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Eaton KM, Krabbenhoft TJ, Backenstose NJC, Bernal MA. The chromosome-scale reference genome for the pinfish (Lagodon rhomboides) provides insights into their evolutionary and demographic history. G3 (BETHESDA, MD.) 2024; 14:jkae096. [PMID: 38739549 DOI: 10.1093/g3journal/jkae096] [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: 03/18/2024] [Revised: 03/18/2024] [Accepted: 05/06/2024] [Indexed: 05/16/2024]
Abstract
The pinfish (Lagodon rhomboides) is an ecologically, economically, and culturally relevant member of the family Sparidae, playing crucial roles in the marine food webs of the western Atlantic Ocean and Gulf of Mexico. Despite their high abundance and ecological importance, there is a scarcity of genomic resources for this species. We assembled and annotated a chromosome-scale genome for the pinfish, resulting in a highly contiguous 785 Mb assembly of 24 scaffolded chromosomes. The high-quality assembly contains 98.9% complete BUSCOs and shows strong synteny to other chromosome-scale genomes of fish in the family Sparidae, with a limited number of large-scale genomic rearrangements. Leveraging this new genomic resource, we found evidence of significant expansions of dietary gene families over the evolutionary history of the pinfish, which may be associated with an ontogenetic shift from carnivory to herbivory seen in this species. Estimates of historical patterns of population demography using this new reference genome identified several periods of population growth and contraction which were associated with ancient climatic shifts and sea level changes. This genome serves as a valuable reference for future studies of population genomics and differentiation and provides a much-needed genomic resource for this western Atlantic sparid.
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Affiliation(s)
- Katherine M Eaton
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
| | - Trevor J Krabbenhoft
- Department of Biological Sciences, University at Buffalo, Buffalo, NY 14260, USA
- Research and Education in Energy, Environment, and Water (RENEW) Institute, University at Buffalo, Buffalo, NY 14260, USA
| | | | - Moisés A Bernal
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
- Smithsonian Tropical Research Institute (STRI), Panama City, 0843-03092, Panama
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2
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Li L, Zhang H, Jin H, Guo J, Liu P, Yang J, Wang Z, Zhang E, Yu B, Shi L, He J, Wang P, Wei J, Zhong Y, Li W. Identification and characterization of two Bacillus anthracis bacteriophages. Arch Virol 2024; 169:134. [PMID: 38834736 DOI: 10.1007/s00705-024-06005-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Accepted: 02/05/2024] [Indexed: 06/06/2024]
Abstract
Anthrax is an acute infectious zoonotic disease caused by Bacillus anthracis, a bacterium that is considered a potential biological warfare agent. Bacillus bacteriophages shape the composition and evolution of bacterial communities in nature and therefore have important roles in the ecosystem community. B. anthracis phages are not only used in etiological diagnostics but also have promising prospects in clinical therapeutics or for disinfection in anthrax outbreaks. In this study, two temperate B. anthracis phages, vB_BanS_A16R1 (A16R1) and vB_BanS_A16R4 (A16R4), were isolated and showed siphovirus-like morphological characteristics. Genome sequencing showed that the genomes of phages A16R1 and A16R4 are 36,569 bp and 40,059 bp in length, respectively. A16R1 belongs to the genus Wbetavirus, while A16R4 belongs to the genus Hubeivirus and is the first phage of that genus found to lyse B. anthracis. Because these two phages can comparatively specifically lyse B. anthracis, they could be used as alternative diagnostic tools for identification of B. anthracis infections.
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Affiliation(s)
- Lun Li
- Yunnan Institute for Endemic Disease Control and Prevention, Dali, China
- Yunnan Key Laboratory for Zoonosis Control and Prevention, Dali, China
- School of Public Health, Dali University, Dali, China
- National Institute for Communicable Disease Control and Prevention (ICDC), China CDC, Beijing, China
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Beijing, China
| | - Huijuan Zhang
- National Institute for Communicable Disease Control and Prevention (ICDC), China CDC, Beijing, China
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Beijing, China
| | - Haixiao Jin
- National Institute for Communicable Disease Control and Prevention (ICDC), China CDC, Beijing, China
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Beijing, China
| | - Jin Guo
- National Institute for Communicable Disease Control and Prevention (ICDC), China CDC, Beijing, China
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Beijing, China
| | - Pan Liu
- Yunnan Institute for Endemic Disease Control and Prevention, Dali, China
- Yunnan Key Laboratory for Zoonosis Control and Prevention, Dali, China
| | - Jiao Yang
- Yunnan Institute for Endemic Disease Control and Prevention, Dali, China
- Yunnan Key Laboratory for Zoonosis Control and Prevention, Dali, China
| | - Zijian Wang
- Yunnan Institute for Endemic Disease Control and Prevention, Dali, China
- Yunnan Key Laboratory for Zoonosis Control and Prevention, Dali, China
| | - Enmin Zhang
- National Institute for Communicable Disease Control and Prevention (ICDC), China CDC, Beijing, China
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Beijing, China
| | - Binbin Yu
- Yunnan Institute for Endemic Disease Control and Prevention, Dali, China
- Yunnan Key Laboratory for Zoonosis Control and Prevention, Dali, China
| | - Liyuan Shi
- Yunnan Institute for Endemic Disease Control and Prevention, Dali, China
- Yunnan Key Laboratory for Zoonosis Control and Prevention, Dali, China
| | - Jinrong He
- National Institute for Communicable Disease Control and Prevention (ICDC), China CDC, Beijing, China
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Beijing, China
| | - Peng Wang
- Yunnan Institute for Endemic Disease Control and Prevention, Dali, China
- Yunnan Key Laboratory for Zoonosis Control and Prevention, Dali, China
| | - Jianchun Wei
- National Institute for Communicable Disease Control and Prevention (ICDC), China CDC, Beijing, China
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Beijing, China
| | - Youhong Zhong
- Yunnan Institute for Endemic Disease Control and Prevention, Dali, China.
- Yunnan Key Laboratory for Zoonosis Control and Prevention, Dali, China.
| | - Wei Li
- National Institute for Communicable Disease Control and Prevention (ICDC), China CDC, Beijing, China.
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Beijing, China.
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Wang Y, Shen M, Xu G, Yu H, Jia C, Zhu F, Meng Q, Xu D, Du S, Zhang D, Zhang Z. Comprehensive analysis of histophysiology, transcriptome and metabolome tolerance mechanisms in black porgy (Acanthopagrus schlegelii) under low temperature stress. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 927:172318. [PMID: 38608886 DOI: 10.1016/j.scitotenv.2024.172318] [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: 12/05/2023] [Revised: 04/05/2024] [Accepted: 04/06/2024] [Indexed: 04/14/2024]
Abstract
Low temperature stress has adverse effects on fish growth and reproduction, causing huge economic losses to the aquaculture industry. Especially, black porgy (Acanthopagrus schlegelii) farming industry in north of Yangtze River has been severely affected by low temperature for a long time. To explore the tolerance mechanism of black porgy to low temperature stress, the experiment was designed. The liver and gill tissues of black porgy were taken from the water temperature point of 15 °C (control group named as CG), 3.8 °C (cold sensitive group named as CS) and 2.8 °C (cold tolerant group named as CT) with a cooling rate of 3 °C/d from 15 °C for histophysiology, transcriptomics and metabolomics analysis. After cold stress, the histological results showed that the nucleus of the black porgy liver tissue appeared swelling, the cell arrangement was disordered; meanwhile the gill lamellae were twisted and broken, the epidermis was detached and aneurysm appeared. In addition, the expression of antioxidant, glucose metabolism and immune-related enzymes in the liver and gill of black porgy also changed significantly after low temperature stress. By analyzing the transcriptome and metabolome dates of black porgy liver, 3474 differentially expressed genes (DEGs) and 689 differentially expressed metabolites (DEMs) involved in low temperature stress were identified, respectively. The results of the transcriptome and metabolome combined analysis showed that individuals in the CS group mainly supplied energy to the body through lipid metabolism and amino acid metabolism, and meanwhile the apoptosis pathway was activated. While, individuals in the CT group mainly through glucose metabolism and steroid hormone biosynthesis to supply energy for the body. The validation results of qPCR on eight functional genes further demonstrated the reliability of RNA-Seq data. In summary, the results provide molecular information about adaptation to climate change and genetic selection of black porgy.
