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Jian J, Wang Z, Chen C, Workman CT, Fang X, Larsen TO, Guo J, Sonnenschein EC. Two high-quality Prototheca zopfii genomes provide new insights into their evolution as obligate algal heterotrophs and their pathogenicity. Microbiol Spectr 2024:e0414823. [PMID: 38940543 DOI: 10.1128/spectrum.04148-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Accepted: 05/24/2024] [Indexed: 06/29/2024] Open
Abstract
The majority of the nearly 10,000 described species of green algae are photoautotrophs; however, some species have lost their ability to photosynthesize and become obligate heterotrophs that rely on parasitism for survival. Two high-quality genomes of the heterotrophic algae Prototheca zopfii Pz20 and Pz23 were obtained using short- and long-read genomic as well as transcriptomic data. The genome sizes were 31.2 Mb and 31.3 Mb, respectively, and contig N50 values of 1.99 Mb and 1.26 Mb. Although P. zopfii maintained its plastid genome, the transition to heterotrophy led to a reduction in both plastid and nuclear genome size, including the loss of photosynthesis-related genes from both the nuclear and plastid genomes and the elimination of genes encoding for carotenoid oxygenase and pheophorbide an oxygenase. The loss of genes, including basic leucine-zipper (bZIP) transcription factors, flavin adenine dinucleotide-linked oxidase, and helicase, could have played a role in the transmission of autotrophy to heterotrophs and in the processes of abiotic stress resistance and pathogenicity. A total of 66 (1.37%) and 73 (1.49%) genes were identified as potential horizontal gene transfer events in the two P. zopfii genomes, respectively. Genes for malate synthase and isocitrate lyase, which are horizontally transferred from bacteria, may play a pivotal role in carbon and nitrogen metabolism as well as the pathogenicity of Prototheca and non-photosynthetic organisms. The two high-quality P. zopfii genomes provide new insights into their evolution as obligate heterotrophs and pathogenicity. IMPORTANCE The genus Prototheca, characterized by its heterotrophic nature and pathogenicity, serves as an exemplary model for investigating pathobiology. The limited understanding of the protothecosis infectious disease is attributed to the lack of genomic resources. Using HiFi long-read sequencing, both nuclear and plastid genomes were generated for two strains of P. zopfii. The findings revealed a concurrent reduction in both plastid and nuclear genome size, accompanied by the loss of genes associated with photosynthesis, carotenoid oxygenase, basic leucine-zipper (bZIP) transcription factors, and others. The analysis of horizontal gene transfer revealed the presence of 1.37% and 1.49% bacterial genes, including malate synthase and isocitrate lyase, which play crucial roles in carbon and nitrogen metabolism, as well as pathogenicity and obligate heterotrophy. The two high-quality P. zopfii genomes represent valuable resources for investigating their adaptation and evolution as obligate heterotrophs, as well as for developing future prevention and treatment strategies against protothecosis.
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Affiliation(s)
- Jianbo Jian
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
- BGI Genomics, Shenzhen, China
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, China
| | | | | | - Christopher T Workman
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | | | - Thomas Ostenfeld Larsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Jian Guo
- Department of Laboratory Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Eva C Sonnenschein
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
- Department of Biosciences, Swansea University, Swansea, United Kingdom
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2
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Ren X, Sun D, Lv J, Gao B, Jia S, Bian X, Zhao K, Li J, Liu P, Li J. Chromosome-level genome of the long-tailed marine-living ornate spiny lobster, Panulirus ornatus. Sci Data 2024; 11:662. [PMID: 38909031 PMCID: PMC11193758 DOI: 10.1038/s41597-024-03512-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 06/12/2024] [Indexed: 06/24/2024] Open
Abstract
Recent conservation efforts to protect rare and endangered aquatic species have intensified. Nevertheless, the ornate spiny lobster (Panulirus ornatus), which is prevalent in the Indo-Pacific waters, has been largely ignored. In the absence of a detailed genomic reference, the conservation and population genetics of this crustacean are poorly understood. Here, We assembled a comprehensive chromosome-level genome for P. ornatus. This genome-among the most detailed for lobsters-spans 2.65 Gb with a contig N50 of 51.05 Mb, and 99.11% of the sequences with incorporated to 73 chromosomes. The ornate spiny lobster genome comprises 65.67% repeat sequences and 22,752 protein-coding genes with 99.20% of the genes functionally annotated. The assembly of the P. ornatus genome provides valuable insights into comparative crustacean genomics and endangered species conservation, and lays the groundwork for future research on the speciation, ecology, and evolution of the ornate spiny lobster.
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Affiliation(s)
- Xianyun Ren
- National Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, 266071, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Qingdao, Shandong, 266237, China
| | - Dongfang Sun
- National Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, 266071, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Qingdao, Shandong, 266237, China
| | - Jianjian Lv
- National Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, 266071, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Qingdao, Shandong, 266237, China
| | - Baoquan Gao
- National Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, 266071, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Qingdao, Shandong, 266237, China
| | - Shaoting Jia
- National Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, 266071, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Qingdao, Shandong, 266237, China
| | - Xueqiong Bian
- National Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, 266071, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Qingdao, Shandong, 266237, China
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, PR China
| | - Kuangcheng Zhao
- National Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, 266071, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Qingdao, Shandong, 266237, China
| | - Jitao Li
- National Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, 266071, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Qingdao, Shandong, 266237, China
| | - Ping Liu
- National Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, 266071, China.
- Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Qingdao, Shandong, 266237, China.
| | - Jian Li
- National Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, 266071, China.
- Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Qingdao, Shandong, 266237, China.
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3
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Yuan Y, Zhong T, Wang Y, Yang J, Gui L, Shen Y, Zhou J, Chung-Davidson YW, Li W, Xu J, Li J, Li M, Ren J. Chromosome-scale genome assemblies of sexually dimorphic male and female Acrossocheilus fasciatus. Sci Data 2024; 11:653. [PMID: 38906919 PMCID: PMC11192953 DOI: 10.1038/s41597-024-03504-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 06/10/2024] [Indexed: 06/23/2024] Open
Abstract
Acrossocheilus fasciatus is a stream-dwelling fish species of the Barbinae subfamily. It is valued for its colorfully striped appearance and delicious meat. This species is also characterized by apparent sexual dimorphism and toxic ovum. Biology and aquaculture researches of A. fasciatus are hindered by the lack of a high-quality reference genome. Here, we report chromosome-level genome assemblies of the male and female A. fasciatus. The HiFi-only genome assemblies for both female and male individuals were 899.13 Mb (N50 length of 32.58 Mb) and 885.68 Mb (N50 length of 33.06 Mb), respectively. Notably, a substantial proportion of the assembled sequences, accounting for 96.15% and 98.35% for female and male genomes, respectively, were successfully anchored onto 25 chromosomes utilizing Hi-C data. We annotated the female assembly as a reference genome and identified a total of 400.62 Mb (44.56%) repetitive sequences, 27,392 protein-coding genes, and 35,869 ncRNAs. The high-quality male and female reference genomes will provide genomic resources for developing sex-specific molecular markers, inform single-sex breeding, and elucidate genetic mechanisms of sexual dimorphism.
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Affiliation(s)
- Yixin Yuan
- Key Laboratory of Freshwater Aquatic Genetic Resources certificated by the Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, 201306, China
| | - Tianxing Zhong
- Key Laboratory of Freshwater Aquatic Genetic Resources certificated by the Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, 201306, China
| | - Yifei Wang
- Key Laboratory of Freshwater Aquatic Genetic Resources certificated by the Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, 201306, China
| | - Jinquan Yang
- Key Laboratory of Freshwater Aquatic Genetic Resources certificated by the Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, 201306, China
| | - Lang Gui
- Key Laboratory of Freshwater Aquatic Genetic Resources certificated by the Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, 201306, China
| | - Yubang Shen
- Key Laboratory of Freshwater Aquatic Genetic Resources certificated by the Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, 201306, China
| | - Jiajun Zhou
- Zhejiang Forest Resource Monitoring Center, Hangzhou, 310020, China
| | - Yu-Wen Chung-Davidson
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI, 48824, USA
| | - Weiming Li
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI, 48824, USA
| | - Jinkai Xu
- Huangshan Dingxin Ecological Agriculture Co., Ltd, Huangshan, 245431, China
| | - Jiale Li
- Key Laboratory of Freshwater Aquatic Genetic Resources certificated by the Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, 201306, China
| | - Mingyou Li
- Key Laboratory of Freshwater Aquatic Genetic Resources certificated by the Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, 201306, China.
| | - Jianfeng Ren
- Key Laboratory of Freshwater Aquatic Genetic Resources certificated by the Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, 201306, China.
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Joglekar A, Hu W, Zhang B, Narykov O, Diekhans M, Marrocco J, Balacco J, Ndhlovu LC, Milner TA, Fedrigo O, Jarvis ED, Sheynkman G, Korkin D, Ross ME, Tilgner HU. Single-cell long-read sequencing-based mapping reveals specialized splicing patterns in developing and adult mouse and human brain. Nat Neurosci 2024; 27:1051-1063. [PMID: 38594596 PMCID: PMC11156538 DOI: 10.1038/s41593-024-01616-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Accepted: 03/07/2024] [Indexed: 04/11/2024]
Abstract
RNA isoforms influence cell identity and function. However, a comprehensive brain isoform map was lacking. We analyze single-cell RNA isoforms across brain regions, cell subtypes, developmental time points and species. For 72% of genes, full-length isoform expression varies along one or more axes. Splicing, transcription start and polyadenylation sites vary strongly between cell types, influence protein architecture and associate with disease-linked variation. Additionally, neurotransmitter transport and synapse turnover genes harbor cell-type variability across anatomical regions. Regulation of cell-type-specific splicing is pronounced in the postnatal day 21-to-postnatal day 28 adolescent transition. Developmental isoform regulation is stronger than regional regulation for the same cell type. Cell-type-specific isoform regulation in mice is mostly maintained in the human hippocampus, allowing extrapolation to the human brain. Conversely, the human brain harbors additional cell-type specificity, suggesting gain-of-function isoforms. Together, this detailed single-cell atlas of full-length isoform regulation across development, anatomical regions and species reveals an unappreciated degree of isoform variability across multiple axes.
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Affiliation(s)
- Anoushka Joglekar
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
- Center for Neurogenetics, Weill Cornell Medicine, New York, NY, USA
- New York Genome Center, New York, NY, USA
| | - Wen Hu
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
- Center for Neurogenetics, Weill Cornell Medicine, New York, NY, USA
| | - Bei Zhang
- Spatial Genomics, Inc., Pasadena, CA, USA
| | - Oleksandr Narykov
- Bioinformatics and Computational Biology Program, Worcester Polytechnic Institute, Worcester, MA, USA
- Computer Science Department, Worcester Polytechnic Institute, Worcester, MA, USA
- Data Science Program, Worcester Polytechnic Institute, Worcester, MA, USA
| | - Mark Diekhans
- UC Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Jordan Marrocco
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
- Department of Biology, Touro University, New York, NY, USA
- Laboratory of Neuroendocrinology, The Rockefeller University, New York, NY, USA
| | - Jennifer Balacco
- Vertebrate Genome Lab, The Rockefeller University, New York, NY, USA
| | - Lishomwa C Ndhlovu
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York, NY, USA
| | - Teresa A Milner
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Olivier Fedrigo
- Vertebrate Genome Lab, The Rockefeller University, New York, NY, USA
| | - Erich D Jarvis
- Vertebrate Genome Lab, The Rockefeller University, New York, NY, USA
- Laboratory of Neurogenetics of Language, The Rockefeller University, New York, NY, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Gloria Sheynkman
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
- UVA Comprehensive Cancer Center, University of Virginia, Charlottesville, VA, USA
| | - Dmitry Korkin
- Bioinformatics and Computational Biology Program, Worcester Polytechnic Institute, Worcester, MA, USA
- Computer Science Department, Worcester Polytechnic Institute, Worcester, MA, USA
- Data Science Program, Worcester Polytechnic Institute, Worcester, MA, USA
| | - M Elizabeth Ross
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
- Center for Neurogenetics, Weill Cornell Medicine, New York, NY, USA
| | - Hagen U Tilgner
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA.
- Center for Neurogenetics, Weill Cornell Medicine, New York, NY, USA.
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5
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Ji G, Long Y, Cai G, Wang A, Yan G, Li H, Gao G, Xu K, Huang Q, Chen B, Li L, Li F, Nishio T, Shen J, Wu X. A new chromosome-scale genome of wild Brassica oleracea provides insights into the domestication of Brassica crops. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:2882-2899. [PMID: 38421062 DOI: 10.1093/jxb/erae079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 02/28/2024] [Indexed: 03/02/2024]
Abstract
The cultivated diploid Brassica oleracea is an important vegetable crop, but the genetic basis of its domestication remains largely unclear in the absence of high-quality reference genomes of wild B. oleracea. Here, we report the first chromosome-level assembly of the wild Brassica oleracea L. W03 genome (total genome size, 630.7 Mb; scaffold N50, 64.6 Mb). Using the newly assembled W03 genome, we constructed a gene-based B. oleracea pangenome and identified 29 744 core genes, 23 306 dispensable genes, and 1896 private genes. We re-sequenced 53 accessions, representing six potential wild B. oleracea progenitor species. The results of the population genomic analysis showed that the wild B. oleracea populations had the highest level of diversity and represents the most closely related population to modern-day horticultural B. oleracea. In addition, the WUSCHEL gene was found to play a decisive role in domestication and to be involved in cauliflower and broccoli curd formation. We also illustrate the loss of disease-resistance genes during selection for domestication. Our results provide new insights into the domestication of B. oleracea and will facilitate the future genetic improvement of Brassica crops.
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Affiliation(s)
- Gaoxiang Ji
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Ying Long
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Guangqin Cai
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Aihua Wang
- Wuhan Vegetable Research Institute, Wuhan Academy of Agricultural Sciences, Wuhan,China
| | - Guixin Yan
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Hao Li
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Guizhen Gao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Kun Xu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Qian Huang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Biyun Chen
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Lixia Li
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Feng Li
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Takeshi Nishio
- Graduate School of Agricultural Science, Tohoku University, 468-1, Aza-Aoba, Aramaki, Aoba-ku, Sendai, 980-0845, Japan
| | - Jinxiong Shen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Xiaoming Wu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
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Wang Y, Li P, Zhu Y, Zhang F, Zhang S, He Y, Wu Y, Lin Y, Wang H, Ren W, Wang L, Yang Y, Wang R, Zheng P, Liu Y, Wang S, Yue J. Graph-Based Pangenome of Actinidia chinensis Reveals Structural Variations Mediating Fruit Degreening. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2400322. [PMID: 38757662 DOI: 10.1002/advs.202400322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 04/19/2024] [Indexed: 05/18/2024]
Abstract
Fruit ripening is associated with the degreening process (loss of chlorophyll) that occurs in most fruit species. Kiwifruit is one of the special species whose fruits may maintain green flesh by accumulating a large amount of chlorophyll even after ripening. However, little is known about the genetic variations related to the fruit degreening process. Here, a graph-based kiwifruit pangenome by analyzing 14 chromosome-scale haplotype-resolved genome assemblies from seven representative cultivars or lines in Actinidia chinensis is built. A total of 49,770 non-redundant gene families are identified, with core genes constituting 46.6%, and dispensable genes constituting 53.4%. A total of 84,591 non-redundant structural variations (SVs) are identified. The pangenome graph integrating both reference genome sequences and variant information facilitates the identification of SVs related to fruit color. The SV in the promoter of the AcBCM gene determines its high expression in the late developmental stage of fruits, which causes chlorophyll accumulation in the green-flesh fruits by post-translationally regulating AcSGR2, a key enzyme of chlorophyll catabolism. Taken together, a high-quality pangenome is constructed, unraveled numerous genetic variations, and identified a novel SV mediating fruit coloration and fruit quality, providing valuable information for further investigating genome evolution and domestication, QTL genes function, and genomics-assisted breeding.
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Affiliation(s)
- Yingzhen Wang
- Anhui Province Key Laboratory of Horticultural Crop Quality Biology, School of Horticulture, Anhui Agricultural University, Hefei, 230036, China
- School of Forestry Science and Technology, Lishui Vocational and Technical College, Lishui, 323000, China
| | - Pengwei Li
- Anhui Province Key Laboratory of Horticultural Crop Quality Biology, School of Horticulture, Anhui Agricultural University, Hefei, 230036, China
| | - Yanyan Zhu
- Anhui Province Key Laboratory of Horticultural Crop Quality Biology, School of Horticulture, Anhui Agricultural University, Hefei, 230036, China
| | - Feng Zhang
- Anhui Province Key Laboratory of Horticultural Crop Quality Biology, School of Horticulture, Anhui Agricultural University, Hefei, 230036, China
| | - Sijia Zhang
- Anhui Province Key Laboratory of Horticultural Crop Quality Biology, School of Horticulture, Anhui Agricultural University, Hefei, 230036, China
| | - Yan He
- Anhui Province Key Laboratory of Horticultural Crop Quality Biology, School of Horticulture, Anhui Agricultural University, Hefei, 230036, China
| | - Ying Wu
- Anhui Province Key Laboratory of Horticultural Crop Quality Biology, School of Horticulture, Anhui Agricultural University, Hefei, 230036, China
| | - Yunzhi Lin
- Ministry of Education Key Laboratory for Bio-resource and Eco-environment, College of Life Science, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, 610064, China
| | - Hongtao Wang
- Anhui Province Key Laboratory of Horticultural Crop Quality Biology, School of Horticulture, Anhui Agricultural University, Hefei, 230036, China
| | - Wangmei Ren
- Anhui Province Key Laboratory of Horticultural Crop Quality Biology, School of Horticulture, Anhui Agricultural University, Hefei, 230036, China
| | - Lihuan Wang
- Anhui Province Key Laboratory of Horticultural Crop Quality Biology, School of Horticulture, Anhui Agricultural University, Hefei, 230036, China
| | - Ying Yang
- Anhui Province Key Laboratory of Horticultural Crop Quality Biology, School of Horticulture, Anhui Agricultural University, Hefei, 230036, China
| | - Runze Wang
- Anhui Province Key Laboratory of Horticultural Crop Quality Biology, School of Horticulture, Anhui Agricultural University, Hefei, 230036, China
| | - Pengpeng Zheng
- Anhui Province Key Laboratory of Horticultural Crop Quality Biology, School of Horticulture, Anhui Agricultural University, Hefei, 230036, China
| | - Yongsheng Liu
- Anhui Province Key Laboratory of Horticultural Crop Quality Biology, School of Horticulture, Anhui Agricultural University, Hefei, 230036, China
- Ministry of Education Key Laboratory for Bio-resource and Eco-environment, College of Life Science, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, 610064, China
| | - Songhu Wang
- Anhui Province Key Laboratory of Horticultural Crop Quality Biology, School of Horticulture, Anhui Agricultural University, Hefei, 230036, China
| | - Junyang Yue
- Anhui Province Key Laboratory of Horticultural Crop Quality Biology, School of Horticulture, Anhui Agricultural University, Hefei, 230036, China
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7
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Li X, Mao C, He J, Bin X, Liu G, Dong Z, Zhao R, Wan X, Li X. The first chromosome-level genome of the stag beetle Dorcus hopei Saunders, 1854 (Coleoptera: Lucanidae). Sci Data 2024; 11:396. [PMID: 38637640 PMCID: PMC11026507 DOI: 10.1038/s41597-024-03251-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 04/10/2024] [Indexed: 04/20/2024] Open
Abstract
Stag beetles (Coleoptera: Lucanidae) represent a significant saproxylic assemblage in forest ecosystems and are noted for their enlarged mandibles and male polymorphism. Despite their relevance as ideal models for the study of exaggerated mandibles that aid in attracting mates, the regulatory mechanisms associated with these traits remain understudied, and restricted by the lack of high-quality reference genomes for stag beetles. To address this limitation, we successfully assembled the first chromosome-level genome of a representative species Dorcus hopei. The genome was 496.58 Mb in length, with a scaffold N50 size of 54.61 Mb, BUSCO values of 99.8%, and 96.8% of scaffolds anchored to nine pairs of chromosomes. We identified 285.27 Mb (57.45%) of repeat sequences and annotated 11,231 protein-coding genes. This genome will be a valuable resource for further understanding the evolution and ecology of stag beetles, and provides a basis for studying the mechanisms of exaggerated mandibles through comparative analysis.
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Affiliation(s)
- Xiaolu Li
- Department of Ecology, School of Resources and Environmental Engineering, Anhui University, Hefei, 230601, China
| | - Chuyang Mao
- Key Laboratory of Genetic Evolution & Animal Models, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), Kunming, Yunnan, 650223, China
- Yunnan Key Laboratory of Biodiversity Information, Kunming, Yunnan, 650223, China
| | - Jinwu He
- Key Laboratory of Genetic Evolution & Animal Models, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), Kunming, Yunnan, 650223, China
- Yunnan Key Laboratory of Biodiversity Information, Kunming, Yunnan, 650223, China
| | - Xiaoyan Bin
- Department of Ecology, School of Resources and Environmental Engineering, Anhui University, Hefei, 230601, China
| | - Guichun Liu
- Key Laboratory of Genetic Evolution & Animal Models, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), Kunming, Yunnan, 650223, China
- Yunnan Key Laboratory of Biodiversity Information, Kunming, Yunnan, 650223, China
| | - Zhiwei Dong
- Key Laboratory of Genetic Evolution & Animal Models, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), Kunming, Yunnan, 650223, China
- Yunnan Key Laboratory of Biodiversity Information, Kunming, Yunnan, 650223, China
| | - Ruoping Zhao
- Key Laboratory of Genetic Evolution & Animal Models, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), Kunming, Yunnan, 650223, China
- Yunnan Key Laboratory of Biodiversity Information, Kunming, Yunnan, 650223, China
| | - Xia Wan
- Department of Ecology, School of Resources and Environmental Engineering, Anhui University, Hefei, 230601, China.
| | - Xueyan Li
- Key Laboratory of Genetic Evolution & Animal Models, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), Kunming, Yunnan, 650223, China.
- Yunnan Key Laboratory of Biodiversity Information, Kunming, Yunnan, 650223, China.
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8
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Huang X, Yang S, Zhang Y, Shi Y, Shen L, Zhang Q, Qiu A, Guan D, He S. Temperature-dependent action of pepper mildew resistance locus O 1 in inducing pathogen immunity and thermotolerance. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:2064-2083. [PMID: 38011680 DOI: 10.1093/jxb/erad479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 11/25/2023] [Indexed: 11/29/2023]
Abstract
Plant diseases tend to be more serious under conditions of high-temperature/high-humidity (HTHH) than under moderate conditions, and hence disease resistance under HTHH is an important determinant for plant survival. However, how plants cope with diseases under HTHH remains poorly understood. In this study, we used the pathosystem consisting of pepper (Capsicum annuum) and Ralstonia solanacearum (bacterial wilt) as a model to examine the functions of the protein mildew resistance locus O 1 (CaMLO1) and U-box domain-containing protein 21 (CaPUB21) under conditions of 80% humidity and either 28 °C or 37 °C. Expression profiling, loss- and gain-of-function assays involving virus-induced gene-silencing and overexpression in pepper plants, and protein-protein interaction assays were conducted, and the results showed that CaMLO1 acted negatively in pepper immunity against R. solanacearum at 28 °C but positively at 37 °C. In contrast, CaPUB21 acted positively in immunity at 28 °C but negatively at 37 °C. Importantly, CaPUB21 interacted with CaMLO1 under all of the tested conditions, but only the interaction in response to R. solanacearum at 37 °C or to exposure to 37 °C alone led to CaMLO1 degradation, thereby turning off defence responses against R. solanacearum at 37 °C and under high-temperature stress to conserve resources. Thus, we show that CaMLO1 and CaPUB21 interact with each other and function distinctly in pepper immunity against R. solanacearum in an environment-dependent manner.
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Affiliation(s)
- Xueying Huang
- National Education Ministry Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Sheng Yang
- National Education Ministry Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Yapeng Zhang
- National Education Ministry Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Yuanyuan Shi
- National Education Ministry Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Lei Shen
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China
| | - Qixiong Zhang
- National Education Ministry Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Ailian Qiu
- National Education Ministry Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Deyi Guan
- National Education Ministry Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Shuilin He
- National Education Ministry Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
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9
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Bhavsar D, Kutre S, Shikhare P, Kumar S, Behera SK, Chauthe SK. Pharmacoinformatics approach for type 2 diabetes mellitus therapeutics using phytocompounds from Costus genus: an in-silico investigation. J Biomol Struct Dyn 2024:1-17. [PMID: 38511497 DOI: 10.1080/07391102.2024.2330712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 03/08/2024] [Indexed: 03/22/2024]
Abstract
Type 2 Diabetes Mellitus (T2DM), as a significant health concern globally, particularly in India, underscoring the vital need for effective therapeutics. Current drug therapies for T2DM may have limitations, leading researchers to explore natural products as alternatives. In this study. We have investigated the anti-diabetic compounds from the Costus genus, known as the insulin plant, which is abundant in southern India. The bioinformatics tools and software used for in-silico analysis to identify potential therapeutic compounds and hub genes associated with T2DM in the Indian population that could cut short the in-vitro and in-vivo experimental approaches in near future. The systematic review and combinatorial in-silico analysis revealed IGF2BP2, INS and TCF as the key targets that are associated with T2DM. The compounds stigmasterol, cycloartenol, and diosgenone were explored to be potent among all the 38 phytocompounds from genus Costus with binding energies -8.48, -10.07, and -10.31 kcal/mol against IGF2BP2, INS and TCF. The molecular dynamics (MD) simulation studies of these complexes demonstrated stable and consistent dynamic behavior, particularly in the INS-cycloartenol, IGF2BP2-stigmasterol and TCF7L2-diosgenone complexes. The identified compounds and associated targets represent potential candidates for T2DM therapeutics in the Indian population. The pharmacoinformatics approach presented in the study could streamline the drug discovery process by prioritizing compounds for further experimental validation.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Drashti Bhavsar
- Department of Natural Products, National Institute of Pharmaceutical Education and Research, Ahmedabad, Gujarat, India
| | - Suraj Kutre
- Department of Natural Products, National Institute of Pharmaceutical Education and Research, Ahmedabad, Gujarat, India
| | - Priti Shikhare
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research, Ahmedabad, Gujarat, India
| | - Sunil Kumar
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute (IASRI), New Delhi, India
| | - Santosh Kumar Behera
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research, Ahmedabad, Gujarat, India
| | - Siddheshwar Kisan Chauthe
- Department of Natural Products, National Institute of Pharmaceutical Education and Research, Ahmedabad, Gujarat, India
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10
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Cucić S, Ells T, Guri A, Kropinski AM, Khursigara CM, Anany H. Degradation of Listeria monocytogenes biofilm by phages belonging to the genus Pecentumvirus. Appl Environ Microbiol 2024; 90:e0106223. [PMID: 38315006 PMCID: PMC10952537 DOI: 10.1128/aem.01062-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 11/29/2023] [Indexed: 02/07/2024] Open
Abstract
Listeria monocytogenes is a pathogenic foodborne bacterium that is a significant cause of mortality associated with foodborne illness and causes many food recalls attributed to a bacteriological cause. Their ability to form biofilms contributes to the persistence of Listeria spp. in food processing environments. When growing as biofilms, L. monocytogenes are more resistant to sanitizers used in the food industry, such as benzalkonium chloride (BAC), as well as to physical stresses like desiccation and starvation. Lytic phages of Listeria are antagonistic to a broad range of Listeria spp. and may, therefore, have utility in reducing the occurrence of Listeria-associated food recalls by preventing food contamination. We screened nine closely related Listeria phages, including the commercially available Listex P100, for host range and ability to degrade microtiter plate biofilms of L. monocytogenes ATCC 19111 (serovar 1/2a). One phage, CKA15, was selected and shown to rapidly adsorb to its host under conditions relevant to applying the phage in dairy processing environments. Under simulated dairy processing conditions (SDPC), CKA15 caused a 2-log reduction in Lm19111 biofilm bacteria. This work supports the biosanitation potential of phage CKA15 and provides a basis for further investigation of phage-bacteria interactions in biofilms grown under SDPC. IMPORTANCE Listeria monocytogenes is a pathogenic bacterium that is especially dangerous for children, the elderly, pregnant women, and immune-compromised people. Because of this, the food industry takes its presence in their plants seriously. Food recalls due to L. monocytogenes are common with a high associated economic cost. In food-processing plants, Listeria spp. typically reside in biofilms, which are structures produced by bacteria that shield them from environmental stressors and are often attached to surfaces. The significance of our work is that we show a bacteriophage-a virus-infecting bacteria-can reduce Listeria counts by two orders of magnitude when the bacterial biofilms were grown under simulated dairy processing conditions. This work provides insights into how phages may be tested and used to develop biosanitizers that are effective but are not harmful to the environment or human health.
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Affiliation(s)
- Stevan Cucić
- Guelph Research and Development Centre, Agriculture and Agri-Food Canada, Guelph, Ontario, Canada
- Department of Molecular and Cellular Biology, College of Biological Science, University of Guelph, Guelph, Ontario, Canada
| | - Tim Ells
- Kentville Research and Development Centre, Agriculture and Agri-Food Canada, Kentville, Nova Scotia, Canada
| | - Anilda Guri
- Gay Lea Foods Co-operative, Research and Development Centre, Hamilton, Ontario, Canada
| | - Andrew M. Kropinski
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
| | - Cezar M. Khursigara
- Department of Molecular and Cellular Biology, College of Biological Science, University of Guelph, Guelph, Ontario, Canada
| | - Hany Anany
- Guelph Research and Development Centre, Agriculture and Agri-Food Canada, Guelph, Ontario, Canada
- Department of Molecular and Cellular Biology, College of Biological Science, University of Guelph, Guelph, Ontario, Canada
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11
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Zhai X, Wu D, Chen C, Yang X, Cheng S, Sha L, Deng S, Cheng Y, Fan X, Kang H, Wang Y, Liu D, Zhou Y, Zhang H. A chromosome level genome assembly of Pseudoroegneria Libanotica reveals a key Kcs gene involves in the cuticular wax elongation for drought resistance. BMC Genomics 2024; 25:253. [PMID: 38448864 PMCID: PMC10916072 DOI: 10.1186/s12864-024-10140-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 02/19/2024] [Indexed: 03/08/2024] Open
Abstract
BACKGROUND The genus Pseudoroegneria (Nevski) Löve (Triticeae, Poaceae), whose genome symbol was designed as "St", accounts for more than 60% of perennial Triticeae species. The diploid species Psudoroegneria libanotica (2n = 14) contains the most ancient St genome, exhibited strong drought resistance, and was morphologically covered by cuticular wax on the aerial part. Therefore, the St-genome sequencing data could provide fundamental information for studies of genome evolution and reveal its mechanisms of cuticular wax and drought resistance. RESULTS In this study, we reported the chromosome-level genome assembly for the St genome of Pse. libanotica, with a total size of 2.99 Gb. 46,369 protein-coding genes annotated and 71.62% was repeat sequences. Comparative analyses revealed that the genus Pseudoroegneria diverged during the middle and late Miocene. During this period, unique genes, gene family expansion, and contraction in Pse. libanotica were enriched in biotic and abiotic stresses, such as fatty acid biosynthesis which may greatly contribute to its drought adaption. Furthermore, we investigated genes associated with the cuticular wax formation and water deficit and found a new Kcs gene evm.TU.CTG175.54. It plays a critical role in the very long chain fatty acid (VLCFA) elongation from C18 to C26 in Pse. libanotica. The function needs more evidence to be verified. CONCLUSIONS We sequenced and assembled the St genome in Triticeae and discovered a new KCS gene that plays a role in wax extension to cope with drought. Our study lays a foundation for the genome diversification of Triticeae species and deciphers cuticular wax formation genes involved in drought resistance.
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Affiliation(s)
- Xingguang Zhai
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Dandan Wu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Chen Chen
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Xunzhe Yang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Shaobo Cheng
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Lina Sha
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Shuhan Deng
- Glbizzia Biosciences Co., Ltd, Liandong U Valley, Huatuo Road 50, Daxing, Beijing, 102600, China
| | - Yiran Cheng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Xing Fan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Houyang Kang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Yi Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Dengcai Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Yonghong Zhou
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.
| | - Haiqin Zhang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.
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12
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Cassiano GC, Martinelli A, Mottin M, Neves BJ, Andrade CH, Ferreira PE, Cravo P. Whole genome sequencing identifies novel mutations in malaria parasites resistant to artesunate (ATN) and to ATN + mefloquine combination. Front Cell Infect Microbiol 2024; 14:1353057. [PMID: 38495651 PMCID: PMC10940360 DOI: 10.3389/fcimb.2024.1353057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Accepted: 02/14/2024] [Indexed: 03/19/2024] Open
Abstract
Introduction The global evolution of resistance to Artemisinin-based Combination Therapies (ACTs) by malaria parasites, will severely undermine our ability to control this devastating disease. Methods Here, we have used whole genome sequencing to characterize the genetic variation in the experimentally evolved Plasmodium chabaudi parasite clone AS-ATNMF1, which is resistant to artesunate + mefloquine. Results and discussion Five novel single nucleotide polymorphisms (SNPs) were identified, one of which was a previously undescribed E738K mutation in a 26S proteasome subunit that was selected for under artesunate pressure (in AS-ATN) and retained in AS-ATNMF1. The wild type and mutated three-dimensional (3D) structure models and molecular dynamics simulations of the P. falciparum 26S proteasome subunit Rpn2 suggested that the E738K mutation could change the toroidal proteasome/cyclosome domain organization and change the recognition of ubiquitinated proteins. The mutation in the 26S proteasome subunit may therefore contribute to altering oxidation-dependent ubiquitination of the MDR-1 and/or K13 proteins and/or other targets, resulting in changes in protein turnover. In light of the alarming increase in resistance to artemisin derivatives and ACT partner drugs in natural parasite populations, our results shed new light on the biology of resistance and provide information on novel molecular markers of resistance that may be tested (and potentially validated) in the field.
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Affiliation(s)
- Gustavo Capatti Cassiano
- Global Health and Tropical Medicine (GHTM), Associate Laboratory in Translation and Innovation Towards Global Health, (LA-REAL), Instituto de Higiene e Medicina Tropical, (IHMT), Universidade NOVA de Lisboa, (UNL), Lisbon, Portugal
| | | | - Melina Mottin
- Laboratory for Molecular Modeling and Drug Design (LabMol), Faculty of Pharmacy, Universidade Federal de Goiás, Goiânia, Brazil
| | - Bruno Junior Neves
- Laboratory or Cheminformatics (LabChem), Faculty of Pharmacy, Universidade Federal de Goiás, Goiânia, Brazil
| | - Carolina Horta Andrade
- Laboratory for Molecular Modeling and Drug Design (LabMol), Faculty of Pharmacy, Universidade Federal de Goiás, Goiânia, Brazil
- Center for the Research and Advancement in Fragments and Molecular Targets (CRAFT), School of Pharmaceutical Sciences at Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
| | - Pedro Eduardo Ferreira
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal
| | - Pedro Cravo
- Global Health and Tropical Medicine (GHTM), Associate Laboratory in Translation and Innovation Towards Global Health, (LA-REAL), Instituto de Higiene e Medicina Tropical, (IHMT), Universidade NOVA de Lisboa, (UNL), Lisbon, Portugal
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13
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Newman TE, Jacques S, Grime C, Mobegi FM, Kamphuis FL, Khentry Y, Lee R, Kamphuis LG. Genetic dissection of domestication traits in interspecific chickpea populations. THE PLANT GENOME 2024; 17:e20408. [PMID: 37961823 DOI: 10.1002/tpg2.20408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 10/11/2023] [Accepted: 10/16/2023] [Indexed: 11/15/2023]
Abstract
Chickpea (Cicer arietinum) is a pulse crop that provides an integral source of nutrition for human consumption. The close wild relatives Cicer reticulatum and Cicer echinospermum harbor untapped genetic diversity that can be exploited by chickpea breeders to improve domestic varieties. Knowledge of genomic loci that control important chickpea domestication traits will expedite the development of improved chickpea varieties derived from interspecific crosses. Therefore, we set out to identify genomic loci underlying key chickpea domestication traits by both association and quantitative trait locus (QTL) mapping using interspecific F2 populations. Diverse phenotypes were recorded for various agronomic traits. A total of 11 high-confidence markers were detected on chromosomes 1, 3, and 7 by both association and QTL mapping; these were associated with growth habit, flowering time, and seed traits. Furthermore, we identified candidate genes linked to these markers, which advanced our understanding of the genetic basis of domestication traits and validated known genes such as the FLOWERING LOCUS gene cluster that regulates flowering time. Collectively, this study has elucidated the genetic basis of chickpea domestication traits, which can facilitate the development of superior chickpea varieties.