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Affiliation(s)
- Yue Wang
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China; Jiangsu Marine Fishery Research Institute, Nantong 226007, China
| | - Mingjun Shen
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China; Jiangsu Marine Fishery Research Institute, Nantong 226007, China
| | - Guangping Xu
- Jiangsu Marine Fishery Research Institute, Nantong 226007, China
| | - Han Yu
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China; Jiangsu Marine Fishery Research Institute, Nantong 226007, China
| | - Chaofeng Jia
- Jiangsu Marine Fishery Research Institute, Nantong 226007, China
| | - Fei Zhu
- Jiangsu Marine Fishery Research Institute, Nantong 226007, China
| | - Qian Meng
- Jiangsu Marine Fishery Research Institute, Nantong 226007, China
| | - Dafeng Xu
- Jiangsu Marine Fishery Research Institute, Nantong 226007, China
| | - Shuran Du
- Jiangsu Marine Fishery Research Institute, Nantong 226007, China
| | - Dianchang Zhang
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China; South China Sea Fishery Research Institute, Chinese Academy of Fishery Sciences Guangzhou 510300, China
| | - Zhiwei Zhang
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China; Jiangsu Marine Fishery Research Institute, Nantong 226007, China.
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4
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Jiang MZ, Liu C, Xu C, Jiang H, Wang Y, Liu SJ. Gut microbial interactions based on network construction and bacterial pairwise cultivation. SCIENCE CHINA. LIFE SCIENCES 2024:10.1007/s11427-023-2537-0. [PMID: 38600293 DOI: 10.1007/s11427-023-2537-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Accepted: 01/27/2024] [Indexed: 04/12/2024]
Abstract
Association networks are widely applied for the prediction of bacterial interactions in studies of human gut microbiomes. However, the experimental validation of the predicted interactions is challenging due to the complexity of gut microbiomes and the limited number of cultivated bacteria. In this study, we addressed this challenge by integrating in vitro time series network (TSN) associations and co-cultivation of TSN taxon pairs. Fecal samples were collected and used for cultivation and enrichment of gut microbiome on YCFA agar plates for 13 days. Enriched cells were harvested for DNA extraction and metagenomic sequencing. A total of 198 metagenome-assembled genomes (MAGs) were recovered. Temporal dynamics of bacteria growing on the YCFA agar were used to infer microbial association networks. To experimentally validate the interactions of taxon pairs in networks, we selected 24 and 19 bacterial strains from this study and from the previously established human gut microbial biobank, respectively, for pairwise co-cultures. The co-culture experiments revealed that most of the interactions between taxa in networks were identified as neutralism (51.67%), followed by commensalism (21.67%), amensalism (18.33%), competition (5%) and exploitation (3.33%). Genome-centric analysis further revealed that the commensal gut bacteria (helpers and beneficiaries) might interact with each other via the exchanges of amino acids with high biosynthetic costs, short-chain fatty acids, and/or vitamins. We also validated 12 beneficiaries by adding 16 additives into the basic YCFA medium and found that the growth of 66.7% of these strains was significantly promoted. This approach provides new insights into the gut microbiome complexity and microbial interactions in association networks. Our work highlights that the positive relationships in gut microbial communities tend to be overestimated, and that amino acids, short-chain fatty acids, and vitamins are contributed to the positive relationships.
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Affiliation(s)
- Min-Zhi Jiang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266000, China
| | - Chang Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266000, China
| | - Chang Xu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266000, China
| | - He Jiang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266000, China
| | - Yulin Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266000, China.
| | - Shuang-Jiang Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266000, China.
- State Key Laboratory of Microbial Resources, and Environmental Microbiology Research Center (EMRC), Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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5
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Xue S, Wang H, Ma Y, Sun T, Wang Y, Meng F, Wang X, Yang Z, Zhang J, Du J, Li S, Li Z. Fine mapping of powdery mildew resistance gene PmXNM in a Chinese wheat landrace Xiaonanmai. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:35. [PMID: 38286845 DOI: 10.1007/s00122-024-04544-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 01/05/2024] [Indexed: 01/31/2024]
Abstract
KEY MESSAGE Powdery mildew resistance gene PmXNM, originated from the Chinese wheat landrace Xiaonanmai, was delimited to a 300.7-kb interval enriched with resistance genes. Powdery mildew, caused by Blumeria graminis f. sp. tritici (Bgt), is a globally devastating disease threatening the yield and quality of wheat worldwide. The use of broad-spectrum disease resistance genes from wheat landraces is an effective strategy to prevent this pathogen. Chinese wheat landrace Xiaonanmai (XNM) was immune to 23 tested Bgt isolates at the seedling stage. The F1, F2, and F2:4 progenies derived from the cross between XNM and Chinese Spring (CS) were used in this study. Genetic analysis revealed that powdery mildew resistance in XNM was controlled by a single dominant gene, temporarily designated PmXNM. Bulked segregant analysis and molecular mapping delimited PmXNM to the distal terminal region of chromosome 4AL flanked by markers caps213923 and kasp511718. The region carrying the PmXNM locus was approximately 300.7 kb and contained nine high-confidence genes according to the reference genome sequence of CS. Five of these genes, annotated as disease resistance RPP13-like proteins 1, were clustered in the target region. Haplotype analysis using the candidate gene-specific markers indicated that the majority of 267 common wheat accessions (75.3%) exhibited extensive gene losses at the PmXNM locus, as confirmed by aligning the targeted genome sequences of CS with those of other sequenced wheat cultivars. Seven candidate gene-specific markers have proven effective for marker-assisted introgression of PmXNM into modern elite cultivars.
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Affiliation(s)
- Shulin Xue
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, Henan, China.
| | - Huan Wang
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, Henan, China
| | - Yuyu Ma
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, Henan, China
| | - Tiepeng Sun
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, Henan, China
| | - Yingxue Wang
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, Henan, China
| | - Fan Meng
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, Henan, China
| | - Xintian Wang
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, Henan, China
| | - Zihan Yang
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, Henan, China
| | - Jieli Zhang
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, Henan, China
| | - Jinxuan Du
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, Henan, China
| | - Suoping Li
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, Henan, China
| | - Zhifang Li
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, Henan, China.
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6
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Yan N, Feng H, Sun Y, Xin Y, Zhang H, Lu H, Zheng J, He C, Zuo Z, Yuan T, Li N, Xie L, Wei W, Sun Y, Zuo E. Cytosine base editors induce off-target mutations and adverse phenotypic effects in transgenic mice. Nat Commun 2023; 14:1784. [PMID: 36997536 PMCID: PMC10063651 DOI: 10.1038/s41467-023-37508-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 03/20/2023] [Indexed: 04/03/2023] Open
Abstract
Base editors have been reported to induce off-target mutations in cultured cells, mouse embryos and rice, but their long-term effects in vivo remain unknown. Here, we develop a Systematic evaluation Approach For gene Editing tools by Transgenic mIce (SAFETI), and evaluate the off-target effects of BE3, high fidelity version of CBE (YE1-BE3-FNLS) and ABE (ABE7.10F148A) in ~400 transgenic mice over 15 months. Whole-genome sequence analysis reveals BE3 expression generated de novo mutations in the offspring of transgenic mice. RNA-seq analysis reveals both BE3 and YE1-BE3-FNLS induce transcriptome-wide SNVs, and the numbers of RNA SNVs are positively correlated with CBE expression levels across various tissues. By contrast, ABE7.10F148A shows no detectable off-target DNA or RNA SNVs. Notably, we observe abnormal phenotypes including obesity and developmental delay in mice with permanent genomic BE3 overexpression during long-time monitoring, elucidating a potentially overlooked aspect of side effects of BE3 in vivo.