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Affiliation(s)
- Toby E Newman
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia
| | - Silke Jacques
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia
| | - Christy Grime
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia
| | - Fredrick M Mobegi
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia
| | - Fiona L Kamphuis
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia
| | - Yuphin Khentry
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia
| | - Robert Lee
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia
| | - Lars G Kamphuis
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia
- The UWA Institute of Agriculture, The University of Western Australia, Crawley, Western Australia, Australia
- CSIRO Agriculture and Food, Floreat, Western Australia, Australia
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14
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Wang R, Liu CN, Segar ST, Jiang YT, Zhang KJ, Jiang K, Wang G, Cai J, Chen LF, Chen S, Cheng J, Compton SG, Deng JY, Ding YY, Du FK, Hu XD, Hu XH, Kang L, Li DH, Lu L, Li YY, Tang L, Tong X, Wang ZS, Xu WW, Yang Y, Zang RG, Zu ZX, Zhang YY, Chen XY. Dipterocarpoidae genomics reveal their demography and adaptations to Asian rainforests. Nat Commun 2024; 15:1683. [PMID: 38395938 PMCID: PMC10891123 DOI: 10.1038/s41467-024-45836-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 02/01/2024] [Indexed: 02/25/2024] Open
Abstract
Dipterocarpoideae species form the emergent layer of Asian rainforests. They are the indicator species for Asian rainforest distribution, but they are severely threatened. Here, to understand their adaptation and population decline, we assemble high-quality genomes of seven Dipterocarpoideae species including two autotetraploid species. We estimate the divergence time between Dipterocarpoideae and Malvaceae and within Dipterocarpoideae to be 108.2 (97.8‒118.2) and 88.4 (77.7‒102.9) million years ago, and we identify a whole genome duplication event preceding dipterocarp lineage diversification. We find several genes that showed a signature of selection, likely associated with the adaptation to Asian rainforests. By resequencing of two endangered species, we detect an expansion of effective population size after the last glacial period and a recent sharp decline coinciding with the history of local human activities. Our findings contribute to understanding the diversification and adaptation of dipterocarps and highlight anthropogenic disturbances as a major factor in their endangered status.
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Affiliation(s)
- Rong Wang
- Zhejiang Tiantong Forest Ecosystem National Observation and Research Station, Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China.
| | - Chao-Nan Liu
- Zhejiang Tiantong Forest Ecosystem National Observation and Research Station, Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China
| | - Simon T Segar
- Agriculture & Environment Department, Harper Adams University, Newport, United Kingdom
| | - Yu-Ting Jiang
- Zhejiang Tiantong Forest Ecosystem National Observation and Research Station, Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China
| | | | - Kai Jiang
- Zhejiang Tiantong Forest Ecosystem National Observation and Research Station, Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, China
| | - Gang Wang
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan, China
| | - Jing Cai
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Lu-Fan Chen
- Zhejiang Tiantong Forest Ecosystem National Observation and Research Station, Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China
| | - Shan Chen
- Zhejiang Tiantong Forest Ecosystem National Observation and Research Station, Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China
| | - Jing Cheng
- Zhejiang Tiantong Forest Ecosystem National Observation and Research Station, Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China
| | | | - Jun-Yin Deng
- Zhejiang Tiantong Forest Ecosystem National Observation and Research Station, Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China
| | - Yuan-Yuan Ding
- Zhejiang Tiantong Forest Ecosystem National Observation and Research Station, Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China
| | - Fang K Du
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Xiao-Di Hu
- Novogene Bioinformatics Institute, Beijing, China
| | - Xing-Hua Hu
- Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and the Chinese Academy of Sciences, Guilin, China
| | - Ling Kang
- Novogene Bioinformatics Institute, Beijing, China
| | - Dong-Hai Li
- College of Ecology and Environment, Hainan University, Haikou, China
| | - Ling Lu
- Zhejiang Tiantong Forest Ecosystem National Observation and Research Station, Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China
| | - Yuan-Yuan Li
- Zhejiang Tiantong Forest Ecosystem National Observation and Research Station, Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China
| | - Liang Tang
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Hainan University, Haikou, China
| | - Xin Tong
- Zhejiang Tiantong Forest Ecosystem National Observation and Research Station, Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, China
| | - Zheng-Shi Wang
- Zhejiang Tiantong Forest Ecosystem National Observation and Research Station, Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China
| | - Wei-Wei Xu
- Novogene Bioinformatics Institute, Beijing, China
| | - Yang Yang
- Zhejiang Tiantong Forest Ecosystem National Observation and Research Station, Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China
| | - Run-Guo Zang
- Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing, China
| | - Zhuo-Xin Zu
- Novogene Bioinformatics Institute, Beijing, China
| | - Yuan-Ye Zhang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, China.
| | - Xiao-Yong Chen
- Zhejiang Tiantong Forest Ecosystem National Observation and Research Station, Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China.
- Shanghai Engineering Research Center of Sustainable Plant Innovation, Shanghai, China.
- Shanghai Institute of Pollution Control and Ecological Security, Shanghai, China.
- Institute of Eco-Chongming, Shanghai, China.
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15
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Li H, Zhai X, Peng H, Qing Y, Deng Y, Zhou S, Bei T, Tian J, Zhang J, Hu Y, Qin X, Lu Y, Yao Y, Wang S, Zheng Y. Chromosomal level genome assemblies of two Malus crabapple cultivars Flame and Royalty. Sci Data 2024; 11:201. [PMID: 38351118 PMCID: PMC10864326 DOI: 10.1038/s41597-024-03049-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 02/05/2024] [Indexed: 02/16/2024] Open
Abstract
Malus hybrid 'Flame' and Malus hybrid 'Royalty' are representative ornamental crabapples, rich in flavonoids and serving as the preferred materials for studying the coloration mechanism. We generated two sets of high-quality chromosome-level and haplotype-resolved genome of 'Flame' with sizes of 688.2 Mb and 675.7 Mb, and those of 'Royalty' with sizes of 674.1 Mb and 663.6 Mb, all anchored to 17 chromosomes and with a high BUSCO completeness score nearly 99.0%. A total of 47,833 and 47,307 protein-coding genes were annotated in the two haplotype genomes of 'Flame', and the numbers of 'Royalty' were 46,305 and 46,920 individually. The assembled high-quality genomes offer new resources for studying the origin and adaptive evolution of crabapples and the molecular basis of the accumulation of flavonoids and anthocyanins, facilitating molecular breeding of Malus plants.
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Affiliation(s)
- Hua Li
- Beijing Key Laboratory for Agriculture Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing, 102206, China
- Bioinformatics Center, Beijing University of Agriculture, Beijing, 102206, China
| | - Xuyang Zhai
- Beijing Key Laboratory for Agriculture Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing, 102206, China
- Bioinformatics Center, Beijing University of Agriculture, Beijing, 102206, China
| | - Haixu Peng
- Beijing Key Laboratory for Agriculture Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing, 102206, China
- Bioinformatics Center, Beijing University of Agriculture, Beijing, 102206, China
| | - You Qing
- Beijing Key Laboratory for Agriculture Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing, 102206, China
- Bioinformatics Center, Beijing University of Agriculture, Beijing, 102206, China
| | - Yulin Deng
- Beijing Key Laboratory for Agriculture Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing, 102206, China
- Bioinformatics Center, Beijing University of Agriculture, Beijing, 102206, China
| | - Shijie Zhou
- Beijing Key Laboratory for Agriculture Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing, 102206, China
- Bioinformatics Center, Beijing University of Agriculture, Beijing, 102206, China
| | - Tairui Bei
- Bioinformatics Center, Beijing University of Agriculture, Beijing, 102206, China
| | - Ji Tian
- Beijing Key Laboratory for Agriculture Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing, 102206, China
| | - Jie Zhang
- Beijing Key Laboratory for Agriculture Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing, 102206, China
| | - Yujing Hu
- Beijing Key Laboratory for Agriculture Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing, 102206, China
| | - Xiaoxiao Qin
- Beijing Key Laboratory for Agriculture Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing, 102206, China
| | - Yanfen Lu
- Beijing Key Laboratory for Agriculture Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing, 102206, China
| | - Yuncong Yao
- Beijing Key Laboratory for Agriculture Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing, 102206, China
| | - Sen Wang
- Beijing Key Laboratory for Agriculture Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing, 102206, China.
- Bioinformatics Center, Beijing University of Agriculture, Beijing, 102206, China.
| | - Yi Zheng
- Beijing Key Laboratory for Agriculture Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing, 102206, China.
- Bioinformatics Center, Beijing University of Agriculture, Beijing, 102206, China.
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16
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Wadapurkar RM, Sivaram A, Vyas R. Computational investigations into structure and function impact of novel mutations identified in targeted exons from ovarian cancer cell lines. J Biomol Struct Dyn 2024:1-15. [PMID: 38334284 DOI: 10.1080/07391102.2024.2310776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 01/20/2024] [Indexed: 02/10/2024]
Abstract
The lack of sensitive and specific biomarkers for ovarian cancer leads to late stage diagnosis of the disease in a majority of the cases. Mutation accumulation is the basis for cancer progression, thus identifying mutations is an important step in the disease diagnosis. In the present study, a comprehensive analysis of fifteen Next Generation Sequencing samples from thirteen ovarian cancer cell lines was carried out for the identification of new mutations. The study revealed eight clinically significant novel mutations in six ovarian cancer oncogenes, viz. SMARCA4, ARID1A, PPP2R1A, CTNNB1, DICER1 and PIK3CA. In-depth computational analysis revealed that the mutations affected the structure of the proteins in terms of stability, solvent accessible surface area and molecular dynamics. Moreover, the mutations were present in functionally significant domains of the proteins, thereby adversely affecting the protein functionality. PPI network for SMARCA4, CTNNB1, DICER1, PIK3CA, PPP2R1A and ARID1A showed that these genes were involved in certain significant pathways affecting various hallmarks of cancer. For further validation, in vitro studies were performed that revealed hypermutability of the CTNNB1 gene. Through this study we have identified some key mutations and have analysed their structural and functional impact. The study establishes some key mutations, which can be potentially explored as biomarker and drug target.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Rucha M Wadapurkar
- MIT School of Bioengineering Sciences & Research, MIT-ADT University, Pune, Maharashtra, India
| | - Aruna Sivaram
- MIT School of Bioengineering Sciences & Research, MIT-ADT University, Pune, Maharashtra, India
| | - Renu Vyas
- MIT School of Bioengineering Sciences & Research, MIT-ADT University, Pune, Maharashtra, India
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de la Fuente C, Grondin A, Sine B, Debieu M, Belin C, Hajjarpoor A, Atkinson JA, Passot S, Salson M, Orjuela J, Tranchant-Dubreuil C, Brossier JR, Steffen M, Morgado C, Dinh HN, Pandey BK, Darmau J, Champion A, Petitot AS, Barrachina C, Pratlong M, Mounier T, Nakombo-Gbassault P, Gantet P, Gangashetty P, Guedon Y, Vadez V, Reichheld JP, Bennett MJ, Kane NA, Guyomarc'h S, Wells DM, Vigouroux Y, Laplaze L. Glutaredoxin regulation of primary root growth is associated with early drought stress tolerance in pearl millet. eLife 2024; 12:RP86169. [PMID: 38294329 PMCID: PMC10945517 DOI: 10.7554/elife.86169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2024] Open
Abstract
Seedling root traits impact plant establishment under challenging environments. Pearl millet is one of the most heat and drought tolerant cereal crops that provides a vital food source across the sub-Saharan Sahel region. Pearl millet's early root system features a single fast-growing primary root which we hypothesize is an adaptation to the Sahelian climate. Using crop modeling, we demonstrate that early drought stress is an important constraint in agrosystems in the Sahel where pearl millet was domesticated. Furthermore, we show that increased pearl millet primary root growth is correlated with increased early water stress tolerance in field conditions. Genetics including genome-wide association study and quantitative trait loci (QTL) approaches identify genomic regions controlling this key root trait. Combining gene expression data, re-sequencing and re-annotation of one of these genomic regions identified a glutaredoxin-encoding gene PgGRXC9 as the candidate stress resilience root growth regulator. Functional characterization of its closest Arabidopsis homolog AtROXY19 revealed a novel role for this glutaredoxin (GRX) gene clade in regulating cell elongation. In summary, our study suggests a conserved function for GRX genes in conferring root cell elongation and enhancing resilience of pearl millet to its Sahelian environment.
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Affiliation(s)
| | - Alexandre Grondin
- DIADE, Université de Montpellier, IRD, CIRADMontpellierFrance
- LMI LAPSEDakarSenegal
- CERAAS, ISRAThiesSenegal
| | | | - Marilyne Debieu
- DIADE, Université de Montpellier, IRD, CIRADMontpellierFrance
| | | | - Amir Hajjarpoor
- DIADE, Université de Montpellier, IRD, CIRADMontpellierFrance
| | - Jonathan A Atkinson
- School of Biosciences, University of NottinghamSutton BoningtonUnited Kingdom
| | - Sixtine Passot
- DIADE, Université de Montpellier, IRD, CIRADMontpellierFrance
| | - Marine Salson
- DIADE, Université de Montpellier, IRD, CIRADMontpellierFrance
| | - Julie Orjuela
- DIADE, Université de Montpellier, IRD, CIRADMontpellierFrance
| | | | | | - Maxime Steffen
- DIADE, Université de Montpellier, IRD, CIRADMontpellierFrance
| | | | - Hang Ngan Dinh
- DIADE, Université de Montpellier, IRD, CIRADMontpellierFrance
| | - Bipin K Pandey
- School of Biosciences, University of NottinghamSutton BoningtonUnited Kingdom
| | - Julie Darmau
- DIADE, Université de Montpellier, IRD, CIRADMontpellierFrance
| | - Antony Champion
- DIADE, Université de Montpellier, IRD, CIRADMontpellierFrance
| | | | | | | | | | | | - Pascal Gantet
- DIADE, Université de Montpellier, IRD, CIRADMontpellierFrance
| | | | - Yann Guedon
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut AgroMontpellierFrance
| | - Vincent Vadez
- DIADE, Université de Montpellier, IRD, CIRADMontpellierFrance
- LMI LAPSEDakarSenegal
- CERAAS, ISRAThiesSenegal
| | | | - Malcolm J Bennett
- School of Biosciences, University of NottinghamSutton BoningtonUnited Kingdom
| | | | | | - Darren M Wells
- School of Biosciences, University of NottinghamSutton BoningtonUnited Kingdom
| | - Yves Vigouroux
- DIADE, Université de Montpellier, IRD, CIRADMontpellierFrance
| | - Laurent Laplaze
- DIADE, Université de Montpellier, IRD, CIRADMontpellierFrance
- LMI LAPSEDakarSenegal
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18
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Sang H, Li Y, Tan S, Gao P, Wang B, Guo S, Luo S, Sun C. Conservation genomics analysis reveals recent population decline and possible causes in bumblebee Bombus opulentus. INSECT SCIENCE 2024. [PMID: 38297451 DOI: 10.1111/1744-7917.13324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 11/29/2023] [Accepted: 12/07/2023] [Indexed: 02/02/2024]
Abstract
Bumblebees are a genus of pollinators (Bombus) that play important roles in natural ecosystem and agricultural production. Several bumblebee species have been recorded as under population decline, and the proportion of species experiencing population decline within subgenus Thoracobombus is higher than average. Bombus opulentus is 1 species in Thoracobombus, but little is known about its recent population dynamics. Here, we employed conservation genomics methods to investigate the population dynamics of B. opulentus during the recent past and identify the likely environmental factors that may cause population decline. Firstly, we placed the scaffold-level of B. opulentus reference genome sequence onto chromosome-level using Hi-C technique. Then, based on this reference genome and whole-genome resequencing data for 51 B. opulentus samples, we reconstructed the population structure and effective population size (Ne ) trajectories of B. opulentus and identified genes that were under positive selection. Our results revealed that the collected B. opulentus samples could be divided into 2 populations, and 1 of them experienced a recent population decline; the declining population also exhibited lower genetic diversity and higher inbreeding levels. Genes related to high-temperature tolerance, immune response, and detoxication showed signals of positive selection in the declining population, suggesting that climate warming and pathogen/pesticide exposures may contribute to the decline of this B. opulentus population. Taken together, our study provided insights into the demography of B. opulentus populations and highlighted that populations of the same bumblebee species could have contrasting Ne trajectories and population decline could be caused by a combination of various stressors.
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Affiliation(s)
- Huiling Sang
- College of Life Sciences, Capital Normal University, Beijing, China
- State Key Laboratory of Resource Insects, Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yancan Li
- State Key Laboratory of Resource Insects, Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China
- Western Research Institute, Chinese Academy of Agricultural Sciences, Changji, Xinjiang, China
| | - Shuxin Tan
- College of Life Sciences, Capital Normal University, Beijing, China
| | - Pu Gao
- College of Life Sciences, Capital Normal University, Beijing, China
| | - Bei Wang
- Yan'an Beekeeping Experimental Station, Yan'an, Shannxi, China
| | - Shengnan Guo
- Hengshui center for Disease Prevention and Control, Hengshui, Hebei, China
| | - Shudong Luo
- State Key Laboratory of Resource Insects, Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China
- Western Research Institute, Chinese Academy of Agricultural Sciences, Changji, Xinjiang, China
| | - Cheng Sun
- College of Life Sciences, Capital Normal University, Beijing, China
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19
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Wang N, Li Y, Meng Q, Chen M, Wu M, Zhang R, Xu Z, Sun J, Zhang X, Nie X, Yuan D, Lin Z. Genome and haplotype provide insights into the population differentiation and breeding improvement of Gossypium barbadense. J Adv Res 2023; 54:15-27. [PMID: 36775017 DOI: 10.1016/j.jare.2023.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 01/10/2023] [Accepted: 02/04/2023] [Indexed: 02/12/2023] Open
Abstract
INTRODUCTION Sea-island cotton (Gossypium barbadense, Gb) is one of the major sources of high-grade natural fiber. Besides the common annual Gb cotton, perennial Gb cotton is also cultivated, but studies on perennial Gb cotton are rare. OBJECTIVES We aimed to make a systematic analysis of perennial sea-island cotton and lay a foundation for its utilization in breeding, and try to identify the representative structural variations (SVs) in sea-island cotton, and to reveal the population differentiation and adaptive improvement of sea-island cotton. METHODS Through genome assembly of one perennial Gb cotton accession (named Gb_M210936) and comparative genome analysis, variations during Gb cotton domestication were identified by comparing Gb_M210936 with annual Gb accession 3-79 and with wild allotetraploid cotton G. darwinii. Six perennial Gb accessions combining with the resequenced 1,129 cotton accessions were used to conduct population and genetic analysis. Large haplotype blocks (haploblocks), generated from interspecific introgressions and intraspecific inversions, were identified and were used to analyze their effects on population differentiation and agronomic traits of sea-island cotton. RESULTS One reference genome of perennial sea-island cotton was assembled. Representative SVs in sea-island cotton were identified, and 31 SVs were found to be associated with agronomic traits. Perennial Gb cotton had a closer kinship with the wild-to-landrace continuum Gb cotton from south America where Gb cotton is originally domesticated. Haploblocks were associated with agronomic traits improvement of sea-island cotton, promoted sea-island cotton differentiation into three subgroups, were suffered from breeding selection, and may drive Gb cotton to be adapted to central Asian. CONCLUSION Our study made up the lack of perennial Gb cotton genome, and clarified that exotic introgressions improved the traits of sea-island cotton, promoted the population differentiation, and drove sea-island cotton adaptive to central Asia, which will provide new insights for the genetic breeding improvement of sea-island cottons.
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Affiliation(s)
- Nian Wang
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China.
| | - Yuanxue Li
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China.
| | - Qingying Meng
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China.
| | - Meilin Chen
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China.
| | - Mi Wu
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China.
| | - Ruiting Zhang
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China.
| | - Zhiyong Xu
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China.
| | - Jie Sun
- Key Laboratory of Oasis Ecology Agricultural of Xinjiang Bingtuan, College of Agriculture, Shihezi University, Shihezi 832000, Xinjiang, China.
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China.
| | - Xinhui Nie
- Key Laboratory of Oasis Ecology Agricultural of Xinjiang Bingtuan, College of Agriculture, Shihezi University, Shihezi 832000, Xinjiang, China.
| | - Daojun Yuan
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China.
| | - Zhongxu Lin
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China; Hubei Hongshan Laboratory, Wuhan 430070, China; Key Laboratory of Oasis Ecology Agricultural of Xinjiang Bingtuan, College of Agriculture, Shihezi University, Shihezi 832000, Xinjiang, China.
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20
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Zhou M, Xu L, Xu D, Chen W, Khan J, Hu Y, Huang H, Wei H, Zhang Y, Chusongsang P, Tanasarnprasert K, Hu X, Limpanont Y, Lv Z. Chromosome-scale genome of the human blood fluke Schistosoma mekongi and its implications for public health. Infect Dis Poverty 2023; 12:104. [PMID: 38017557 PMCID: PMC10683246 DOI: 10.1186/s40249-023-01160-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 11/13/2023] [Indexed: 11/30/2023] Open
Abstract
BACKGROUND Schistosoma mekongi is a human blood fluke causing schistosomiasis that threatens approximately 1.5 million humans in the world. Nonetheless, the limited available S. mekongi genomic resources have hindered understanding of its biology and parasite-host interactions for disease management and pathogen control. The aim of our study was to integrate multiple technologies to construct a high-quality chromosome-level assembly of the S. mekongi genome. METHODS The reference genome for S. mekongi was generated through integrating Illumina, PacBio sequencing, 10 × Genomics linked-read sequencing, and high-throughput chromosome conformation capture (Hi-C) methods. In this study, we conducted de novo assembly, alignment, and gene prediction to assemble and annotate the genome. Comparative genomics allowed us to compare genomes across different species, shedding light on conserved regions and evolutionary relationships. Additionally, our transcriptomic analysis focused on genes associated with parasite-snail interactions in S. mekongi infection. We employed gene ontology (GO) enrichment analysis for functional annotation of these genes. RESULTS In the present study, the S. mekongi genome was both assembled into 8 pseudochromosomes with a length of 404 Mb, with contig N50 and scaffold N50 lengths of 1168 kb and 46,759 kb, respectively. We detected that 43% of the genome consists of repeat sequences and predicted 9103 protein-coding genes. We also focused on proteases, particularly leishmanolysin-like metalloproteases (M8), which are crucial in the invasion of hosts by 12 flatworm species. Through phylogenetic analysis, it was discovered that the M8 gene exhibits lineage-specific amplification among the genus Schistosoma. Lineage-specific expansion of M8 was observed in blood flukes. Additionally, the results of the RNA-seq revealed that a mass of genes related to metabolic and biosynthetic processes were up-regulated, which might be beneficial for cercaria production. CONCLUSIONS This study delivers a high-quality, chromosome-scale reference genome of S. mekongi, enhancing our understanding of the divergence and evolution of Schistosoma. The molecular research conducted here also plays a pivotal role in drug discovery and vaccine development. Furthermore, our work greatly advances the understanding of host-parasite interactions, providing crucial insights for schistosomiasis intervention strategies.
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Affiliation(s)
- Minyu Zhou
- Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-Sen University, Guangzhou, China
- Department of Pathogen Biology and Biosafety, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
| | - Lian Xu
- Key Laboratory of Neuroregeneration, Ministry of Education and Jiangsu Province, Co-Innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong University, Nantong, China
| | - Dahua Xu
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, College of Biomedical Information and Engineering, Hainan Medical University, Haikou, China
| | - Wen Chen
- Key Laboratory of Vascular Biology and Translational Medicine, Medical School, Hunan University of Chinese Medicine, Changsha, China
| | - Jehangir Khan
- Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-Sen University, Guangzhou, China
- Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Haikou, China
| | - Yue Hu
- Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-Sen University, Guangzhou, China
- Department of Pathogen Biology and Biosafety, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
| | - Hui Huang
- Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-Sen University, Guangzhou, China
- Department of Pathogen Biology and Biosafety, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
| | - Hang Wei
- Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-Sen University, Guangzhou, China
- Department of Pathogen Biology and Biosafety, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
| | - Yiqing Zhang
- Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-Sen University, Guangzhou, China
- Department of Pathogen Biology and Biosafety, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
| | - Phiraphol Chusongsang
- Department of Social and Environmental Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Kanthi Tanasarnprasert
- Department of Social and Environmental Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Xiang Hu
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, China.
| | - Yanin Limpanont
- Department of Social and Environmental Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.
| | - Zhiyue Lv
- Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-Sen University, Guangzhou, China.
- Department of Pathogen Biology and Biosafety, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China.
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He Z, Chao H, Zhou X, Ni Q, Hu Y, Yu R, Wang M, Li C, Chen J, Chen Y, Chen Y, Cui C, Zhang L, Chen M, Chen D. A chromosome-level genome assembly provides insights into Cornus wilsoniana evolution, oil biosynthesis, and floral bud development. HORTICULTURE RESEARCH 2023; 10:uhad196. [PMID: 38023476 PMCID: PMC10673659 DOI: 10.1093/hr/uhad196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 09/25/2023] [Indexed: 12/01/2023]
Abstract
Cornus wilsoniana W. is a woody oil plant with high oil content and strong hypolipidemic effects, making it a valuable species for medicinal, landscaping, and ecological purposes in China. To advance genetic research on this species, we employed PacBio together with Hi-C data to create a draft genome assembly for C. wilsoniana. Based on an 11-chromosome anchored chromosome-level assembly, the estimated genome size was determined to be 843.51 Mb. The N50 contig size and N50 scaffold size were calculated to be 4.49 and 78.00 Mb, respectively. Furthermore, 30 474 protein-coding genes were annotated. Comparative genomics analysis revealed that C. wilsoniana diverged from its closest species ~12.46 million years ago (Mya). Furthermore, the divergence between Cornaceae and Nyssaceae occurred >62.22 Mya. We also found evidence of whole-genome duplication events and whole-genome triplication γ, occurring at ~44.90 and 115.86 Mya. We further inferred the origins of chromosomes, which sheds light on the complex evolutionary history of the karyotype of C. wilsoniana. Through transcriptional and metabolic analysis, we identified two FAD2 homologous genes that may play a crucial role in controlling the oleic to linoleic acid ratio. We further investigated the correlation between metabolites and genes and identified 33 MADS-TF homologous genes that may affect flower morphology in C. wilsoniana. Overall, this study lays the groundwork for future research aimed at identifying the genetic basis of crucial traits in C. wilsoniana.
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Affiliation(s)
- Zhenxiang He
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Haoyu Chao
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Xinkai Zhou
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Qingyang Ni
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yueming Hu
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Ranran Yu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Minghuai Wang
- Forest Protection Department, Guangdong Academy of Forestry, Guangzhou 510520, China
| | - Changzhu Li
- State Key Laboratory of Utilization of Woody Oil Resource, Hunan Academy of Forestry, Changsha 410004, China
| | - Jingzhen Chen
- State Key Laboratory of Utilization of Woody Oil Resource, Hunan Academy of Forestry, Changsha 410004, China
| | - Yunzhu Chen
- State Key Laboratory of Utilization of Woody Oil Resource, Hunan Academy of Forestry, Changsha 410004, China
| | - Yong Chen
- Xishan Forest Farm, Dazu District, Chongqing 402360, China
| | - Chunyi Cui
- Longshan Forest Farm, Lechang 512221, China
| | - Liangbo Zhang
- State Key Laboratory of Utilization of Woody Oil Resource, Hunan Academy of Forestry, Changsha 410004, China
- Hunan Horticultural Research Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Ming Chen
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Dijun Chen
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
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22
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Wang Y, Yang T, Wang D, Gou R, Jiang Y, Zhang G, Zheng Y, Gao D, Chen L, Zhang X, Wei Z. Chromosome level genome assembly of colored calla lily (Zantedeschia elliottiana). Sci Data 2023; 10:605. [PMID: 37689767 PMCID: PMC10492805 DOI: 10.1038/s41597-023-02516-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 08/22/2023] [Indexed: 09/11/2023] Open
Abstract
The colored calla lily is an ornamental floral plant native to southern Africa, belonging to the Zantedeschia genus of the Araceae family. We generated a high-quality chromosome-level genome of the colored calla lily, with a size of 1,154 Mb and a contig N50 of 42 Mb. We anchored 98.5% of the contigs (1,137 Mb) into 16 pseudo-chromosomes, and identified 60.18% of the sequences (694 Mb) as repetitive sequences. Functional annotations were assigned to 95.1% of the predicted protein-coding genes (36,165). Additionally, we annotated 469 miRNAs, 1,652 tRNAs, 10,033 rRNAs, and 1,677 snRNAs. Furthermore, Gypsy-type LTR retrotransposons insertions in the genome are the primary factor causing significant genome size variation in Araceae species. This high-quality genome assembly provides valuable resources for understanding genome size differences within the Araceae family and advancing genomic research on colored calla lily.
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Affiliation(s)
- Yi Wang
- Institute of Grassland, Flowers and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Tuo Yang
- College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Di Wang
- Institute of Grassland, Flowers and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
- College of Horticultural Science & Technology, Hebei Key Laboratory of Horticultural Germplasm Excavation and Innovative Utilization/Hebei Higher Institute Application Technology Research and Development Center of Horticultural Plant Biological Breeding, Hebei Normal University of Science & Technology, Qinhuangdao, 66004, China
| | - Rongxin Gou
- Institute of Grassland, Flowers and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
- College of Horticultural Science & Technology, Hebei Key Laboratory of Horticultural Germplasm Excavation and Innovative Utilization/Hebei Higher Institute Application Technology Research and Development Center of Horticultural Plant Biological Breeding, Hebei Normal University of Science & Technology, Qinhuangdao, 66004, China
| | - Yin Jiang
- Institute of Grassland, Flowers and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
- College of Horticultural Science & Technology, Hebei Key Laboratory of Horticultural Germplasm Excavation and Innovative Utilization/Hebei Higher Institute Application Technology Research and Development Center of Horticultural Plant Biological Breeding, Hebei Normal University of Science & Technology, Qinhuangdao, 66004, China
| | - Guojun Zhang
- College of Horticultural Science & Technology, Hebei Key Laboratory of Horticultural Germplasm Excavation and Innovative Utilization/Hebei Higher Institute Application Technology Research and Development Center of Horticultural Plant Biological Breeding, Hebei Normal University of Science & Technology, Qinhuangdao, 66004, China
| | - Yuhong Zheng
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing, 210014, China
| | - Dan Gao
- Smartgenomics Technology Institute, Tianjin, 301700, China
| | - Liyang Chen
- Smartgenomics Technology Institute, Tianjin, 301700, China
| | - Xiuhai Zhang
- Institute of Grassland, Flowers and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China.
| | - Zunzheng Wei
- Institute of Grassland, Flowers and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China.
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Zhang H, Song J, Dong F, Li Y, Ge S, Wei B, Liu Y. Multiple roles of wheat ferritin genes during stress treatment and TaFER5D-1 as a positive regulator in response to drought and salt tolerance. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 202:107921. [PMID: 37544121 DOI: 10.1016/j.plaphy.2023.107921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 05/25/2023] [Accepted: 07/28/2023] [Indexed: 08/08/2023]
Abstract
Ferritin not only regulates the plant's iron content but also plays a significant role in the plant's development and resistance to oxidative damage. However, the role of the FER family in wheat has not been systematically elucidated. In this study, 39 FERs identified from wheat and its ancestral species were clustered into two subgroups, and gene members from the same group contain relatively conservative protein models. The structural analyses indicated that the gene members from the same group contained relatively conserved protein models. The cis-acting elements and expression patterns analysis suggested that TaFERs might play an important role combating to abiotic and biotic stresses. In the transcriptional analysis, the TaFER5D-1 gene was found to be significantly up-regulated under drought and salt stresses and was, therefore, selected to further explore the biological functions Moreover, the GFP expression assay revealed the subcellular localization of TaFER5D-1 proteins in the chloroplast, nucleus, membrane and cytoplasm. Over-expression of TaFER5D-1 in transgenic Arabidopsis lines conferred greater tolerance to drought and salt stress. According to the qRT-PCR data, TaFER5D-1 gene over-expression increased the expression of genes related to root development (Atsweet-17 and AtRSL4), iron storage (AtVIT1 and AtYSL1), and stress response (AtGolS1 and AtCOR47). So it is speculated that TaFER5D-1 could improve stress tolerance by promoting root growth, iron storage, and stress-response ability. Thus, the current study provides insight into the role of TaFER genes in wheat.
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Affiliation(s)
- Huadong Zhang
- Institute of Food Crops, Hubei Academy of Agricultural Sciences/Key Laboratory of Crop Molecular Breeding, Ministry of Agriculture and Rural Affairs/Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Wuhan, 430064, China
| | - Jinghan Song
- National Key Laboratory of Rice Biology/Institute of Crop Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Feiyan Dong
- Institute of Food Crops, Hubei Academy of Agricultural Sciences/Key Laboratory of Crop Molecular Breeding, Ministry of Agriculture and Rural Affairs/Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Wuhan, 430064, China
| | - Yaqian Li
- Institute of Food Crops, Hubei Academy of Agricultural Sciences/Key Laboratory of Crop Molecular Breeding, Ministry of Agriculture and Rural Affairs/Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Wuhan, 430064, China
| | - Shijie Ge
- Institute of Food Crops, Hubei Academy of Agricultural Sciences/Key Laboratory of Crop Molecular Breeding, Ministry of Agriculture and Rural Affairs/Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Wuhan, 430064, China
| | - Bo Wei
- Peking University Institute of Advanced Agricultural Sciences/National Key Laboratory of Wheat Improvement, Weifang, Shandong, 261325, China.
| | - Yike Liu
- Institute of Food Crops, Hubei Academy of Agricultural Sciences/Key Laboratory of Crop Molecular Breeding, Ministry of Agriculture and Rural Affairs/Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Wuhan, 430064, China.
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24
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Meng F, Chu T, Feng P, Li N, Song C, Li C, Leng L, Song X, Chen W. Genome assembly of Polygala tenuifolia provides insights into its karyotype evolution and triterpenoid saponin biosynthesis. HORTICULTURE RESEARCH 2023; 10:uhad139. [PMID: 37671073 PMCID: PMC10476160 DOI: 10.1093/hr/uhad139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Accepted: 07/05/2023] [Indexed: 09/07/2023]
Abstract
Polygala tenuifolia is a perennial medicinal plant that has been widely used in traditional Chinese medicine for treating mental diseases. However, the lack of genomic resources limits the insight into its evolutionary and biological characterization. In the present work, we reported the P. tenuifolia genome, the first genome assembly of the Polygalaceae family. We sequenced and assembled this genome by a combination of Illumnina, PacBio HiFi, and Hi-C mapping. The assembly includes 19 pseudochromosomes covering ~92.68% of the assembled genome (~769.62 Mb). There are 36 463 protein-coding genes annotated in this genome. Detailed comparative genome analysis revealed that P. tenuifolia experienced two rounds of whole genome duplication that occurred ~39-44 and ~18-20 million years ago, respectively. Accordingly, we systematically reconstructed ancestral chromosomes of P. tenuifolia and inferred its chromosome evolution trajectories from the common ancestor of core eudicots to the present species. Based on the transcriptomics data, enzyme genes and transcription factors involved in the synthesis of triterpenoid saponin in P. tenuifolia were identified. Further analysis demonstrated that whole-genome duplications and tandem duplications play critical roles in the expansion of P450 and UGT gene families, which contributed to the synthesis of triterpenoid saponins. The genome and transcriptome data will not only provide valuable resources for comparative and functional genomic researches on Polygalaceae, but also shed light on the synthesis of triterpenoid saponin.