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Affiliation(s)
- Nana Yan
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Hu Feng
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Yongsen Sun
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Ying Xin
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China
| | - Haihang Zhang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Hongjiang Lu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China
| | - Jitan Zheng
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Chenfei He
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Zhenrui Zuo
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Tanglong Yuan
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Nana Li
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China
| | - Long Xie
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Wu Wei
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.
- Lingang Laboratory, Shanghai, China.
| | - Yidi Sun
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China.
| | - Erwei Zuo
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
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7
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Liver Transcriptome Analysis of the Black Porgy (Acanthopagrus schlegelii) under Acute Low-Temperature Stress. Life (Basel) 2023; 13:life13030721. [PMID: 36983876 PMCID: PMC10057800 DOI: 10.3390/life13030721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 02/15/2023] [Accepted: 03/01/2023] [Indexed: 03/10/2023] Open
Abstract
High nutritional value and the development of efficient biotechnological methods of controlled production have made black porgy (Acanthopagrus schlegelii) an economically important fish in Chinese aquaculture in recent years. However, aquaculture production of the species faces multiple issues associated with reduced growth rate, low reproduction ability, and high mortality during production, which are associated with the species’ limited tolerance to low temperatures. To date, comprehensive information on the genetic-based mechanisms of cold tolerance and adaptation to low temperature in the species are still unavailable. In this study, the HiSeq™2500 (Illumina) sequencing platform was used to analyze the transcriptomic profile of the liver tissue in the black porgy subjected to different extents of cold shock, including a control temperature group (AS, T = 15 °C), an intermediate temperature group (AL1, T = 10 °C), and an acute low-temperature stress group (AL2, T = 5 °C). For this purpose, three standardized cDNA libraries of AS, AL1, and AL2 were established. We obtained 43,258,908, 48,239,072, and 38,983,833 clean reads from the AS group, AL1 group, and AL2 group, respectively. After pairwise comparison, 70 differentially expressed genes (DEGs) were identified in the examined fish groups. Among them, 60 genes were found to be significantly differentially expressed after trend analysis. GO annotation and enrichment results showed that they were mainly enriched into three categories: biological processes (12 subcategories), molecular functions (7 subcategories), and cellular components (7 subcategories). KEGG analysis results indicated that all significantly differentially expressed genes were annotated to 102 signaling pathways, including biological rhythm, cholesterol metabolism, glycerolipid metabolism, animal autophagy, FoxO signaling pathway, steroid biosynthesis, and regulation of adipocyte lipolysis and apoptosis. Four of them, namely: G6PC, GPX1, GCK, and HSPE1 were randomly selected for further qRT-PCR verification of data reliability obtained by RNA-Seq technology. In this study, we found that environmental acute cold stress mainly affected the black porgy’s biological processes related to metabolism, apoptosis, and signal transduction. The data that we have reported provides baseline information for further studies concerning the genetic responses of the black porgy under cold stress conditions, the improvement of its aquaculture production, and other economically important matters regarding their limited tolerance to cold shock.
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8
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Microsatellite Genome-Wide Database Development for the Commercial Blackhead Seabream (Acanthopagrus schlegelii). Genes (Basel) 2023; 14:genes14030620. [PMID: 36980892 PMCID: PMC10048070 DOI: 10.3390/genes14030620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 02/26/2023] [Accepted: 02/27/2023] [Indexed: 03/05/2023] Open
Abstract
Simple sequence repeats (SSRs), the markers with the highest polymorphism and co-dominance degrees, offer a crucial genetic research resource. Limited SSR markers in blackhead seabream have been reported. The availability of the blackhead seabream genome assembly provided the opportunity to carry out genome-wide identification for all microsatellite markers, and bioinformatic analyses open the way for developing a microsatellite genome-wide database in blackhead seabream. In this study, a total of 412,381 SSRs were identified in the 688.08 Mb genome by Krait software. Whole-genome sequences (10×) of 42 samples were aligned against the reference genome and genotyped using the HipSTR tools by comparing and counting repeat number variation across the SSR loci. A total of 156,086 SSRs with a 2–4 bp repeat were genotyped by HipSTR tools, which accounted for 55.78% of the 2–4 bp SSRs in the reference genome. High accuracy of genotyping was observed by comparing HipSTR tools and PCR amplification. A set of 109,131 loci with a number of alleles ≥ 3 and with a number of genotyped individuals ≥ 6 were reserved to constitute the polymorphic SSR database. Fifty-one polymorphic SSR loci were identified through PCR amplification. This strategy to develop polymorphic SSR markers not only obtained a large set of polymorphic SSRs but also eliminated the need for laborious experimental screening. SSR markers developed in this study may facilitate blackhead seabream research, which lays a certain foundation for further gene tagging and genetic linkage analysis, such as marker-assisted selection, genetic mapping, as well as comparative genomic analysis.
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9
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Li S, Li W, Jiang S, Jing Y, Xiao L, Yu Y, Liu Y, Li Y, Wang D, Li J, Peng C, Chen J, Lu D, Wu B, Guang X, Ma J, You X, Yang Y, Liu S, Fang X, Gao Q, Shi Q, Lin H, Schartl M, Yue Z, Zhang Y. Mechanisms of sex differentiation and sex reversal in hermaphrodite fish as revealed by the Epinephelus coioides genome. Mol Ecol Resour 2023; 23:920-932. [PMID: 36631404 DOI: 10.1111/1755-0998.13753] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Revised: 12/13/2022] [Accepted: 12/28/2022] [Indexed: 01/13/2023]
Abstract
Most grouper species are functional protogynous hermaphrodites, but the genetic basis and the molecular mechanisms underlying the regulation of this unique reproductive strategy remain enigmatic. In this study, we report a high-quality chromosome-level genome assembly of the representative orange-spotted grouper (Epinephelus coioides). No duplication or deletion of sex differentiation-related genes was found in the genome, suggesting that sex development in this grouper may be related to changes in regulatory sequences or environmental factors. Transcriptomic analyses showed that aromatase and retinoic acid are probably critical to promoting ovarian fate determination, and follicle-stimulating hormone triggers the female-to-male sex change. Socially controlled sex-change studies revealed that, in sex-changing fish, the brain's response to the social environment may be mediated by activation of the phototransduction cascade and the melatonin synthesis pathway. In summary, our genomic and experimental results provide novel insights into the molecular mechanisms of sex differentiation and sex change in the protogynous groupers.