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Affiliation(s)
- Fanbo Meng
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Basic Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
- >State Key Laboratory of Southwestern Chinese Medicine Resources, Innovative Institute of Chengdu University of Traditional Chinese Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Tianzhe Chu
- >State Key Laboratory of Southwestern Chinese Medicine Resources, Innovative Institute of Chengdu University of Traditional Chinese Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Pengmian Feng
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Basic Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Nan Li
- School of Life Sciences, North China University of Science and Technology, Tangshan 063210, China
| | - Chi Song
- >State Key Laboratory of Southwestern Chinese Medicine Resources, Innovative Institute of Chengdu University of Traditional Chinese Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
- Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Chunjin Li
- School of Life Sciences, North China University of Science and Technology, Tangshan 063210, China
| | - Liang Leng
- >State Key Laboratory of Southwestern Chinese Medicine Resources, Innovative Institute of Chengdu University of Traditional Chinese Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
- Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Xiaoming Song
- School of Life Sciences, North China University of Science and Technology, Tangshan 063210, China
| | - Wei Chen
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Basic Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
- >State Key Laboratory of Southwestern Chinese Medicine Resources, Innovative Institute of Chengdu University of Traditional Chinese Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
- School of Life Sciences, North China University of Science and Technology, Tangshan 063210, China
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25
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Fan Z, Wang LY, Xiao L, Tan B, Luo B, Ren TY, Liu N, Zhang ZS, Bai M. Lampshade web spider Ectatosticta davidi chromosome-level genome assembly provides evidence for its phylogenetic position. Commun Biol 2023; 6:748. [PMID: 37463957 PMCID: PMC10354039 DOI: 10.1038/s42003-023-05129-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Accepted: 07/10/2023] [Indexed: 07/20/2023] Open
Abstract
The spider of Ectatosticta davidi, belonging to the lamp-shade web spider family, Hypochilidae, which is closely related to Hypochilidae and Filistatidae and recovered as sister of the rest Araneomorphs spiders. Here we show the final assembled genome of E. davidi with 2.16 Gb in 15 chromosomes. Then we confirm the evolutionary position of Hypochilidae. Moreover, we find that the GMC gene family exhibit high conservation throughout the evolution of true spiders. We also find that the MaSp genes of E. davidi may represent an early stage of MaSp and MiSp genes in other true spiders, while CrSp shares a common origin with AgSp and PySp but differ from MaSp. Altogether, this study contributes to addressing the limited availability of genomic sequences from Hypochilidae spiders, and provides a valuable resource for investigating the genomic evolution of spiders.
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Affiliation(s)
- Zheng Fan
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, 100101, Beijing, China
- School of Life Sciences, Southwest University, 400700, Chongqing, China
| | - Lu-Yu Wang
- School of Life Sciences, Southwest University, 400700, Chongqing, China
| | - Lin Xiao
- School of Life Sciences, Southwest University, 400700, Chongqing, China
| | - Bing Tan
- School of Life Sciences, Southwest University, 400700, Chongqing, China
| | - Bin Luo
- School of Life Sciences, Southwest University, 400700, Chongqing, China
| | - Tian-Yu Ren
- School of Life Sciences, Southwest University, 400700, Chongqing, China
| | - Ning Liu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, 100101, Beijing, China.
| | - Zhi-Sheng Zhang
- School of Life Sciences, Southwest University, 400700, Chongqing, China.
| | - Ming Bai
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, 100101, Beijing, China.
- Northeast Asia Biodiversity Research Center, Northeast Forestry University, 150040, Harbin, China.
- University of Chinese Academy of Sciences, 100049, Beijing, China.
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26
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Ramos-Barbero MD, Gómez-Gómez C, Sala-Comorera L, Rodríguez-Rubio L, Morales-Cortes S, Mendoza-Barberá E, Vique G, Toribio-Avedillo D, Blanch AR, Ballesté E, Garcia-Aljaro C, Muniesa M. Characterization of crAss-like phage isolates highlights Crassvirales genetic heterogeneity and worldwide distribution. Nat Commun 2023; 14:4295. [PMID: 37463935 PMCID: PMC10354031 DOI: 10.1038/s41467-023-40098-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 07/07/2023] [Indexed: 07/20/2023] Open
Abstract
Crassvirales (crAss-like phages) are an abundant group of human gut-specific bacteriophages discovered in silico. The use of crAss-like phages as human fecal indicators is proposed but the isolation of only seven cultured strains of crAss-like phages to date has greatly hindered their study. Here, we report the isolation and genetic characterization of 25 new crAss-like phages (termed crAssBcn) infecting Bacteroides intestinalis, belonging to the order Crassvirales, genus Kehishuvirus and, based on their genomic variability, classified into six species. CrAssBcn phage genomes are similar to ΦCrAss001 but show genomic and aminoacidic differences when compared to other crAss-like phages of the same family. CrAssBcn phages are detected in fecal metagenomes around the world at a higher frequency than ΦCrAss001. This study increases the known crAss-like phage isolates and their abundance and heterogeneity open the question of what member of the Crassvirales group should be selected as human fecal marker.
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Affiliation(s)
- María Dolores Ramos-Barbero
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Diagonal 643. Annex. Floor 0, E-08028, Barcelona, Spain
| | - Clara Gómez-Gómez
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Diagonal 643. Annex. Floor 0, E-08028, Barcelona, Spain
| | - Laura Sala-Comorera
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Diagonal 643. Annex. Floor 0, E-08028, Barcelona, Spain
| | - Lorena Rodríguez-Rubio
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Diagonal 643. Annex. Floor 0, E-08028, Barcelona, Spain
| | - Sara Morales-Cortes
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Diagonal 643. Annex. Floor 0, E-08028, Barcelona, Spain
| | - Elena Mendoza-Barberá
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Diagonal 643. Annex. Floor 0, E-08028, Barcelona, Spain
| | - Gloria Vique
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Diagonal 643. Annex. Floor 0, E-08028, Barcelona, Spain
| | - Daniel Toribio-Avedillo
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Diagonal 643. Annex. Floor 0, E-08028, Barcelona, Spain
| | - Anicet R Blanch
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Diagonal 643. Annex. Floor 0, E-08028, Barcelona, Spain
| | - Elisenda Ballesté
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Diagonal 643. Annex. Floor 0, E-08028, Barcelona, Spain
| | - Cristina Garcia-Aljaro
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Diagonal 643. Annex. Floor 0, E-08028, Barcelona, Spain
| | - Maite Muniesa
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Diagonal 643. Annex. Floor 0, E-08028, Barcelona, Spain.
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27
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Sun L, Jiang C, Su F, Cui W, Yang H. Chromosome-level genome assembly of the sea cucumber Apostichopus japonicus. Sci Data 2023; 10:454. [PMID: 37443361 PMCID: PMC10344927 DOI: 10.1038/s41597-023-02368-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 07/05/2023] [Indexed: 07/15/2023] Open
Abstract
Sea cucumber is a morphologically diverse and ecologically important clade of echinoderms. The sea cucumber Apostichopus japonicus is the most economically valuable species of sea cucumber. The initial assembly of the A. japonicus genome was released in 2017. However, this genome assembly is fragmented and lacks relative position information of genes on chromosomes. In this study, we produced a high-quality chromosome-level genome of A. japonicus using Pacbio HiFi long-reads and Hi-C sequencing data. The assembled A. japonicus genome spanned 671.60 Mb with a contig N50 size of 17.20 Mb and scaffold N50 size of 29.65 Mb. A total of 99.9% of the assembly was anchored to 23 chromosomes. In total, 19,828 genes were annotated, and 97.2% of BUSCO genes were fully represented. This high-quality genome of A. japonicus will not only aid in the development of sustainable aquaculture practices, but also lay a foundation for a deeper understanding of their genetic makeup, evolutionary history, and ecological adaptation.
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Affiliation(s)
- Lina Sun
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Chunxi Jiang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Fang Su
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wei Cui
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hongsheng Yang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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28
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Pan K, Dai S, Tian J, Zhang J, Liu J, Li M, Li S, Zhang S, Gao B. Chromosome-level genome and multi-omics analyses provide insights into the geo-herbalism properties of Alpinia oxyphylla. FRONTIERS IN PLANT SCIENCE 2023; 14:1161257. [PMID: 37360712 PMCID: PMC10285302 DOI: 10.3389/fpls.2023.1161257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 05/17/2023] [Indexed: 06/28/2023]
Abstract
Introduction Alpinia oxyphylla Miquel (A. oxyphylla), one of the "Four Famous South Medicines" in China, is an essential understory cash crop that is planted widely in the Hainan, Guangdong, Guangxi, and Fujian provinces. Particularly, A. oxyphylla from Hainan province is highly valued as the best national product for geo-herbalism and is an important indicator of traditional Chinese medicine efficacy. However, the molecular mechanism underlying the formation of its quality remains unspecified. Methods To this end, we employed a multi-omics approach to investigate the authentic quality formation of A. oxyphylla. Results In this study, we present a high-quality chromosome-level genome assembly of A. oxyphylla, with contig N50 of 76.96 Mb and a size of approximately 2.08Gb. A total of 38,178 genes were annotated, and the long terminal repeats were found to have a high frequency of 61.70%. Phylogenetic analysis demonstrated a recent whole-genome duplication event (WGD), which occurred before A. oxyphylla's divergence from W. villosa (~14 Mya) and is shared by other species from the Zingiberaceae family (Ks, ~0.3; 4DTv, ~0.125). Further, 17 regions from four provinces were comprehensively assessed for their metabolite content, and the quality of these four regions varied significantly. Finally, genomic, metabolic, and transcriptomic analyses undertaken on these regions revealed that the content of nootkatone in Hainan was significantly different from that in other provinces. Discussion Overall, our findings provide novel insights into germplasm conservation, geo-herbalism evaluation, and functional genomic research for the medicinal plant A. oxyphylla.
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Affiliation(s)
- Kun Pan
- Hainan Provincial Key Laboratory for Research and Development of Tropical Herbs, Haikou Key Laboratory of Li Nationality Medicine, Hainan Ouality Monitoring and Technology Service Center for Chinese Materia MedicaRaw Materials, School of Pharmacy, Hainan Medical University, Haikou, Hainan, China
| | - Shuiping Dai
- Hainan Provincial Key Laboratory for Research and Development of Tropical Herbs, Haikou Key Laboratory of Li Nationality Medicine, Hainan Ouality Monitoring and Technology Service Center for Chinese Materia MedicaRaw Materials, School of Pharmacy, Hainan Medical University, Haikou, Hainan, China
| | - Jianping Tian
- Hainan Provincial Key Laboratory for Research and Development of Tropical Herbs, Haikou Key Laboratory of Li Nationality Medicine, Hainan Ouality Monitoring and Technology Service Center for Chinese Materia MedicaRaw Materials, School of Pharmacy, Hainan Medical University, Haikou, Hainan, China
| | - Junqing Zhang
- Hainan Provincial Key Laboratory for Research and Development of Tropical Herbs, Haikou Key Laboratory of Li Nationality Medicine, Hainan Ouality Monitoring and Technology Service Center for Chinese Materia MedicaRaw Materials, School of Pharmacy, Hainan Medical University, Haikou, Hainan, China
- Academician Workstation of Hainan Province and The Specific Research Fund of The Innovation Platform for Academicians of Hainan Province, Haikou, Hainan, China
| | - Jiaqi Liu
- Hainan Provincial Key Laboratory for Research and Development of Tropical Herbs, Haikou Key Laboratory of Li Nationality Medicine, Hainan Ouality Monitoring and Technology Service Center for Chinese Materia MedicaRaw Materials, School of Pharmacy, Hainan Medical University, Haikou, Hainan, China
| | - Ming Li
- Hainan Provincial Key Laboratory for Research and Development of Tropical Herbs, Haikou Key Laboratory of Li Nationality Medicine, Hainan Ouality Monitoring and Technology Service Center for Chinese Materia MedicaRaw Materials, School of Pharmacy, Hainan Medical University, Haikou, Hainan, China
| | - Shanshan Li
- Hainan Provincial Key Laboratory for Research and Development of Tropical Herbs, Haikou Key Laboratory of Li Nationality Medicine, Hainan Ouality Monitoring and Technology Service Center for Chinese Materia MedicaRaw Materials, School of Pharmacy, Hainan Medical University, Haikou, Hainan, China
| | - Shengkui Zhang
- School of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, Shandong, China
| | - Bingmiao Gao
- Hainan Provincial Key Laboratory for Research and Development of Tropical Herbs, Haikou Key Laboratory of Li Nationality Medicine, Hainan Ouality Monitoring and Technology Service Center for Chinese Materia MedicaRaw Materials, School of Pharmacy, Hainan Medical University, Haikou, Hainan, China
- Academician Workstation of Hainan Province and The Specific Research Fund of The Innovation Platform for Academicians of Hainan Province, Haikou, Hainan, China
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29
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Ma F, Wang Y, Su B, Zhao C, Yin D, Chen C, Yang Y, Wang C, Luo B, Wang H, Deng Y, Xu P, Yin G, Jian J, Liu K. Gap-free genome assembly of anadromous Coilia nasus. Sci Data 2023; 10:360. [PMID: 37280262 DOI: 10.1038/s41597-023-02278-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 05/30/2023] [Indexed: 06/08/2023] Open
Abstract
The Chinese tapertail anchovy, Coilia nasus, is a socioeconomically important anadromous fish that migrates from near ocean waters to freshwater to spawn every spring. The analysis of genomic architecture and information of C. nasus were hindered by the previously released versions of reference genomes with gaps. Here, we report the assembly of a chromosome-level gap-free genome of C. nasus by incorporating high-coverage and accurate long-read sequence data with multiple assembly strategies. All 24 chromosomes were assembled without gaps, representing the highest completeness and assembly quality. We assembled the genome with a size of 851.67 Mb and used BUSCO to estimate the completeness of the assembly as 92.5%. Using a combination of de novo prediction, protein homology and RNA-seq annotation, 21,900 genes were functionally annotated, representing 99.68% of the total predicted protein-coding genes. The availability of gap-free reference genomes for C. nasus will provide the opportunity for understanding genome structure and function, and will also lay a solid foundation for further management and conservation of this important species.
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Affiliation(s)
- Fengjiao Ma
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, 214081, China
| | - Yinping Wang
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, 214081, China
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, China
| | - Bixiu Su
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Chenxi Zhao
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Denghua Yin
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, China
| | - Chunhai Chen
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Yanping Yang
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, China
| | - Chenhe Wang
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Bei Luo
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Hongqi Wang
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Yanmin Deng
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, China
| | - Pao Xu
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, 214081, China.
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, China.
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, China.
| | - Guojun Yin
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, 214081, China.
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, China.
| | - Jianbo Jian
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China.
| | - Kai Liu
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, 214081, China.
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, China.
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, China.
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Pieplow C, Wessel G. Functional annotation of a hugely expanded nanos repertoire in Lytechinus variegatus, the green sea urchin. Mol Reprod Dev 2023; 90:310-322. [PMID: 37039283 PMCID: PMC10225336 DOI: 10.1002/mrd.23684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 02/17/2023] [Accepted: 03/18/2023] [Indexed: 04/12/2023]
Abstract
Nanos genes encode essential RNA-binding proteins involved in germline determination and germline stem cell maintenance. When examining diverse classes of echinoderms, typically three, sometimes four, nanos genes are present. In this analysis, we identify and annotate nine nanos orthologs in the green sea urchin, Lytechinus variegatus (Lv). All nine genes are transcribed and grouped into three distinct classes. Class one includes the germline Nanos, with one member: Nanos2. Class two includes Nanos3-like genes, with significant sequence similarity to Nanos3 in the purple sea urchin, Strongylocentrotus purpuratus (Sp), but with wildly variable expression patterns. The third class includes several previously undescribed nanos zinc-finger genes that may be the result of duplications of Nanos2. All nine nanos transcripts occupy unique genomic loci and are expressed with unique temporal profiles during development. Importantly, here we describe and characterize the unique genomic location, conservation, and phylogeny of the Lv ortholog of the well-studied Sp Nanos2. However, in addition to the conserved germline functioning Nanos2, the green sea urchin appears to be an outlier in the echinoderm phyla with eight additional nanos genes. We hypothesize that this expansion of nanos gene members may be the result of a previously uncharacterized L1-class transposon encoded on the opposite strand of a nanos2 pseudogene present on chromosome 12 in this species. The expansion of nanos genes described here represents intriguing insights into germline specification and nanos evolution in this species of sea urchin.
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Affiliation(s)
- Cosmo Pieplow
- MCB Department, Division of Biomedicine, Brown University, Providence RI 02912
| | - Gary Wessel
- MCB Department, Division of Biomedicine, Brown University, Providence RI 02912
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31
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Wang C, Wu DD, Yuan YH, Yao MC, Han JL, Wu YJ, Shan F, Li WP, Zhai JQ, Huang M, Peng SM, Cai QH, Yu JY, Liu QX, Liu ZY, Li LX, Teng MS, Huang W, Zhou JY, Zhang C, Chen W, Tu XL. Population genomic analysis provides evidence of the past success and future potential of South China tiger captive conservation. BMC Biol 2023; 21:64. [PMID: 37069598 PMCID: PMC10111772 DOI: 10.1186/s12915-023-01552-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 02/21/2023] [Indexed: 04/19/2023] Open
Abstract
BACKGROUND Among six extant tiger subspecies, the South China tiger (Panthera tigris amoyensis) once was widely distributed but is now the rarest one and extinct in the wild. All living South China tigers are descendants of only two male and four female wild-caught tigers and they survive solely in zoos after 60 years of effective conservation efforts. Inbreeding depression and hybridization with other tiger subspecies were believed to have occurred within the small, captive South China tiger population. It is therefore urgently needed to examine the genomic landscape of existing genetic variation among the South China tigers. RESULTS In this study, we assembled a high-quality chromosome-level genome using long-read sequences and re-sequenced 29 high-depth genomes of the South China tigers. By combining and comparing our data with the other 40 genomes of six tiger subspecies, we identified two significantly differentiated genomic lineages among the South China tigers, which harbored some rare genetic variants introgressed from other tiger subspecies and thus maintained a moderate genetic diversity. We noticed that the South China tiger had higher FROH values for longer runs of homozygosity (ROH > 1 Mb), an indication of recent inbreeding/founder events. We also observed that the South China tiger had the least frequent homozygous genotypes of both high- and moderate-impact deleterious mutations, and lower mutation loads than both Amur and Sumatran tigers. Altogether, our analyses indicated an effective genetic purging of deleterious mutations in homozygous states from the South China tiger, following its population contraction with a controlled increase in inbreeding based on its pedigree records. CONCLUSIONS The identification of two unique founder/genomic lineages coupled with active genetic purging of deleterious mutations in homozygous states and the genomic resources generated in our study pave the way for a genomics-informed conservation, following the real-time monitoring and rational exchange of reproductive South China tigers among zoos.