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Affiliation(s)
- Shuisheng Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory for Aquatic Economic Animals, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | | | - Shoujia Jiang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory for Aquatic Economic Animals, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, China.,Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, Shenzhen, China
| | - Yi Jing
- BGI-Shenzhen, Shenzhen, China.,BGI-Sanya, BGI-Shenzhen, Sanya, China
| | - Ling Xiao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory for Aquatic Economic Animals, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | | | - Yun Liu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory for Aquatic Economic Animals, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Yanhong Li
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Dengdong Wang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory for Aquatic Economic Animals, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Jiang Li
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Cheng Peng
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory for Aquatic Economic Animals, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Jiaxing Chen
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory for Aquatic Economic Animals, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Danqi Lu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory for Aquatic Economic Animals, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Bin Wu
- BGI-Shenzhen, Shenzhen, China
| | | | - Junping Ma
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Xinxin You
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, Shenzhen, China
| | - Yuqing Yang
- Marine Fisheries Development Center of Guangdong Province, Huizhou, China
| | - Su Liu
- Marine Fisheries Development Center of Guangdong Province, Huizhou, China
| | | | - Qiang Gao
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Qiong Shi
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, Shenzhen, China
| | - Haoran Lin
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory for Aquatic Economic Animals, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Manfred Schartl
- Developmental Biochemistry, University of Würzburg, Biozentrum, Am Hubland, Würzburg, and Comprehensive Cancer Center, University Clinic Würzburg, Würzburg, Germany.,Hagler Institute for Advanced Study and Department of Biology, Texas A&M University, College Station, Texas, USA
| | - Zhen Yue
- BGI-Shenzhen, Shenzhen, China.,BGI-Sanya, BGI-Shenzhen, Sanya, China
| | - Yong Zhang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory for Aquatic Economic Animals, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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10
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Davoudi P, Do DN, Rathgeber B, Colombo SM, Sargolzaei M, Plastow G, Wang Z, Karimi K, Hu G, Valipour S, Miar Y. Genome-wide detection of copy number variation in American mink using whole-genome sequencing. BMC Genomics 2022; 23:649. [PMID: 36096727 PMCID: PMC9468235 DOI: 10.1186/s12864-022-08874-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 09/05/2022] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Copy number variations (CNVs) represent a major source of genetic diversity and contribute to the phenotypic variation of economically important traits in livestock species. In this study, we report the first genome-wide CNV analysis of American mink using whole-genome sequence data from 100 individuals. The analyses were performed by three complementary software programs including CNVpytor, DELLY and Manta. RESULTS A total of 164,733 CNVs (144,517 deletions and 20,216 duplications) were identified representing 5378 CNV regions (CNVR) after merging overlapping CNVs, covering 47.3 Mb (1.9%) of the mink autosomal genome. Gene Ontology and KEGG pathway enrichment analyses of 1391 genes that overlapped CNVR revealed potential role of CNVs in a wide range of biological, molecular and cellular functions, e.g., pathways related to growth (regulation of actin cytoskeleton, and cAMP signaling pathways), behavior (axon guidance, circadian entrainment, and glutamatergic synapse), lipid metabolism (phospholipid binding, sphingolipid metabolism and regulation of lipolysis in adipocytes), and immune response (Wnt signaling, Fc receptor signaling, and GTPase regulator activity pathways). Furthermore, several CNVR-harbored genes associated with fur characteristics and development (MYO5A, RAB27B, FGF12, SLC7A11, EXOC2), and immune system processes (SWAP70, FYN, ORAI1, TRPM2, and FOXO3). CONCLUSIONS This study presents the first genome-wide CNV map of American mink. We identified 5378 CNVR in the mink genome and investigated genes that overlapped with CNVR. The results suggest potential links with mink behaviour as well as their possible impact on fur quality and immune response. Overall, the results provide new resources for mink genome analysis, serving as a guideline for future investigations in which genomic structural variations are present.
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Affiliation(s)
- Pourya Davoudi
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
| | - Duy Ngoc Do
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
| | - Bruce Rathgeber
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
| | - Stefanie M Colombo
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
| | - Mehdi Sargolzaei
- Department of Pathobiology, University of Guelph, Guelph, ON, Canada
- Select Sires Inc., Plain City, OH, USA
| | - Graham Plastow
- Livestock Gentec, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Zhiquan Wang
- Livestock Gentec, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Karim Karimi
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
| | - Guoyu Hu
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
| | - Shafagh Valipour
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
| | - Younes Miar
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada.
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11
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Jia Y, Zhao S, Guo W, Peng L, Zhao F, Wang L, Fan G, Zhu Y, Xu D, Liu G, Wang R, Fang X, Zhang H, Kristiansen K, Zhang W, Chen J. Sequencing introduced false positive rare taxa lead to biased microbial community diversity, assembly, and interaction interpretation in amplicon studies. ENVIRONMENTAL MICROBIOME 2022; 17:43. [PMID: 35978448 PMCID: PMC9387074 DOI: 10.1186/s40793-022-00436-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 07/21/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Increasing studies have demonstrated potential disproportionate functional and ecological contributions of rare taxa in a microbial community. However, the study of the microbial rare biosphere is hampered by their inherent scarcity and the deficiency of currently available techniques. Sample-wise cross contaminations might be introduced by sample index misassignment in the most widely used metabarcoding amplicon sequencing approach. Although downstream bioinformatic quality control and clustering or denoising algorithms could remove sequencing errors and non-biological artifact reads, no algorithm could eliminate high quality reads from sample-wise cross contaminations introduced by index misassignment, making it difficult to distinguish between bona fide rare taxa and potential false positives in metabarcoding studies. RESULTS We thoroughly evaluated the rate of index misassignment of the widely used NovaSeq 6000 and DNBSEQ-G400 sequencing platforms using both commercial and customized mock communities, and observed significant lower (0.08% vs. 5.68%) fraction of potential false positive reads for DNBSEQ-G400 as compared to NovaSeq 6000. Significant batch effects could be caused by stochastically introduced false positive or false negative rare taxa. These false detections could also lead to inflated alpha diversity of relatively simple microbial communities and underestimated that of complex ones. Further test using a set of cow rumen samples reported differential rare taxa by different sequencing platforms. Correlation analysis of the rare taxa detected by each sequencing platform demonstrated that the rare taxa identified by DNBSEQ-G400 platform had a much higher possibility to be correlated with the physiochemical properties of rumen fluid as compared to NovaSeq 6000 platform. Community assembly mechanism and microbial network correlation analysis indicated that false positive or negative rare taxa detection could lead to biased community assembly mechanism and identification of fake keystone species of the community. CONCLUSIONS We highly suggest proper positive/negative/blank controls, technical replicate settings, and proper sequencing platform selection in future amplicon studies, especially when the microbial rare biosphere would be focused.
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Affiliation(s)
- Yangyang Jia
- BGI-Shenzhen, Shenzhen, 518083, China
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
| | - Shengguo Zhao
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Wenjie Guo
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
| | - Ling Peng
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
| | - Fang Zhao
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
| | - Lushan Wang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Guangyi Fan
- BGI-Shenzhen, Shenzhen, 518083, China
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
| | - Yuanfang Zhu
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
| | - Dayou Xu
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
| | - Guilin Liu
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
| | - Ruoqing Wang
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
| | | | - He Zhang
- BGI-Shenzhen, Shenzhen, 518083, China
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Karsten Kristiansen
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Universitetsparken 13, 2100, Copenhagen, Denmark.
- Qingdao-Europe Advanced Institute for Life Sciences, BGI-Shenzhen, Qingdao, 266555, China.
| | - Wenwei Zhang
- BGI-Shenzhen, Shenzhen, 518083, China.
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China.
| | - Jianwei Chen
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China.
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Universitetsparken 13, 2100, Copenhagen, Denmark.
- Qingdao-Europe Advanced Institute for Life Sciences, BGI-Shenzhen, Qingdao, 266555, China.
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12
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The mitochondrial genome and phylogenetic analysis of Rhacophorus rhodopus. Sci Rep 2022; 12:13693. [PMID: 35953583 PMCID: PMC9372073 DOI: 10.1038/s41598-022-17814-8] [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: 04/25/2022] [Accepted: 08/01/2022] [Indexed: 11/08/2022] Open
Abstract
Classification of the genus Rhacophorus has been problematic. In particular there has been considerable controversy surrounding the phylogenetic relationships among Rhacophorus rhodopus, R. bipunctatus, and R. reinwardtii. To examine the relationship among these Rhacophorus species, we assembled the complete mitochondrial genome sequence of R. rhodopus. The R. rhodopus genome is 15,789 bp in length with 12 protein-coding genes (PCGs) (losing ND5), two ribosomal genes, 22 transfer RNA genes, and a control region (D-loop). Base composition of the overall sequence was 60.86% for A + T content and 39.14% for C + G content. Most of the PCGs used ATG as a start codon, except for the COX I gene, which used the ATA start codon. COX I and ND6 used AGG and ATP8 stop codons respectively, while ND3 and ND4L used the TAA stop codon. For the remaining seven genes, the stop codons was incomplete. In addition, both 5' and 3' of the control areas had distinct repeating regions. Based on three datasets and two methods (Bayesian inference (BI) and maximum likelihood (ML)), we reconstructed three phylogenetic trees to explore the taxonomic status of the species and the phylogenetic relationship among R. rhodopus, R. bipunctatus and R. reinwardtii. Our results indicated that these three species are non-monophyletic; thus, the phylogenetic relationship among them is complex and difficult to determine. Further, R. rhodopus is divided into three lineages from different parts of China. The two Rhacophorus samples showed very close phylogenetic relationship with R. rhodopus. Our results add to the mitochondrial genome database of amphibians and will help to disentangle the phylogenetic relationships within the Rhacophoridae.
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13
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Liu J, Xue CX, Wang J, Crombie AT, Carrión O, Johnston AWB, Murrell JC, Liu J, Zheng Y, Zhang XH, Todd JD. Oceanospirillales containing the DMSP lyase DddD are key utilisers of carbon from DMSP in coastal seawater. MICROBIOME 2022; 10:110. [PMID: 35883169 PMCID: PMC9327192 DOI: 10.1186/s40168-022-01304-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Accepted: 05/27/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Ubiquitous and diverse marine microorganisms utilise the abundant organosulfur molecule dimethylsulfoniopropionate (DMSP), the main precursor of the climate-active gas dimethylsulfide (DMS), as a source of carbon, sulfur and/or signalling molecules. However, it is currently difficult to discern which microbes actively catabolise DMSP in the environment, why they do so and the pathways used. RESULTS Here, a novel DNA-stable isotope probing (SIP) approach, where only the propionate and not the DMS moiety of DMSP was 13C-labelled, was strategically applied to identify key microorganisms actively using DMSP and also likely DMS as a carbon source, and their catabolic enzymes, in North Sea water. Metagenomic analysis of natural seawater suggested that Rhodobacterales (Roseobacter group) and SAR11 bacteria were the major microorganisms degrading DMSP via demethylation and, to a lesser extent, DddP-driven DMSP lysis pathways. However, neither Rhodobacterales and SAR11 bacteria nor their DMSP catabolic genes were prominently labelled in DNA-SIP experiments, suggesting they use DMSP as a sulfur source and/or in signalling pathways, and not primarily for carbon requirements. Instead, DNA-SIP identified gammaproteobacterial Oceanospirillales, e.g. Amphritea, and their DMSP lyase DddD as the dominant microorganisms/enzymes using DMSP as a carbon source. Supporting this, most gammaproteobacterial (with DddD) but few alphaproteobacterial seawater isolates grew on DMSP as sole carbon source and produced DMS. Furthermore, our DNA-SIP strategy also identified Methylophaga and other Piscirickettsiaceae as key bacteria likely using the DMS, generated from DMSP lysis, as a carbon source. CONCLUSIONS This is the first study to use DNA-SIP with 13C-labelled DMSP and, in a novel way, it identifies the dominant microbes utilising DMSP and DMS as carbon sources. It highlights that whilst metagenomic analyses of marine environments can predict microorganisms/genes that degrade DMSP and DMS based on their abundance, it cannot disentangle those using these important organosulfur compounds for their carbon requirements. Note, the most abundant DMSP degraders, e.g. Rhodobacterales with DmdA, are not always the key microorganisms using DMSP for carbon and releasing DMS, which in this coastal system were Oceanospirillales containing DddD. Video abstract.
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Affiliation(s)
- Jingli Liu
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and College of Marine Life Sciences , Ocean University of China, Qingdao, China
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Chun-Xu Xue
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and College of Marine Life Sciences , Ocean University of China, Qingdao, China
| | - Jinyan Wang
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and College of Marine Life Sciences , Ocean University of China, Qingdao, China
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Andrew T Crombie
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Ornella Carrión
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Andrew W B Johnston
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - J Colin Murrell
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Ji Liu
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and College of Marine Life Sciences , Ocean University of China, Qingdao, China
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Yanfen Zheng
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and College of Marine Life Sciences , Ocean University of China, Qingdao, China
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Xiao-Hua Zhang
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and College of Marine Life Sciences , Ocean University of China, Qingdao, China.
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
| | - Jonathan D Todd
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, UK.
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14
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Jin M, Fei X, Li T, Lu Z, Chu M, Di R, He X, Wang X, Wei C. Transcriptome study digs out BMP2 involved in adipogenesis in sheep tails. BMC Genomics 2022; 23:457. [PMID: 35725366 PMCID: PMC9210821 DOI: 10.1186/s12864-022-08657-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Accepted: 05/25/2022] [Indexed: 12/22/2022] Open
Abstract
Background Hu sheep and Tibetan sheep in China are characterized by fat tails and thin tails, respectively. Several transcriptomes have been conducted in different sheep breeds to identify the differentially expressed genes (DEGs) underlying this trait. However, these studies identified different DEGs in different sheep breeds. Results Hence, RNA sequencing was performed on Hu sheep and Tibetan sheep. We obtained a total of 45.57 and 43.82 million sequencing reads, respectively. Two libraries mapped reads from 36.93 and 38.55 million reads after alignment to the reference sequences. 2108 DEGs were identified, including 1247 downregulated and 861 upregulated DEGs. GO and KEGG analyses of all DEGs demonstrated that pathways were enriched in the regulation of lipolysis in adipocytes and terms related to the chemokine signalling pathway, lysosomes, and glycosaminoglycan degradation. Eight genes were selected for validation by RT–qPCR. In addition, the transfection of BMP2 overexpression into preadipocytes resulted in increased PPAR-γ expression and expression. BMP2 potentially induces adipogenesis through LOX in preadipocytes. The number of lipid drops in BMP2 overexpression detected by oil red O staining was also greater than that in the negative control. Conclusion In summary, these results showed that significant genes (BMP2, HOXA11, PPP1CC and LPIN1) are involved in the regulation of adipogenesis metabolism and suggested novel insights into metabolic molecules in sheep fat tails. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08657-8.
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Affiliation(s)
- Meilin Jin
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.,College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Xiaojuan Fei
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Taotao Li
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zengkui Lu
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
| | - Mingxing Chu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ran Di
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaoyun He
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiangyu Wang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Caihong Wei
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
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15
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Isolation of Three Coliphages and the Evaluation of Their Phage Cocktail for Biocontrol of Shiga Toxin-Producing Escherichia coli O157 in Milk. Curr Microbiol 2022; 79:216. [PMID: 35678865 DOI: 10.1007/s00284-022-02908-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 05/16/2022] [Indexed: 11/03/2022]
Abstract
Shiga toxin-producing Escherichia coli (STEC) O157 is a well-known foodborne pathogen and a leading cause of many intestinal diseases. In this study, we explore the use of a phage cocktail to help control STEC O157 in broth and milk. We isolated three virulent phages from sanitary sewages using a STEC O157 as the indicator bacterium. Phenotypical characterizations revealed that these three phages belong to the Myoviridae family and were stable at different temperatures and pH. They displayed a short latent period between 10 and 20 min, and a burst size (32-65 per infected cell). No virulence factors and drug resistance genes were found in their genomes. Bacterial lysis assays showed that a phage cocktail comprising these three phages was more effective (at least 4.32 log reduction) against STEC O157 at 25 °C with multiplicity of infection (MOI) = 1000 in broth medium. At 4 °C, a 3.8 log reduction in the number of viable STEC O157 after 168-h treatment with phage cocktail at MOI = 1000 was observed in milk, compared to phage-free bacterial control group. Characterizations of phages suggest they could be developed into novel therapeutic agents to control STEC O157 in milk production.