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Affiliation(s)
- Chen Wang
- Guangzhou Zoo & Guangzhou Wildlife Research Center, Guangzhou, 510070, China
| | - Dong-Dong Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, China
- Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China
- Kunming College of Life Science, University of the Chinese Academy of Sciences, Kunming, 650204, China
| | | | - Meng-Cheng Yao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, China
- Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China
- Kunming College of Life Science, University of the Chinese Academy of Sciences, Kunming, 650204, China
| | - Jian-Lin Han
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China
- International Livestock Research Institute (ILRI), Nairobi, 00100, Kenya
| | - Ya-Jiang Wu
- Guangzhou Zoo & Guangzhou Wildlife Research Center, Guangzhou, 510070, China
| | - Fen Shan
- Guangzhou Zoo & Guangzhou Wildlife Research Center, Guangzhou, 510070, China
| | - Wan-Ping Li
- Guangzhou Zoo & Guangzhou Wildlife Research Center, Guangzhou, 510070, China
| | - Jun-Qiong Zhai
- Guangzhou Zoo & Guangzhou Wildlife Research Center, Guangzhou, 510070, China
| | - Mian Huang
- Guangzhou Zoo & Guangzhou Wildlife Research Center, Guangzhou, 510070, China
| | - Shi-Ming Peng
- Guangzhou Zoo & Guangzhou Wildlife Research Center, Guangzhou, 510070, China
| | - Qin-Hui Cai
- Guangzhou Zoo & Guangzhou Wildlife Research Center, Guangzhou, 510070, China
| | | | | | | | - Lin-Xiang Li
- Suzhou Shangfangshan Forest Zoo, Suzhou, 215009, China
| | | | - Wei Huang
- Nanchang Zoo, Nanchang, 330025, China
| | - Jun-Ying Zhou
- Chinese Association of Zoological Gardens, Beijing, 100037, China
| | - Chi Zhang
- Qinghai Province Key Laboratory of Crop Molecular Breeding, Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810008, Qinghai, China
| | - Wu Chen
- Guangzhou Zoo & Guangzhou Wildlife Research Center, Guangzhou, 510070, China.
| | - Xiao-Long Tu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, China.
- Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China.
- Kunming College of Life Science, University of the Chinese Academy of Sciences, Kunming, 650204, China.
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Joglekar A, Hu W, Zhang B, Narykov O, Diekhans M, Balacco J, Ndhlovu LC, Milner TA, Fedrigo O, Jarvis ED, Sheynkman G, Korkin D, Ross ME, Tilgner HU. Single-cell long-read mRNA isoform regulation is pervasive across mammalian brain regions, cell types, and development. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.02.535281. [PMID: 37066387 PMCID: PMC10103983 DOI: 10.1101/2023.04.02.535281] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/22/2023]
Abstract
RNA isoforms influence cell identity and function. Until recently, technological limitations prevented a genome-wide appraisal of isoform influence on cell identity in various parts of the brain. Using enhanced long-read single-cell isoform sequencing, we comprehensively analyze RNA isoforms in multiple mouse brain regions, cell subtypes, and developmental timepoints from postnatal day 14 (P14) to adult (P56). For 75% of genes, full-length isoform expression varies along one or more axes of phenotypic origin, underscoring the pervasiveness of isoform regulation across multiple scales. As expected, splicing varies strongly between cell types. However, certain gene classes including neurotransmitter release and reuptake as well as synapse turnover, harbor significant variability in the same cell type across anatomical regions, suggesting differences in network activity may influence cell-type identity. Glial brain-region specificity in isoform expression includes strong poly(A)-site regulation, whereas neurons have stronger TSS regulation. Furthermore, developmental patterns of cell-type specific splicing are especially pronounced in the murine adolescent transition from P21 to P28. The same cell type traced across development shows more isoform variability than across adult anatomical regions, indicating a coordinated modulation of functional programs dictating neural development. As most cell-type specific exons in P56 mouse hippocampus behave similarly in newly generated data from human hippocampi, these principles may be extrapolated to human brain. However, human brains have evolved additional cell-type specificity in splicing, suggesting gain-of-function isoforms. Taken together, we present a detailed single-cell atlas of full-length brain isoform regulation across development and anatomical regions, providing a previously unappreciated degree of isoform variability across multiple scales of the brain.
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Affiliation(s)
- Anoushka Joglekar
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
- Center for Neurogenetics, Weill Cornell Medicine, New York, NY, USA
| | - Wen Hu
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
- Center for Neurogenetics, Weill Cornell Medicine, New York, NY, USA
| | | | - Oleksandr Narykov
- Bioinformatics and Computational Biology Program, Worcester Polytechnic Institute, Worcester, MA, USA
- Computer Science Department, Worcester Polytechnic Institute, Worcester, MA, USA
- Data Science Program, Worcester Polytechnic Institute, Worcester, MA, USA
| | - Mark Diekhans
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | | | - Lishomwa C Ndhlovu
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York, NY, USA
| | - Teresa A Milner
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Olivier Fedrigo
- Vertebrate Genome Lab, the Rockefeller University, New York, NY
| | - Erich D Jarvis
- Vertebrate Genome Lab, the Rockefeller University, New York, NY
- Laboratory of Neurogenetics of Language, the Rockefeller University, New York, NY
- Howard Hughes Medical Institute, Chevy Chase, MD
| | - Gloria Sheynkman
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
- UVA Comprehensive Cancer Center, University of Virginia, Charlottesville, Virginia, USA
| | - Dmitry Korkin
- Bioinformatics and Computational Biology Program, Worcester Polytechnic Institute, Worcester, MA, USA
- Computer Science Department, Worcester Polytechnic Institute, Worcester, MA, USA
- Data Science Program, Worcester Polytechnic Institute, Worcester, MA, USA
| | - M Elizabeth Ross
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
- Center for Neurogenetics, Weill Cornell Medicine, New York, NY, USA
| | - Hagen U Tilgner
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
- Center for Neurogenetics, Weill Cornell Medicine, New York, NY, USA
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Huang F, Chen P, Tang X, Zhong T, Yang T, Nwafor CC, Yang C, Ge X, An H, Li Z, Cahoon EB, Zhang C. Genome assembly of the Brassicaceae diploid Orychophragmus violaceus reveals complex whole-genome duplication and evolution of dihydroxy fatty acid metabolism. PLANT COMMUNICATIONS 2023; 4:100432. [PMID: 36071666 PMCID: PMC10030321 DOI: 10.1016/j.xplc.2022.100432] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 07/27/2022] [Accepted: 09/05/2022] [Indexed: 05/04/2023]
Abstract
Orychophragmus violaceus is a Brassicaceae species widely cultivated in China, particularly as a winter cover crop in northern China because of its low-temperature tolerance and low water demand. Recently, O. violaceus has also been cultivated as a potential industrial oilseed crop because of its abundant 24-carbon dihydroxy fatty acids (diOH-FAs), which contribute to superior high-temperature lubricant properties. In this study, we performed de novo assembly of the O. violaceus genome. Whole-genome synteny analysis of the genomes of its relatives demonstrated that O. violaceus is a diploid that has undergone an extra whole-genome duplication (WGD) after the Brassicaceae-specific α-WGD event, with a basic chromosome number of x = 12. Formation of diOH-FAs is hypothesized to have occurred after the WGD event. Based on the genome and the transcriptome data from multiple stages of seed development, we predicted that OvDGAT1-1 and OvDGAT1-2 are candidate genes for the regulation of diOH-FA storage in O. violaceus seeds. These results may greatly facilitate the development of heat-tolerant and eco-friendly plant-based lubricants using O. violaceus seed oil and improve our understanding of the genomic evolution of Brassicaceae.
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Affiliation(s)
- Fan Huang
- National Key Lab of Crop Genetic Improvement and College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Peng Chen
- National Key Lab of Crop Genetic Improvement and College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Xinyu Tang
- National Key Lab of Crop Genetic Improvement and College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Ting Zhong
- National Key Lab of Crop Genetic Improvement and College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Taihua Yang
- National Key Lab of Crop Genetic Improvement and College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Chinedu Charles Nwafor
- National Key Lab of Crop Genetic Improvement and College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Chao Yang
- National Key Lab of Crop Genetic Improvement and College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Xianhong Ge
- National Key Lab of Crop Genetic Improvement and College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Hong An
- Bioinformatics and Analytics Core, University of Missouri-Columbia, Columbia, MO, USA
| | - Zaiyun Li
- National Key Lab of Crop Genetic Improvement and College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Edgar B Cahoon
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, USA; Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, USA.
| | - Chunyu Zhang
- National Key Lab of Crop Genetic Improvement and College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China.
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Wang M, Ruan L, Liu M, Liu Z, He J, Zhang L, Wang Y, Shi H, Chen M, Yang F, Zeng R, He J, Guo C, Chen J. The genome of a vestimentiferan tubeworm (Ridgeia piscesae) provides insights into its adaptation to a deep-sea environment. BMC Genomics 2023; 24:72. [PMID: 36774470 PMCID: PMC9921365 DOI: 10.1186/s12864-023-09166-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 02/03/2023] [Indexed: 02/13/2023] Open
Abstract
BACKGROUND Vestimentifera (Polychaeta, Siboglinidae) is a taxon of deep-sea worm-like animals living in deep-sea hydrothermal vents, cold seeps, and organic falls. The morphology and lifespan of Ridgeia piscesae, which is the only vestimentiferan tubeworm species found in the hydrothermal vents on the Juan de Fuca Ridge, vary greatly according to endemic environment. Recent analyses have revealed the genomic basis of adaptation in three vent- and seep-dwelling vestimentiferan tubeworms. However, the evolutionary history and mechanism of adaptation in R. piscesae, a unique species in the family Siboglinidae, remain to be investigated. RESULT We assembled a draft genome of R. piscesae collected at the Cathedral vent of the Juan de Fuca Ridge. Comparative genomic analysis showed that vent-dwelling tubeworms with a higher growth rate had smaller genome sizes than seep-dwelling tubeworms that grew much slower. A strong positive correlation between repeat content and genome size but not intron size and the number of protein-coding genes was identified in these deep-sea tubeworm species. Evolutionary analysis revealed that Ridgeia pachyptila and R. piscesae, the two tubeworm species that are endemic to hydrothermal vents of the eastern Pacific, started to diverge between 28.5 and 35 million years ago. Four genes involved in cell proliferation were found to be subject to positive selection in the genome of R. piscesae. CONCLUSION Ridgeia pachyptila and R. piscesae started to diverge after the formation of the Gorda/Juan de Fuca/Explorer ridge systems and the East Pacific Rise. The high growth rates of vent-dwelling tubeworms might be derived from their small genome sizes. Cell proliferation is important for regulating the growth rate in R. piscesae.
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Affiliation(s)
- Muhua Wang
- grid.12981.330000 0001 2360 039XState Key Laboratory for Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082 China ,grid.12981.330000 0001 2360 039XChina-ASEAN Belt and Road Joint Laboratory On Mariculture Technology, Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275 China
| | - Lingwei Ruan
- grid.453137.70000 0004 0406 0561State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources of Ministry of Natural Resources, Fujian Key Laboratory of Marine Genetic Resources, Ministry of Natural Resources, Third Institute of Oceanography, Xiamen, 361005 China
| | - Meng Liu
- grid.410753.4Novogene Bioinformatics Institute, Beijing, 100083 China
| | - Zixuan Liu
- grid.12981.330000 0001 2360 039XState Key Laboratory for Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082 China
| | - Jian He
- grid.12981.330000 0001 2360 039XState Key Laboratory for Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082 China ,grid.12981.330000 0001 2360 039XChina-ASEAN Belt and Road Joint Laboratory On Mariculture Technology, Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275 China
| | - Long Zhang
- grid.12981.330000 0001 2360 039XState Key Laboratory for Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082 China
| | - Yuanyuan Wang
- grid.12981.330000 0001 2360 039XState Key Laboratory for Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082 China
| | - Hong Shi
- grid.453137.70000 0004 0406 0561State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources of Ministry of Natural Resources, Fujian Key Laboratory of Marine Genetic Resources, Ministry of Natural Resources, Third Institute of Oceanography, Xiamen, 361005 China
| | - Mingliang Chen
- grid.453137.70000 0004 0406 0561State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources of Ministry of Natural Resources, Fujian Key Laboratory of Marine Genetic Resources, Ministry of Natural Resources, Third Institute of Oceanography, Xiamen, 361005 China
| | - Feng Yang
- grid.453137.70000 0004 0406 0561State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources of Ministry of Natural Resources, Fujian Key Laboratory of Marine Genetic Resources, Ministry of Natural Resources, Third Institute of Oceanography, Xiamen, 361005 China
| | - Runying Zeng
- grid.453137.70000 0004 0406 0561State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources of Ministry of Natural Resources, Fujian Key Laboratory of Marine Genetic Resources, Ministry of Natural Resources, Third Institute of Oceanography, Xiamen, 361005 China
| | - Jianguo He
- State Key Laboratory for Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082, China. .,China-ASEAN Belt and Road Joint Laboratory On Mariculture Technology, Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China.
| | - Changjun Guo
- State Key Laboratory for Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082, China. .,China-ASEAN Belt and Road Joint Laboratory On Mariculture Technology, Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China.
| | - Jianming Chen
- State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources of Ministry of Natural Resources, Fujian Key Laboratory of Marine Genetic Resources, Ministry of Natural Resources, Third Institute of Oceanography, Xiamen, 361005, China. .,Fujian Key Laboratory On Conservation and Sustainable Utilization of Marine Biodiversity, Fuzhou Institute of Oceanography, Minjiang University, Fuzhou, 350108, China.
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35
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Sun G, Xie S, Tang L, Zhao C, Zhang M, Huang L. Comparative genomics of five Valsa species gives insights on their pathogenicity evolution. G3 (BETHESDA, MD.) 2023; 13:jkac312. [PMID: 36454665 PMCID: PMC9911072 DOI: 10.1093/g3journal/jkac312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 01/21/2022] [Accepted: 11/07/2022] [Indexed: 12/03/2022]
Abstract
Valsa is a genus of ascomycetes within the Valsaceae family. This family includes many wood destructive pathogens such as the well known Valsa mali and Valsa pyri which cause canker diseases in fruit trees and threaten the global fruit production. Lack of genomic information of this family is impeding our understandings about their evolution and genetic basis of their pathogenicity divergence. Here, we report genome assemblies of Valsa malicola, Valsa persoonii, and Valsa sordida which represent close relatives of Valsa mali and Valsa pyri with different host preferences. Comparative genomics analysis revealed that segmental rearrangements, inversions, and translocations frequently occurred among Valsa spp. genomes. Gene families that exhibited gene copy expansions tended to be associated with secondary metabolism, transmembrane transport, and pyrophosphatase activities. Orthologous genes in regions lost synteny exhibited significantly higher rate of synonymous substitution (KS) than those in regions retained synteny. Moreover, among these genes, membrane transporter families associated with antidrug (MFS, DHA) activities and nutrient transportation (SP and APCs) activities were significantly over-represented. Lineage specific synonymous substitution (KS) and nonsynonymous substitution (KA) analysis based on the phylogeny constructed from 11 fungal species identified a set of genes with selection signatures in Valsa clade and these genes were significantly enriched in functions associated with fatty acid beta-oxidation, DNA helicase activity, and ATPase activity. Furthermore, unique genes that possessed or retained by each of the five Valsa species are more likely part of the secondary metabolic (SM) gene clusters. SM gene clusters conserved across five Valsa species showed various degrees of diversification in both identity and completeness. All 11 syntenically conserved SM clusters showed differential expression during the infection of apple branch with Valsa mali suggesting involvements of secondary metabolism in the pathogenicity of Valsa species.
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Affiliation(s)
- Guangchao Sun
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling 712100, Shaanxi, China
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Shichang Xie
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Lin Tang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Chao Zhao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Mian Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Lili Huang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling 712100, Shaanxi, China
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Zhao L, Li XD, Jiang T, Wang H, Dan Z, Xu SQ, Guan DL. The Chromosome-Level Genome of Hestina assimilis (Lepidoptera: Nymphalidae) Reveals the Evolution of Saprophagy-Related Genes in Brush-Footed Butterflies. Int J Mol Sci 2023; 24:ijms24032087. [PMID: 36768416 PMCID: PMC9917059 DOI: 10.3390/ijms24032087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 01/06/2023] [Accepted: 01/16/2023] [Indexed: 01/21/2023] Open
Abstract
Most butterflies feed on nectar, while some saprophagous butterflies forage on various non-nectar foods. To date, little is known about the genomic and molecular shifts associated with the evolution of the saprophagous feeding strategy. Here, we assembled the high-quality chromosome-level genome of Hestina assimilis to explore its saprophagous molecular and genetic mechanisms. This chromosome-level genome of H. assimilis is 412.82 Mb, with a scaffold N50 of 15.70 Mb. In total, 98.11% of contigs were anchored to 30 chromosomes. Compared with H. assimilis and other Nymphalidae butterflies, the genes of metabolism and detoxification experienced expansions. We annotated 80 cytochrome P450 (CYP) genes in the H. assimilis genome, among which genes belonging to the CYP4 subfamily were significantly expanded (p < 0.01). These P450 genes were unevenly distributed and mainly concentrated on chromosomes 6-9. We identified 33 olfactory receptor (OR), 20 odorant-binding protein (OBP), and six gustatory receptor (GR) genes in the H. assimilis genome, which were fewer than in the nectarivorous Danaus plexippus. A decreased number of OBP, OR, and GR genes implied that H. assimilis should resort less to olfaction and gustation than their nectarivorous counterparts, which need highly specialized olfactory and gustatory functions. Moreover, we found one site under positive selection occurred in residue 996 (phenylalanine) of GR genes exclusive to H. assimilis, which is conservative in most lineages. Our study provides support for the adaptive evolution of feeding habits in butterflies.
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Affiliation(s)
- Lu Zhao
- College of Life Sciences, Shaanxi Normal University, Xi’an 710119, China
| | - Xiao-Dong Li
- School of Chemistry and Bioengineering, Hechi University, Yizhou 546300, China
| | - Tao Jiang
- College of Life Sciences, Shaanxi Normal University, Xi’an 710119, China
| | - Hang Wang
- College of Life Sciences, Shaanxi Normal University, Xi’an 710119, China
| | - Zhicuo Dan
- College of Life Sciences, Shaanxi Normal University, Xi’an 710119, China
| | - Sheng-Quan Xu
- College of Life Sciences, Shaanxi Normal University, Xi’an 710119, China
- Correspondence: (S.-Q.X.); (D.-L.G.)
| | - De-Long Guan
- College of Life Sciences, Shaanxi Normal University, Xi’an 710119, China
- School of Chemistry and Bioengineering, Hechi University, Yizhou 546300, China
- Correspondence: (S.-Q.X.); (D.-L.G.)