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16
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Guo Z, Yuan Y, Chen C, Lin J, Ma Q, Liu G, Gao Y, Huang Y, Chen L, Chen LZ, Huang YF, Wang H, Li B, Chen Y, Zhang X. Durable complete response to neoantigen-loaded dendritic-cell vaccine following anti-PD-1 therapy in metastatic gastric cancer. NPJ Precis Oncol 2022; 6:34. [PMID: 35661819 PMCID: PMC9166775 DOI: 10.1038/s41698-022-00279-3] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 04/15/2022] [Indexed: 12/13/2022] Open
Abstract
ABSRACT Neoantigens are ideal targets for dendritic cell (DC) vaccines. So far, only a few neoantigen-based DC vaccines have been investigated in clinical trials. Here, we reported a case of a patient with metastatic gastric cancer who received personalized neoantigen-loaded monocyte-derived dendritic cell (Neo-MoDC) vaccines followed by combination therapy of the Neo-MoDC and immune checkpoint inhibitor (ICI). The patient developed T cell responses against neoantigens after receiving the Neo-MoDC vaccine alone. The following combination therapy triggered a stronger immune response and mediated complete regression of all tumors for over 25 months till October, 2021. Peripheral blood mononuclear cells recognized seven of the eight vaccine neoantigens. And the frequency of neoantigen-specific T cell clones increased obviously after vaccination. Overall, this report describing a complete tumor regression in a gastric cancer patient mediated by Neo-MoDC vaccine in combination with ICI, and suggesting a promising treatment for patients with metastatic gastric cancer.
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Affiliation(s)
- Zengqing Guo
- Department of Medical Oncology, Fujian Medical University Cancer Hospital & Fujian Cancer Hospital, Fuzhou, Fujian Province, China.,Cancer Bio-immunotherapy Center, Fujian Medical University Cancer Hospital & Fujian Cancer Hospital, Fuzhou, Fujian Province, China.,Fujian Provincial Key Laboratory of Translational Cancer Medicine, Fuzhou, Fujian Province, China
| | - Yuan Yuan
- BGI-Shenzhen, Shenzhen, 518083, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chao Chen
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Jing Lin
- Department of Medical Oncology, Fujian Medical University Cancer Hospital & Fujian Cancer Hospital, Fuzhou, Fujian Province, China.,Cancer Bio-immunotherapy Center, Fujian Medical University Cancer Hospital & Fujian Cancer Hospital, Fuzhou, Fujian Province, China.,Fujian Provincial Key Laboratory of Translational Cancer Medicine, Fuzhou, Fujian Province, China
| | - Qiwang Ma
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Geng Liu
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Yan Gao
- BGI-Shenzhen, Shenzhen, 518083, China
| | | | - Ling Chen
- Department of Medical Oncology, Fujian Medical University Cancer Hospital & Fujian Cancer Hospital, Fuzhou, Fujian Province, China.,Cancer Bio-immunotherapy Center, Fujian Medical University Cancer Hospital & Fujian Cancer Hospital, Fuzhou, Fujian Province, China.,Fujian Provincial Key Laboratory of Translational Cancer Medicine, Fuzhou, Fujian Province, China
| | - Li-Zhu Chen
- Department of Medical Oncology, Fujian Medical University Cancer Hospital & Fujian Cancer Hospital, Fuzhou, Fujian Province, China.,Cancer Bio-immunotherapy Center, Fujian Medical University Cancer Hospital & Fujian Cancer Hospital, Fuzhou, Fujian Province, China.,Fujian Provincial Key Laboratory of Translational Cancer Medicine, Fuzhou, Fujian Province, China
| | - Yu-Fang Huang
- Department of Medical Oncology, Fujian Medical University Cancer Hospital & Fujian Cancer Hospital, Fuzhou, Fujian Province, China.,Cancer Bio-immunotherapy Center, Fujian Medical University Cancer Hospital & Fujian Cancer Hospital, Fuzhou, Fujian Province, China.,Fujian Provincial Key Laboratory of Translational Cancer Medicine, Fuzhou, Fujian Province, China
| | | | - Bo Li
- BGI-Shenzhen, Shenzhen, 518083, China.
| | - Yu Chen
- Department of Medical Oncology, Fujian Medical University Cancer Hospital & Fujian Cancer Hospital, Fuzhou, Fujian Province, China. .,Cancer Bio-immunotherapy Center, Fujian Medical University Cancer Hospital & Fujian Cancer Hospital, Fuzhou, Fujian Province, China. .,Fujian Provincial Key Laboratory of Translational Cancer Medicine, Fuzhou, Fujian Province, China.
| | - Xi Zhang
- BGI-Shenzhen, Shenzhen, 518083, China.
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17
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Ohtsuki H, Norimatsu H, Makino T, Urabe J. Invasions of an obligate asexual daphnid species support the nearly neutral theory. Sci Rep 2022; 12:7305. [PMID: 35508526 PMCID: PMC9068809 DOI: 10.1038/s41598-022-11218-4] [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: 12/23/2021] [Accepted: 04/20/2022] [Indexed: 11/09/2022] Open
Abstract
To verify the "nearly neutral theory (NNT)," the ratio of nonsynonymous to synonymous substitutions (dN/dS) was compared among populations of different species. To determine the validity of NNT, however, populations that are genetically isolated from each other but share the same selection agents and differ in size should be compared. Genetically different lineages of obligate asexual Daphnia pulex invading Japan from North America are an ideal example as they satisfy these prerequisites. Therefore, we analyzed the whole-genome sequences of 18 genotypes, including those of the two independently invaded D. pulex lineages (JPN1 and JPN2) and compared the dN/dS ratio between the lineages. The base substitution rate of each genotype demonstrated that the JPN1 lineage having a larger distribution range diverged earlier and thus was older than the JPN2 lineage. Comparisons of the genotypes within lineages revealed that changes in dN/dS occurred after the divergence and were larger in the younger lineage, JPN2. These results imply that the JPN1 lineage has been more effectively subjected to purification selections, while slightly deteriorating mutations are less purged in JPN2 with smaller population size. Altogether, the lineage-specific difference in the dN/dS ratio for the obligate asexual D. pulex was well explained by the NNT.
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Affiliation(s)
- Hajime Ohtsuki
- Graduate School of Life Sciences, Tohoku University, 6-3 Aoba, Aramaki, Aoba-ku, Sendai, 980-8578, Japan
| | - Hirotomo Norimatsu
- Graduate School of Life Sciences, Tohoku University, 6-3 Aoba, Aramaki, Aoba-ku, Sendai, 980-8578, Japan
| | - Takashi Makino
- Graduate School of Life Sciences, Tohoku University, 6-3 Aoba, Aramaki, Aoba-ku, Sendai, 980-8578, Japan
| | - Jotaro Urabe
- Graduate School of Life Sciences, Tohoku University, 6-3 Aoba, Aramaki, Aoba-ku, Sendai, 980-8578, Japan.
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Xue S, Hu S, Chen X, Ma Y, Lu M, Bai S, Wang X, Sun T, Wang Y, Wan H, An X, Li S. Fine mapping of Pm58 from Aegilops tauschii conferring powdery mildew resistance. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:1657-1669. [PMID: 35234985 DOI: 10.1007/s00122-022-04061-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 02/11/2022] [Indexed: 05/26/2023]
Abstract
The powdery mildew resistance gene Pm58 was traced to a 141.3-kb interval with the co-segregating marker Xkasp68500 in wheat breeding. Pm58 is a powdery mildew resistance gene identified in Aegilops tauschii accession TA1662 and effective in a common wheat background. To finely map Pm58, an F2 population of 676 plants derived from the cross T093 × TA1662 was used for recombinant screening. We obtained 13 recombinants that occurred between the flanking markers Xhnu670 and Xhnu186. Genotyping and phenotyping these recombinant F2:3 families delimited Pm58 to a 0.22-cM interval (Xsts20220-Xkasp61553) on chromosome arm 2DS. The region carrying the Pm58 locus was approximately 141.3-kb, which contained eight annotated genes according to the reference genome sequence of Ae. tauschii AL8/78. Haplotype analysis of 178 Ae. tauschii accessions using the candidate gene-specific markers identified a disease resistance gene AET2Gv20068500 as a candidate for Pm58. Comparative mapping of the Pm58-containing interval revealed two presence/absence variations (PAVs) between AL8/78 and common wheat Chinese Spring. PAV-1 resides in the 3'-end of AET2Gv20068500. The majority of 158 common wheat cultivars (84.8%) displayed the absence of a 14.1-kb fragment in the PAV-1 region, which was confirmed by aligning the targeted genome sequences of the other sequenced Ae. tauschii accessions and common wheat cultivars. A co-segregating marker Xkasp68500 developed from AET2Gv20068500 can distinguish TA1662 from all randomly selected common wheat cultivars and will be instrumental for tracking Pm58 in breeding programs.