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Wadapurkar RM, Sivaram A, Vyas R. Computational studies reveal co-occurrence of two mutations in IL7R gene of high-grade serous carcinoma patients. J Biomol Struct Dyn 2022; 40:13310-13324. [PMID: 34657565 DOI: 10.1080/07391102.2021.1987326] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Major cause of mortality in ovarian cancer can be attributed to a lack of specific and sensitive biomarkers for diagnosis and prognosis of the disease. Uncovering the mutations in genes involved in crucial oncogenic pathways is a key step in discovery and development of novel biomarkers. Whole exome sequencing (WES) is a powerful method for the detection of cancer driver mutations. The present work focuses on identifying functionally damaging mutations in patients with high-grade serous ovarian carcinoma (HGSC) through computational analysis of WES. In this study, WES data of HGSC patients was retrieved from the genomic literature available in sequence read archive, the variants were identified and comprehensive structural and functional analysis was performed. Interestingly, I66T and V138I mutations were found to be co-occurring in the IL7R gene in four out of five HGSC patient samples investigated in this study. The V138I mutation was located in the fibronectin type-3 domain and computationally assessed to be causing disruptive effects on the structure and dynamics of IL7R protein. This mutation was found to be co-occurring with the neutral I66T mutation in the same domain which compensated the disruptive effects of V138I variant. These comprehensive studies point to a hitherto unexplored significant role of the IL7R gene in ovarian carcinoma. It is envisaged that the work will lay the foundation for the development of a novel biomarker with potential application in molecular profiling and in estimation of the disease prognosis.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Rucha M Wadapurkar
- MIT School of Bioengineering Sciences & Research, MIT-ADT University, Pune, Maharashtra, India
| | - Aruna Sivaram
- MIT School of Bioengineering Sciences & Research, MIT-ADT University, Pune, Maharashtra, India
| | - Renu Vyas
- MIT School of Bioengineering Sciences & Research, MIT-ADT University, Pune, Maharashtra, India
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Yin D, Chen C, Lin D, Zhang J, Ying C, Liu Y, Liu W, Cao Z, Zhao C, Wang C, Liang L, Xu P, Jian J, Liu K. Gapless genome assembly of East Asian finless porpoise. Sci Data 2022; 9:765. [PMID: 36513679 PMCID: PMC9747978 DOI: 10.1038/s41597-022-01868-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 11/23/2022] [Indexed: 12/14/2022] Open
Abstract
In recent years, conservation efforts have increased for rare and endangered aquatic wildlife, especially cetaceans. However, the East Asian finless porpoise (Neophocaena asiaeorientalis sunameri), which has a wide distribution in China, has received far less attention and protection. As an endangered small cetacean, the lack of a chromosomal-level reference for the East Asian finless porpoise limits our understanding of its population genetics and conservation biology. To address this issue, we combined PacBio HiFi long reads and Hi-C sequencing data to generate a gapless genome of the East Asian finless porpoise that is approximately 2.5 Gb in size over its 21 autosomes and two sex chromosomes (X and Y). A total of 22,814 protein-coding genes were predicted where ~97.31% were functionally annotated. This high-quality genome assembly of East Asian finless porpoise will not only provide new resources for the comparative genomics of cetaceans and conservation biology of threatened species, but also lay a foundation for more speciation, ecology, and evolutionary studies. Measurement(s) Neophocaena asiaeorientalis sunameri • Gapless genome assembly • sequence annotation Technology Type(s) MGISEQ. 2000 • PacBio HiFi Sequencing • Hi-C Sample Characteristic - Organism Neophocaena asiaeorientalis sunameri Sample Characteristic - Environment seawater Sample Characteristic - Location Yellow Sea near Lianyungang City, Jiangsu Province, China.
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Affiliation(s)
- Denghua Yin
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, China
| | - Chunhai Chen
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Danqing Lin
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, China
| | - Jialu Zhang
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, China
| | - Congping Ying
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, 214081, China
| | - Yan Liu
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, China
| | - Wang Liu
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, 214081, China
| | - Zhichen Cao
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, China
| | - Chenxi Zhao
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Chenhe Wang
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Liping Liang
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Pao Xu
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, China.
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, 214081, China.
| | - Jianbo Jian
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China.
| | - Kai Liu
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, China.
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, 214081, China.
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, China.
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Chi G, Cao X, Li Q, Yao C, Lu F, Liu Y, Cao M, He N. Computationally Guided Enzymatic Studies on Schizochytrium-Sourced Malonyl-CoA:ACP Transacylase. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:13922-13934. [PMID: 36264009 DOI: 10.1021/acs.jafc.2c05447] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The malonyl-CoA:ACP transacylase (MAT) domain is responsible for the selection and incorporation of malonyl building blocks in the biosynthesis of polyunsaturated fatty acids (PUFAs) in eukaryotic microalgae (Schizochytrium) and marine bacteria (Moritella marina, Photobacterium profundum, and Shewanella). Elucidation of the structural basis underlying the substrate specificity and catalytic mechanism of the MAT will help to improve the yield and quality of PUFAs. Here, a methodology guided by molecular dynamics simulations was carried out to identify and mutate specificity-conferring residues within the MAT domain of Schizochytrium. Combining mutagenesis, cell-free protein synthesis, and in vitro biochemical assay, we dissected nearby interactions and molecular mechanisms relevant for binding and catalysis and found that the reorientation of the Ser154 Cβ-Oγ bond establishes distinctive proton-transfer chains (His153-Ser154 and Asn235-His153-Ser154) for catalysis. Gln66 can be replaced by tyrosine to shorten the distance between His153 (Nε2) and Ser154 (Oγ), which facilitates a faster proton-transfer rate, allowing better use of acyl substrates than the wild type. Furthermore, we screened a mutant that displayed an 18.4% increase in PUFA accumulation. These findings provide important insights into the study of MAT through protein engineering and will benefit dissecting the molecular mechanisms of other PUFA-related catalytic domains.
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Affiliation(s)
- Guoxiang Chi
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
- The Key Laboratory for Synthetic Biotechnology of Xiamen City, Xiamen University, Xiamen 361005, China
| | - Xingyu Cao
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
- The Key Laboratory for Synthetic Biotechnology of Xiamen City, Xiamen University, Xiamen 361005, China
| | - Qi Li
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
- The Key Laboratory for Synthetic Biotechnology of Xiamen City, Xiamen University, Xiamen 361005, China
| | - Chuanyi Yao
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
- The Key Laboratory for Synthetic Biotechnology of Xiamen City, Xiamen University, Xiamen 361005, China
| | - Fuping Lu
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Yihan Liu
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Mingfeng Cao
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
- The Key Laboratory for Synthetic Biotechnology of Xiamen City, Xiamen University, Xiamen 361005, China
| | - Ning He
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
- The Key Laboratory for Synthetic Biotechnology of Xiamen City, Xiamen University, Xiamen 361005, China
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Yang Z, Tian S, Li X, Dai Z, Yan A, Chen Z, Chen J, Tang Q, Cheng C, Xu Y, Deng C, Liu C, Kang L, Xie D, Zhao J, Chen X, Zhang X, Wu Y, Li A, Su J. Multi-omics provides new insights into the domestication and improvement of dark jute (Corchorus olitorius). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 112:812-829. [PMID: 36129373 DOI: 10.1111/tpj.15983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 08/31/2022] [Accepted: 09/15/2022] [Indexed: 06/15/2023]
Abstract
Jute (Corchorus sp.) is the most important bast fiber crop worldwide; however, the mechanisms underlying domestication and improvement remain largely unknown. We performed multi-omics analysis by integrating de novo sequencing, resequencing, and transcriptomic and epigenetic sequencing to clarify the domestication and improvement of dark jute Corchorus olitorius. We demonstrated that dark jute underwent early domestication and a relatively moderate genetic bottleneck during improvement breeding. A genome-wide association study of 11 important agronomic traits identified abundant candidate loci. We characterized the selective sweeps in the two breeding stages of jute, prominently, soil salinity differences played an important role in environmental adaptation during domestication, and the strongly selected genes for improvement had an increased frequency of favorable haplotypes. Furthermore, we speculated that an encoding auxin/indole-3-acetic acid protein COS07g_00652 could enhance the flexibility and strength of the stem to improve fiber yield. Our study not only provides valuable genetic resources for future fiber breeding in jute, but also is of great significance for reviewing the genetic basis of early crop breeding.
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Affiliation(s)
- Zemao Yang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China
| | - Shilin Tian
- Novogene Bioinformatics Institute, Beijing, 100015, China
- Department of Ecology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Xiangkong Li
- Novogene Bioinformatics Institute, Beijing, 100015, China
| | - Zhigang Dai
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China
| | - An Yan
- Natural Sciences and Science Education, National Institute of Education, Nanyang Technological University, 637616, Singapore
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, 117543, Singapore
| | - Zhong Chen
- Natural Sciences and Science Education, National Institute of Education, Nanyang Technological University, 637616, Singapore
| | - Jiquan Chen
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China
| | - Qing Tang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China
| | - Chaohua Cheng
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China
| | - Ying Xu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China
| | - Canhui Deng
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China
| | - Chan Liu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China
| | - Ling Kang
- Novogene Bioinformatics Institute, Beijing, 100015, China
| | - Dongwei Xie
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China
| | - Jian Zhao
- Novogene Bioinformatics Institute, Beijing, 100015, China
| | - Xiaojun Chen
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China
| | - Xiaoyu Zhang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China
| | - Yupeng Wu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China
| | - Alei Li
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China
| | - Jianguang Su
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China
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Zhang M, Wang Z, Jian S. Genome-Wide Identification and Functional Analysis of the GASA Gene Family Responding to Multiple Stressors in Canavalia rosea. Genes (Basel) 2022; 13:1988. [PMID: 36360226 PMCID: PMC9690345 DOI: 10.3390/genes13111988] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 10/25/2022] [Accepted: 10/26/2022] [Indexed: 08/15/2023] Open
Abstract
In plants, the Gibberellic Acid-Stimulated Arabidopsis (GASA) gene family is unique and responds to ubiquitous stress and hormones, playing important regulatory roles in the growth and development of plants, as well as in the resistance mechanisms to biotic and abiotic stress. In this study, a total of 23 CrGASAs were characterized in C. rosea using a genome-wide approach, and their phylogenetic relationships, gene structures, conserved motifs, chromosomal locations, gene duplications, and promoter regions were systematically analyzed. Expression profile analysis derived from transcriptome data showed that CrGASAs are expressed at higher levels in the flowers or fruit than in the leaves, vines, and roots. The expression of CrGASAs also showed habitat- and environmental-stress-regulated patterns in C. rosea analyzed by transcriptome and quantitative reverse transcription PCR (qRT-PCR). The heterologous induced expression of some CrGASAs in yeast enhanced the tolerance to H2O2, and some CrGASAs showed elevated heat tolerance and heavy metal (HM) Cd/Cu tolerance. These findings will provide an important foundation to elucidate the biological functions of CrGASA genes, especially their role in the ecological adaptation of specific plant species to tropical islands and reefs in C. rosea.
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Affiliation(s)
- Mei Zhang
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Zhengfeng Wang
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- Key Laboratory of Carbon Sequestration in Terrestrial Ecosystem, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Shuguang Jian
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
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Li Z, Yang Y, Chen B, Xia B, Li H, Zhou Y, He M. Genome-wide identification and expression analysis of SBP-box gene family reveal their involvement in hormone response and abiotic stresses in Chrysanthemum nankingense. PeerJ 2022; 10:e14241. [PMID: 36320567 PMCID: PMC9618261 DOI: 10.7717/peerj.14241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 09/23/2022] [Indexed: 01/24/2023] Open
Abstract
SQUAMOSA promoter-binding-protein (SBP)-box family proteins are a class of plant-specific transcription factors, and widely regulate the development of floral and leaf morphology in plant growth and involve in environment and hormone signal response. In this study, we isolated and identified 21 non-redundant SBP-box genes in Chrysanthemum nankingense with bioinformatics analysis. Sequence alignments of 21 CnSBP proteins discovered a highly conserved SBP domain including two zinc finger-like structures and a nuclear localization signal region. According to the amino acid sequence alignments, 67 SBP-box genes from Arabidopsis thaliana, rice, Artemisia annua and C. nankingense were clustered into eight groups, and the motif and gene structure analysis also sustained this classification. The gene evolution analysis indicated the CnSBP genes experienced a duplication event about 10 million years ago (Mya), and the CnSBP and AtSPL genes occurred a divergence at 24 Mya. Transcriptome data provided valuable information for tissue-specific expression profiles of the CnSBPs, which highly expressed in floral tissues and differentially expressed in leaf, root and stem organs. Quantitative Real-time Polymerase Chain Reaction data showed expression patterns of the CnSBPs under exogenous hormone and abiotic stress treatments, separately abscisic acid, salicylic acid, gibberellin A3, methyl jasmonate and ethylene spraying as well as salt and drought stresses, indicating that the candidate CnSBP genes showed differentiated spatiotemporal expression patterns in response to hormone and abiotic stresses. Our study provides a systematic genome-wide analysis of the SBP-box gene family in C. nankingense. In general, it provides a fundamental theoretical basis that SBP-box genes may regulate the resistance of stress physiology in chrysanthemum via exogenous hormone pathways.
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Affiliation(s)
- Ziwei Li
- College of Landscape Architecture, Northeast Forestry University, Harbin, Heilongjiang, China
| | - Yujia Yang
- College of Landscape Architecture, Northeast Forestry University, Harbin, Heilongjiang, China
| | - Bin Chen
- College of Landscape Architecture, Northeast Forestry University, Harbin, Heilongjiang, China
| | - Bin Xia
- College of Landscape Architecture, Northeast Forestry University, Harbin, Heilongjiang, China
| | - Hongyao Li
- College of Landscape Architecture, Northeast Forestry University, Harbin, Heilongjiang, China
| | - Yunwei Zhou
- College of Horticulture, Jilin Agricultural University, Jilin, China
| | - Miao He
- College of Landscape Architecture, Northeast Forestry University, Harbin, Heilongjiang, China
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Liu S, Storti M, Finazzi G, Bowler C, Dorrell RG. A metabolic, phylogenomic and environmental atlas of diatom plastid transporters from the model species Phaeodactylum. FRONTIERS IN PLANT SCIENCE 2022; 13:950467. [PMID: 36212359 PMCID: PMC9546453 DOI: 10.3389/fpls.2022.950467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Accepted: 09/02/2022] [Indexed: 06/16/2023]
Abstract
Diatoms are an important group of algae, contributing nearly 40% of total marine photosynthetic activity. However, the specific molecular agents and transporters underpinning the metabolic efficiency of the diatom plastid remain to be revealed. We performed in silico analyses of 70 predicted plastid transporters identified by genome-wide searches of Phaeodactylum tricornutum. We considered similarity with Arabidopsis thaliana plastid transporters, transcriptional co-regulation with genes encoding core plastid metabolic pathways and with genes encoded in the mitochondrial genomes, inferred evolutionary histories using single-gene phylogeny, and environmental expression trends using Tara Oceans meta-transcriptomics and meta-genomes data. Our data reveal diatoms conserve some of the ion, nucleotide and sugar plastid transporters associated with plants, such as non-specific triose phosphate transporters implicated in the transport of phosphorylated sugars, NTP/NDP and cation exchange transporters. However, our data also highlight the presence of diatom-specific transporter functions, such as carbon and amino acid transporters implicated in intricate plastid-mitochondria crosstalk events. These confirm previous observations that substrate non-specific triose phosphate transporters (TPT) may exist as principal transporters of phosphorylated sugars into and out of the diatom plastid, alongside suggesting probable agents of NTP exchange. Carbon and amino acid transport may be related to intricate metabolic plastid-mitochondria crosstalk. We additionally provide evidence from environmental meta-transcriptomic/meta- genomic data that plastid transporters may underpin diatom sensitivity to ocean warming, and identify a diatom plastid transporter (J43171) whose expression may be positively correlated with temperature.
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Affiliation(s)
- Shun Liu
- Institut de Biologie de l’Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, Centre National De La Recherche Scientifique (CNRS), Institut National De La Santé Et De La Recherche Médicale (INSERM), Université Paris Sciences et Lettres (PSL), Paris, France
- CNRS Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, Paris, France
| | - Mattia Storti
- Univ. Grenoble Alpes (UGA), Centre National Recherche Scientifique (CNRS), Commissariat Energie Atomique Energies Alternatives (CEA), Institut National Recherche Agriculture Alimentation Environnement (INRAE), Interdisciplinary Research Institute of Grenoble (IRIG), Laboratoire de Physiologie Cellulaire et Végétale (LPCV), Grenoble, France
| | - Giovanni Finazzi
- Univ. Grenoble Alpes (UGA), Centre National Recherche Scientifique (CNRS), Commissariat Energie Atomique Energies Alternatives (CEA), Institut National Recherche Agriculture Alimentation Environnement (INRAE), Interdisciplinary Research Institute of Grenoble (IRIG), Laboratoire de Physiologie Cellulaire et Végétale (LPCV), Grenoble, France
| | - Chris Bowler
- Institut de Biologie de l’Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, Centre National De La Recherche Scientifique (CNRS), Institut National De La Santé Et De La Recherche Médicale (INSERM), Université Paris Sciences et Lettres (PSL), Paris, France
- CNRS Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, Paris, France
| | - Richard G. Dorrell
- Institut de Biologie de l’Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, Centre National De La Recherche Scientifique (CNRS), Institut National De La Santé Et De La Recherche Médicale (INSERM), Université Paris Sciences et Lettres (PSL), Paris, France
- CNRS Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, Paris, France
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Exploitation of a Bacterium-Encoded Lytic Transglycosylase by a Human Oral Lytic Phage To Facilitate Infection. J Virol 2022; 96:e0106322. [PMID: 36000841 PMCID: PMC9472602 DOI: 10.1128/jvi.01063-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Bacteriophages (phages) are an integral part of the human oral microbiome. Their roles in modulating bacterial physiology and shaping microbial communities have been discussed but remain understudied due to limited isolation and characterization of oral phage. Here, we report the isolation of LC001, a lytic phage targeting human oral Schaalia odontolytica (formerly known as Actinomyces odontolyticus) strain XH001. We showed that LC001 attached to and infected surface-grown, but not planktonic, XH001 cells, and it displayed remarkable host specificity at the strain level. Whole-genome sequencing of spontaneous LC001-resistant, surface-grown XH001 mutants revealed that the majority of the mutants carry nonsense or frameshift mutations in XH001 gene APY09_05145 (renamed ltg-1), which encodes a putative lytic transglycosylase (LT). The mutants are defective in LC001 binding, as revealed by direct visualization of the significantly reduced attachment of phage particles to the XH001 spontaneous mutants compared that to the wild type. Meanwhile, targeted deletion of ltg-1 produced a mutant that is defective in LC001 binding and resistant to LC001 infection even as surface-grown cells, while complementation of ltg-1 in the mutant background restored the LC001-sensitive phenotype. Intriguingly, similar expression levels of ltg-1 were observed in surface-grown and planktonic XH001, which displayed LC001-binding and nonbinding phenotypes, respectively. Furthermore, the overexpression of ltg-1 failed to confer an LC001-binding and -sensitive phenotype to planktonic XH001. Thus, our data suggested that rather than directly serving as a phage receptor, ltg-1-encoded LT may increase the accessibility of phage receptor, possibly via its enzymatic activity, by cleaving the peptidoglycan structure for better receptor exposure during peptidoglycan remodeling, a function that can be exploited by LC001 to facilitate infection. IMPORTANCE The evidence for the presence of a diverse and abundant phage population in the host-associated oral microbiome came largely from metagenomic analysis or the observation of virus-like particles within saliva/plaque samples, while the isolation of oral phage and investigation of their interaction with bacterial hosts are limited. Here, we report the isolation of LC001, the first lytic phage targeting oral Schaalia odontolytica. Our study suggested that LC001 may exploit the host bacterium-encoded lytic transglycosylase function to gain access to the receptor, thus facilitating its infection.