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Affiliation(s)
- Shulin Xue
- State Key Laboratory of Crop Stress Adaptation and Improvement, College of Agriculture, Henan University, Kaifeng, 475004, Henan, China.
| | - Shanshan Hu
- State Key Laboratory of Crop Stress Adaptation and Improvement, College of Agriculture, Henan University, Kaifeng, 475004, Henan, China
| | - Xian Chen
- State Key Laboratory of Crop Stress Adaptation and Improvement, College of Agriculture, Henan University, Kaifeng, 475004, Henan, China
| | - Yuyu Ma
- State Key Laboratory of Crop Stress Adaptation and Improvement, College of Agriculture, Henan University, Kaifeng, 475004, Henan, China
| | - Mingxue Lu
- State Key Laboratory of Crop Stress Adaptation and Improvement, College of Agriculture, Henan University, Kaifeng, 475004, Henan, China
| | - Shenglong Bai
- State Key Laboratory of Crop Stress Adaptation and Improvement, College of Agriculture, Henan University, Kaifeng, 475004, Henan, China
| | - Xintian Wang
- State Key Laboratory of Crop Stress Adaptation and Improvement, College of Agriculture, Henan University, Kaifeng, 475004, Henan, China
| | - Tiepeng Sun
- State Key Laboratory of Crop Stress Adaptation and Improvement, College of Agriculture, Henan University, Kaifeng, 475004, Henan, China
| | - Yingxue Wang
- State Key Laboratory of Crop Stress Adaptation and Improvement, College of Agriculture, Henan University, Kaifeng, 475004, Henan, China
| | - Hongshen Wan
- Key Laboratory of Wheat Biology and Genetic Improvement on Southwestern China, Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, Sichuan, China
| | - Xia An
- Zibo Academy of Agricultural Sciences, Zibo, 255000, Shandong, China
| | - Suoping Li
- State Key Laboratory of Crop Stress Adaptation and Improvement, College of Agriculture, Henan University, Kaifeng, 475004, Henan, China.
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Deletion and tandem duplications of biosynthetic genes drive the diversity of triterpenoids in Aralia elata. Nat Commun 2022; 13:2224. [PMID: 35468919 PMCID: PMC9038795 DOI: 10.1038/s41467-022-29908-y] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 04/06/2022] [Indexed: 11/16/2022] Open
Abstract
Araliaceae species produce various classes of triterpene and triterpenoid saponins, such as the oleanane-type triterpenoids in Aralia species and dammarane-type saponins in Panax, valued for their medicinal properties. The lack of genome sequences of Panax relatives has hindered mechanistic insight into the divergence of triterpene saponins in Araliaceae. Here, we report a chromosome-level genome of Aralia elata with a total length of 1.05 Gb. The loss of 12 exons in the dammarenediol synthase (DDS)-encoding gene in A. elata after divergence from Panax might have caused the lack of dammarane-type saponin production, and a complementation assay shows that overexpression of the PgDDS gene from Panax ginseng in callus of A. elata recovers the accumulation of dammarane-type saponins. Tandem duplication events of triterpene biosynthetic genes are common in the A. elata genome, especially for AeCYP72As, AeCSLMs, and AeUGT73s, which function as tailoring enzymes of oleanane-type saponins and aralosides. More than 13 aralosides are de novo synthesized in Saccharomyces cerevisiae by overexpression of these genes in combination. This study sheds light on the diversity of saponins biosynthetic pathway in Araliaceae and will facilitate heterologous bioproduction of aralosides. Unlike Panax species, which can produce dammarane-type saponins, Aralia elata can only synthesize oleananetype saponins. Here, the authors reveal that the loss of the dammaranediol synthase-encoding gene and tandem duplication of triterpene biosynthetic genes drive structural divergences of saponins between the two genera.
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Chromosome-scale Echinococcus granulosus (genotype G1) genome reveals the Eg95 gene family and conservation of the EG95-vaccine molecule. Commun Biol 2022; 5:199. [PMID: 35241789 PMCID: PMC8894454 DOI: 10.1038/s42003-022-03125-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 02/04/2022] [Indexed: 11/23/2022] Open
Abstract
Cystic echinococcosis is a socioeconomically important parasitic disease caused by the larval stage of the canid tapeworm Echinococcus granulosus, afflicting millions of humans and animals worldwide. The development of a vaccine (called EG95) has been the most notable translational advance in the fight against this disease in animals. However, almost nothing is known about the genomic organisation/location of the family of genes encoding EG95 and related molecules, the extent of their conservation or their functions. The lack of a complete reference genome for E. granulosus genotype G1 has been a major obstacle to addressing these areas. Here, we assembled a chromosomal-scale genome for this genotype by scaffolding to a high quality genome for the congener E. multilocularis, localised Eg95 gene family members in this genome, and evaluated the conservation of the EG95 vaccine molecule. These results have marked implications for future explorations of aspects such as developmentally-regulated gene transcription/expression (using replicate samples) for all E. granulosus stages; structural and functional roles of non-coding genome regions; molecular ‘cross-talk’ between oncosphere and the immune system; and defining the precise function(s) of EG95. Applied aspects should include developing improved tools for the diagnosis and chemotherapy of cystic echinococcosis of humans. A high-quality genome for the parasitic tapeworm, Echinococcus granulosus, provides further insight into the EG95 vaccine target for cystic echinococcosis.
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21
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Complete genome sequence of peony leafroll-associated virus, a novel ampelovirus in subgroup I. Arch Virol 2022; 167:995-998. [PMID: 35133479 DOI: 10.1007/s00705-022-05389-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 01/04/2022] [Indexed: 11/02/2022]
Abstract
The complete genome sequence of peony leafroll-associated virus (PLRaV) was determined by deep sequencing of ribosomal-RNA-depleted total RNA extracted from a peony plant exhibiting leafroll symptoms. Further PCR and RACE analysis showed that the PLRaV genome consists of 15,406 nucleotides and contains 10 putative open reading frames, with an organization typical of members of the genus Ampelovirus, family Closteroviridae. Amino acid sequence comparisons showed that the viral heat shock protein 70 homolog (HSP70h) shared the highest sequence identity (41.7%) with the corresponding region of grapevine leafroll-associated virus 1, and the coat protein (CP) and RNA-dependent RNA polymerase (RdRp) shared the highest sequence identity (32.1% and 52.3%, respectively) with grapevine leafroll-associated virus 13. Phylogenetic analysis of the HSP70h, CP, and RdRp aa sequences showed that PLRaV clustered with members of subgroup I of the genus Ampelovirus.