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Chromosomal-scale genome assembly of the near-extinction big-head schizothorcin (Aspiorhynchus laticeps). Sci Data 2022; 9:556. [PMID: 36085327 PMCID: PMC9463133 DOI: 10.1038/s41597-022-01671-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 08/19/2022] [Indexed: 11/08/2022] Open
Abstract
The big-head schizothorcin (Aspiorhynchus laticeps) is an endemic and near-extinction freshwater fish in Xinjiang, China. In this study, a chromosome-scale genome assembly of A. laticeps was generated using PacBio and Hi-C techniques. The PacBio sequencing data resulted in a 1.58 Gb assembly with a contig N50 of 1.27 Mb. Using Hi-C scaffolding approach, 88.38% of the initial assembled sequences were anchored and oriented into a chromosomal-scale assembly. The final assembly consisted of 25 pseudo-chromosomes that yielded 1.37 Gb of sequence, with a scaffold N50 of 44.02 Mb. BUSCO analysis showed a completeness score of 93.7%. The genome contained 48,537 predicted protein-coding genes and 58.31% of the assembly was annotated as repetitive sequences. Whole genome duplication events were further confirmed using 4dTv analysis. The genome assembly of A. laticeps should be valuable and important to understand the genetic adaptation and endangerment process of this species, which could lead to more effective management and conservation of the big-head schizothorcin and related freshwater fish species. Measurement(s) | Genome Assembly Sequence | Technology Type(s) | Next Generation Sequencing | Sample Characteristic - Organism | Aspiorhynchus laticeps | Sample Characteristic - Location | Xinjiang Autonomous Region |
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Li Y, Zhang H, Dong F, Zou J, Gao C, Zhu Z, Liu Y. Multiple roles of wheat calmodulin genes during stress treatment and TaCAM2-D as a positive regulator in response to drought and salt tolerance. Int J Biol Macromol 2022; 220:985-997. [PMID: 36027985 DOI: 10.1016/j.ijbiomac.2022.08.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Revised: 08/14/2022] [Accepted: 08/17/2022] [Indexed: 11/05/2022]
Abstract
Calmodulin (CaM) and calmodulin-like (CML) proteins are the most prominent calcium (Ca2+) sensing proteins involved in Ca2+-signaling processes. However, the function of these calcium sensors in wheat remains unclear. In this study, 15 TaCAMs and 113 TaCMLs were identified from the wheat reference genome. The analysis of cis-acting elements and expression patterns showed that TaCAMs might play an important role in response to abiotic and biotic stresses. TaCAM2-D gene was found to be significantly upregulated under drought and salt stresses, and thus, it was selected to further explore the biological function. Moreover, TaCAM2-D was observed to be localized in the nucleus, membrane and cytoplasm. Overexpression of TaCAM2-D in Arabidopsis conferred greater tolerance to drought and salt. The prediction analysis, the yeast two-hybrid analysis, and bimolecular fluorescence complementation assay indicated that TaCAM2-D interacted with TaMPK8, which is one of the wheat mitogen-activated protein kinases. Thus, the current study provides insights into the understanding of the TaCAM and TaCML genes in wheat.
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Affiliation(s)
- Yaqian Li
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Institute of Food Crops, Hubei Academy of Agricultural Sciences, Wheat Disease Biology Research Station for Central China, Wuhan, China
| | - Huadong Zhang
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Institute of Food Crops, Hubei Academy of Agricultural Sciences, Wheat Disease Biology Research Station for Central China, Wuhan, China
| | - Feiyan Dong
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Institute of Food Crops, Hubei Academy of Agricultural Sciences, Wheat Disease Biology Research Station for Central China, Wuhan, China
| | - Juan Zou
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Institute of Food Crops, Hubei Academy of Agricultural Sciences, Wheat Disease Biology Research Station for Central China, Wuhan, China
| | - Chunbao Gao
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Institute of Food Crops, Hubei Academy of Agricultural Sciences, Wheat Disease Biology Research Station for Central China, Wuhan, China
| | - Zhanwang Zhu
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Institute of Food Crops, Hubei Academy of Agricultural Sciences, Wheat Disease Biology Research Station for Central China, Wuhan, China.
| | - Yike Liu
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Institute of Food Crops, Hubei Academy of Agricultural Sciences, Wheat Disease Biology Research Station for Central China, Wuhan, China.
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Association of CARD14 Single-Nucleotide Polymorphisms with Psoriasis. Int J Mol Sci 2022; 23:ijms23169336. [PMID: 36012602 PMCID: PMC9409305 DOI: 10.3390/ijms23169336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 08/14/2022] [Accepted: 08/16/2022] [Indexed: 11/17/2022] Open
Abstract
Psoriasis is an immune-mediated chronic and painful disease characterized by red raised patches of inflamed skin that may have desquamation, silvery-white scales, itching and cracks. The susceptibility of developing psoriasis depends on multiple factors, with a complex interplay between genetic and environmental factors. Studies have suggested an association between autosomal dominant CARD14 (caspase recruitment domain-containing protein 14) gain-of-function mutations with the pathophysiology of psoriasis. In this study, non-synonymous single-nucleotide polymorphisms (nsSNPs) of CARD14 gene were assessed to determine their association with psoriasis in Pakistani population. A total of 123 subjects (63 patients with psoriasis and 60 normal controls) were included in this study. DNA was extracted from blood, and PCR analysis was performed followed by Sanger sequencing for 18 CARD14 specific nsSNPs (14 previously reported and the 4 most pathogenic nsSNPs identified using bioinformatics analysis). Among the 18 tested SNPs, only 2 nsSNP, rs2066965 (R547S) and rs34367357 (V585I), were found to be associated with psoriasis. Furthermore, rs2066965 heterozygous genotype was found to be more prevalent in patients with joint pain. Additionally, the 3D structure of CARD14 protein was predicted using alpha-fold2. NMSim web server was used to perform coarse grind simulations of wild-type CARD14 and two mutated structures. R547S increases protein flexibility, whereas V353I is shown to promote CARD14-induced NF-kappa B activation. This study confirms the association between two CARD14 nsSNPs, rs2066965 and rs34367357 with psoriasis in a Pakistani population, and could be helpful in identifying the role of CARD14 gene variants as potential genetic markers in patients with psoriasis.
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Yang Z, Jiang Y, Gong J, Li Q, Dun B, Liu D, Yin F, Yuan L, Zhou X, Wang H, Wang J, Zhan Z, Shah N, Nwafor CC, Zhou Y, Chen P, Zhu L, Li S, Wang B, Xiang J, Zhou Y, Li Z, Piao Z, Yang Q, Zhang C. R gene triplication confers European fodder turnip with improved clubroot resistance. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:1502-1517. [PMID: 35445530 PMCID: PMC9342621 DOI: 10.1111/pbi.13827] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 03/30/2022] [Accepted: 04/10/2022] [Indexed: 05/08/2023]
Abstract
Clubroot is one of the most important diseases for many important cruciferous vegetables and oilseed crops worldwide. Different clubroot resistance (CR) loci have been identified from only limited species in Brassica, making it difficult to compare and utilize these loci. European fodder turnip ECD04 is considered one of the most valuable resources for CR breeding. To explore the genetic and evolutionary basis of CR in ECD04, we sequenced the genome of ECD04 using de novo assembly and identified 978 candidate R genes. Subsequently, the 28 published CR loci were physically mapped to 15 loci in the ECD04 genome, including 62 candidate CR genes. Among them, two CR genes, CRA3.7.1 and CRA8.2.4, were functionally validated. Phylogenetic analysis revealed that CRA3.7.1 and CRA8.2.4 originated from a common ancestor before the whole-genome triplication (WGT) event. In clubroot susceptible Brassica species, CR-gene homologues were affected by transposable element (TE) insertion, resulting in the loss of CR function. It can be concluded that the current functional CR genes in Brassica rapa and non-functional CR genes in other Brassica species were derived from a common ancestral gene before WGT. Finally, a hypothesis for CR gene evolution is proposed for further discussion.
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Affiliation(s)
- Zhiquan Yang
- Hubei Key Laboratory of Agricultural BioinformaticsCollege of InformaticsHuazhong Agricultural UniversityWuhanChina
| | - Yingfen Jiang
- Institute of Crop ScienceAnhui Academy of Agricultural ScienceHefeiChina
- National Key Laboratory of Crop Genetic Improvement and College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Jianfang Gong
- National Key Laboratory of Crop Genetic Improvement and College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Qian Li
- National Key Laboratory of Crop Genetic Improvement and College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Bicheng Dun
- National Key Laboratory of Crop Genetic Improvement and College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
- Yangtze River Rare Plant Research InstituteChina Three Gorges CorporationYichangChina
| | - Dongxu Liu
- Hubei Key Laboratory of Agricultural BioinformaticsCollege of InformaticsHuazhong Agricultural UniversityWuhanChina
| | - Feifan Yin
- Hubei Key Laboratory of Agricultural BioinformaticsCollege of InformaticsHuazhong Agricultural UniversityWuhanChina
| | - Lei Yuan
- National Key Laboratory of Crop Genetic Improvement and College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Xueqing Zhou
- National Key Laboratory of Crop Genetic Improvement and College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Huiying Wang
- National Key Laboratory of Crop Genetic Improvement and College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Jing Wang
- Hubei Key Laboratory of Agricultural BioinformaticsCollege of InformaticsHuazhong Agricultural UniversityWuhanChina
| | - Zongxiang Zhan
- College of HorticultureShenyang Agricultural UniversityShenyangChina
| | - Nadil Shah
- National Key Laboratory of Crop Genetic Improvement and College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Chinedu Charles Nwafor
- National Key Laboratory of Crop Genetic Improvement and College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Yuanwei Zhou
- Yichang Academy of Agricultural ScienceYichangChina
| | - Peng Chen
- National Key Laboratory of Crop Genetic Improvement and College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Li Zhu
- Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains and College of Biology and Agriculture ResourceHuanggang Normal UniversityHuanggangChina
| | - Shisheng Li
- Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains and College of Biology and Agriculture ResourceHuanggang Normal UniversityHuanggangChina
| | - Bingrui Wang
- National Key Laboratory of Crop Genetic Improvement and College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Jun Xiang
- Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains and College of Biology and Agriculture ResourceHuanggang Normal UniversityHuanggangChina
| | - Yongming Zhou
- National Key Laboratory of Crop Genetic Improvement and College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Zaiyun Li
- National Key Laboratory of Crop Genetic Improvement and College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Zhongyun Piao
- College of HorticultureShenyang Agricultural UniversityShenyangChina
| | - Qingyong Yang
- Hubei Key Laboratory of Agricultural BioinformaticsCollege of InformaticsHuazhong Agricultural UniversityWuhanChina
| | - Chunyu Zhang
- National Key Laboratory of Crop Genetic Improvement and College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
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Hilário S, Gonçalves MFM, Fidalgo C, Tacão M, Alves A. Genome Analyses of Two Blueberry Pathogens: Diaporthe amygdali CAA958 and Diaporthe eres CBS 160.32. J Fungi (Basel) 2022; 8:jof8080804. [PMID: 36012791 PMCID: PMC9409727 DOI: 10.3390/jof8080804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 07/27/2022] [Accepted: 07/28/2022] [Indexed: 02/04/2023] Open
Abstract
The genus Diaporthe includes pathogenic species distributed worldwide and affecting a wide variety of hosts. Diaporthe amygdali and Diaporthe eres have been found to cause cankers, dieback, or twig blights on economically important crops such as soybean, almond, grapevine, and blueberry. Despite their importance as plant pathogens, the strategies of species of Diaporthe to infect host plants are poorly explored. To provide a genomic basis of pathogenicity, the genomes of D. amygdali CAA958 and D. eres CBS 160.32 were sequenced and analyzed. Cellular transporters involved in the transport of toxins, ions, sugars, effectors, and genes implicated in pathogenicity were detected in both genomes. Hydrolases and oxidoreductases were the most prevalent carbohydrate-active enzymes (CAZymes). However, analyses of the secreted proteins revealed that the secretome of D. eres CBS 160.32 is represented by 5.4% of CAZymes, whereas the secreted CAZymes repertoire of D. amygdali CAA958 represents 29.1% of all secretomes. Biosynthetic gene clusters (BGCs) encoding compounds related to phytotoxins and mycotoxins were detected in D. eres and D. amygdali genomes. The core gene clusters of the phytotoxin Fusicoccin A in D. amygdali are reported here through a genome-scale assembly. Comparative analyses of the genomes from 11 Diaporthe species revealed an average of 874 CAZymes, 101 secondary metabolite BGCs, 1640 secreted proteins per species, and genome sizes ranging from 51.5 to 63.6 Mbp. This study offers insights into the overall features and characteristics of Diaporthe genomes. Our findings enrich the knowledge about D. eres and D. amygdali, which will facilitate further research into the pathogenicity mechanisms of these species.
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Guo X, Meng X, Li Y, Qu C, Liu Y, Cao M, Yao X, Meng F, Wu J, Peng H, Peng D, Xing S, Jiang W. Comparative proteomics reveals biochemical changes in Salvia miltiorrhiza Bunge during sweating processing. JOURNAL OF ETHNOPHARMACOLOGY 2022; 293:115329. [PMID: 35490901 DOI: 10.1016/j.jep.2022.115329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Revised: 03/31/2022] [Accepted: 04/25/2022] [Indexed: 06/14/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Salvia miltiorrhiza Bunge is a bulk medicinal material used in traditional Chinese medicine, that can cure cardiovascular diseases, neurasthenia, and other conditions. Sweating is a frequently used method of processing S. miltiorrhiza for medical applications. We previously demonstrated changes to the metabolic profile of linoleic acid, glyoxylate, and dicarboxylate after Sweating. However, this alteration has not been explained at the molecular level. MATERIALS AND METHODS Fresh roots of Salvia miltiorrhiza Bunge were treated by the Sweating processing, and then the tandem mass tag technique was used to compare the proteome difference between Sweating S. miltiorrhiza and non-Sweating S. miltiorrhiza. RESULTS We identified a total of 850 differentially expressed proteins after Sweating treatment in S. miltiorrhiza, including 529 upregulated proteins and 321 downregulated proteins. GO enrichment analysis indicated that these differentially expressed proteins are involved in external encapsulating structure, cell wall, oxidoreductase activity, ligase activity, and others. Further analysis showed that CYP450, the pathogenesis-related protein Bet v 1 family, and the peroxidase domain were the major protein domains. KEGG enrichment identified 18 pathways, of which phenylpropanoid biosynthesis is the most important one related to the metabolite profile and is the principal chemical component of S. miltiorrhiza. CONCLUSION This study addressed potential molecular mechanisms in S. miltiorrhiza after Sweating, and the findings provide reasons for the changes in biochemical properties and metabolites changes which might cause pharmacological variation at the proteome level.
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Affiliation(s)
- Xiaohu Guo
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, 230012, China
| | - Xiaoxi Meng
- Department of Horticultural Science, University of Minnesota, MN, 55108, USA
| | - Yan Li
- Hunan Key Laboratory for Conservation and Utilization of Biological Resources in the Nanyue Mountainous Region, College of Life Sciences and Environment, Hengyang Normal University, Hengyang, 421008, China
| | - Changqing Qu
- Engineering Technology Research Center of Anti-aging, Chinese Herbal Medicine, Fuyang Normal University, Fuyang, 236037, China
| | - Yingying Liu
- College of Humanities and International Education Exchange, Anhui University of Chinese Medicine, Hefei, 230012, China
| | - Mengyang Cao
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, 230012, China
| | - Xiaoyan Yao
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, 230012, China
| | - Fei Meng
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, 230012, China
| | - Jing Wu
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, 230012, China
| | - Huasheng Peng
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, 230012, China
| | - Daiyin Peng
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, 230012, China; Institute of Traditional Chinese Medicine Resources Protection and Development, Anhui Academy of Chinese Medicine, Hefei, 230012, China; Synergetic Innovation Center of Anhui Authentic Chinese Medicine Quality Improvement, Hefei, 230038, China
| | - Shihai Xing
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, 230012, China; Synergetic Innovation Center of Anhui Authentic Chinese Medicine Quality Improvement, Hefei, 230038, China; Anhui Province Key Laboratory of Research & Development of Chinese Medicine, Hefei, 230012, China.
| | - Weimin Jiang
- Hunan Key Laboratory for Conservation and Utilization of Biological Resources in the Nanyue Mountainous Region, College of Life Sciences and Environment, Hengyang Normal University, Hengyang, 421008, China.
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