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22
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Chen S, Yang Y, Gao B, Jia C, Zhu F, Meng Q, Zhang Z, Zhang Z, Xu S. Comparative Proteomics of the Acanthopagrus schlegelii Gonad in Different Sex Reversal. Genes (Basel) 2022; 13:genes13020253. [PMID: 35205296 PMCID: PMC8871944 DOI: 10.3390/genes13020253] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 01/23/2022] [Accepted: 01/25/2022] [Indexed: 01/15/2023] Open
Abstract
A substantial proportion of Acanthopagrus schlegelii individuals change sex from male to female during their lifetime. However, the mechanisms underlying sex change are unknown. In this research, iTRAQ analyses of proteins obtained from A.schlegelii gonads in four different stages of development were compared. In total, 4692 proteins were identified, including common sex-specific proteins, such as sperm-associated antigen 6 and cilia- and flagella-associated proteins in males, and zona pellucida sperm-binding proteins in females. Furthermore, proteins involved in the integrin signaling pathway, inflammation mediated by the chemokine and cytokine signaling pathways, pyruvate metabolism, CCKR signaling map, de novo purine biosynthesis and the ubiquitin proteasome pathway were upregulated in female gonads, whereas proteins implicated in DNA replication, the heterotrimeric G-protein signaling pathway, Gi alpha- and Gs alpha-mediated pathways, wnt signaling pathway, and hedgehog signaling pathway were upregulated in male gonads. Interestingly, cathepsins were only identified in ovaries, indicating their potential involvement in rapid ovarian development. Apoptosis-related proteins expressed in ovaries (such as MAPK and Cdc42) may protect them from cancer. This is the first report on the gonad proteome from A.schlegelii in different stages of sex reversal, and the results provide important fundamental data for studying the molecular mechanisms of sex reversal.
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Affiliation(s)
- Shuyin Chen
- Marine Fisheries Research Institute of Jiangsu Province, Nantong 226007, China; (S.C.); (B.G.); (C.J.); (F.Z.); (Q.M.); (Z.Z.)
| | - Yunxia Yang
- Department of Aquaculture, Zhejiang Ocean University, Zhoushan 316022, China;
| | - Bo Gao
- Marine Fisheries Research Institute of Jiangsu Province, Nantong 226007, China; (S.C.); (B.G.); (C.J.); (F.Z.); (Q.M.); (Z.Z.)
| | - Chaofeng Jia
- Marine Fisheries Research Institute of Jiangsu Province, Nantong 226007, China; (S.C.); (B.G.); (C.J.); (F.Z.); (Q.M.); (Z.Z.)
| | - Fei Zhu
- Marine Fisheries Research Institute of Jiangsu Province, Nantong 226007, China; (S.C.); (B.G.); (C.J.); (F.Z.); (Q.M.); (Z.Z.)
| | - Qian Meng
- Marine Fisheries Research Institute of Jiangsu Province, Nantong 226007, China; (S.C.); (B.G.); (C.J.); (F.Z.); (Q.M.); (Z.Z.)
| | - Zhiwei Zhang
- Marine Fisheries Research Institute of Jiangsu Province, Nantong 226007, China; (S.C.); (B.G.); (C.J.); (F.Z.); (Q.M.); (Z.Z.)
| | - Zhiyong Zhang
- Marine Fisheries Research Institute of Jiangsu Province, Nantong 226007, China; (S.C.); (B.G.); (C.J.); (F.Z.); (Q.M.); (Z.Z.)
- Correspondence: (Z.Z.); (S.X.)
| | - Shixia Xu
- College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
- Correspondence: (Z.Z.); (S.X.)
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Wang Y, Yang Z, Shi L, Yang R, Guo H, Zhang S, Geng G. Transcriptome analysis of Auricularia fibrillifera fruit-body responses to drought stress and rehydration. BMC Genomics 2022; 23:58. [PMID: 35033026 PMCID: PMC8760723 DOI: 10.1186/s12864-021-08284-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 12/28/2021] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Drought stress severely restricts edible fungus production. The genus Auricularia has a rare drought tolerance, a rehydration capability, and is nutrient rich. RESULTS The key genes and metabolic pathways involved in drought-stress and rehydration were investigated using a transcriptome analysis to clarify the relevant molecular mechanisms. In total, 173.93 Mb clean reads, 26.09 Gb of data bulk, and 52,954 unigenes were obtained. Under drought-stress and rehydration conditions, 14,235 and 8539 differentially expressed genes, respectively, were detected. 'Tyrosine metabolic', 'caffeine metabolism', 'ribosome', 'phagosome', and 'proline and arginine metabolism', as well as 'peroxisome' and 'mitogen-activated protein kinase signaling' pathways, had major roles in A. fibrillifera responses to drought stress. 'Tyrosine' and 'caffeine metabolism' might reveal unknown mechanisms for the antioxidation of A. fibrillifera under drought-stress conditions. During the rehydration process, 'diterpenoid biosynthesis', 'butanoate metabolism', 'C5-branched dibasic acid', and 'aflatoxin biosynthesis' pathways were significantly enriched. Gibberellins and γ-aminobutyric acid were important in the recovery of A. fibrillifera growth after rehydration. Many genes related to antibiotics, vitamins, and other health-related ingredients were found in A. fibrillifera. CONCLUSION These findings suggested that the candidate genes and metabolites involved in crucial biological pathways might regulate the drought tolerance or rehydration of Auricularia, shedding light on the corresponding mechanisms and providing new potential targets for the breeding and cultivation of drought-tolerant fungi.
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Affiliation(s)
- Yiqin Wang
- College of Agriculture, Guizhou University, Guiyang, Guizhou, China
| | - Zhifen Yang
- College of Agriculture, Guizhou University, Guiyang, Guizhou, China
| | - Luxi Shi
- College of Agriculture, Guizhou University, Guiyang, Guizhou, China
| | - Rui Yang
- College of Agriculture, Guizhou University, Guiyang, Guizhou, China
| | - Hao Guo
- College of Agriculture, Guizhou University, Guiyang, Guizhou, China
| | - Suqin Zhang
- College of Agriculture, Guizhou University, Guiyang, Guizhou, China.
| | - Guangdong Geng
- College of Agriculture, Guizhou University, Guiyang, Guizhou, China.
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Zhang Y, Li J, Li C, Chen S, Tang Q, Xiao Y, Zhong L, Chen Y, Chen B. Gene expression programs during callus development in tissue culture of two Eucalyptus species. BMC PLANT BIOLOGY 2022; 22:1. [PMID: 34979920 PMCID: PMC8722213 DOI: 10.1186/s12870-021-03391-x] [Citation(s) in RCA: 71] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 12/09/2021] [Indexed: 05/09/2023]
Abstract
BACKGROUND Eucalyptus is a highly diverse genus of the Myrtaceae family and widely planted in the world for timber and pulp production. Tissue culture induced callus has become a common tool for Eucalyptus breeding, however, our knowledge about the genes related to the callus maturation and shoot regeneration is still poor. RESULTS We set up an experiment to monitor the callus induction and callus development of two Eucalyptus species - E. camaldulensis (high embryogenic potential) and E. grandis x urophylla (low embryogenic potential). Then, we performed transcriptome sequencing for primary callus, mature callus, shoot regeneration stage callus and senescence callus. We identified 707 upregulated and 694 downregulated genes during the maturation process of the two Eucalyptus species and most of them were involved in the signaling pathways like plant hormone and MAPK. Next, we identified 135 and 142 genes that might play important roles during the callus development of E. camaldulensis and E. grandis x urophylla, respectively. Further, we found 15 DEGs shared by these two Eucalyptus species during the callus development, including Eucgr.D00640 (stem-specific protein TSJT1), Eucgr.B00171 (BTB/POZ and TAZ domain-containing protein 1), Eucgr.C00948 (zinc finger CCCH domain-containing protein 20), Eucgr.K01667 (stomatal closure-related actinbinding protein 3), Eucgr.C00663 (glutaredoxin-C10) and Eucgr.C00419 (UPF0481 protein At3g47200). Interestingly, the expression patterns of these genes displayed "N" shape in the samples. Further, we found 51 genes that were dysregulated during the callus development of E. camaldulensis but without changes in E. grandis x urophylla, such as Eucgr.B02127 (GRF1-interacting factor 1), Eucgr.C00947 (transcription factor MYB36), Eucgr.B02752 (laccase-7), Eucgr.B03985 (transcription factor MYB108), Eucgr.D00536 (GDSL esterase/lipase At5g45920) and Eucgr.B02347 (scarecrow-like protein 34). These 51 genes might be associated with the high propagation ability of Eucalyptus and 22 might be induced after the dedifferentiation. Last, we performed WGCNA to identify the co-expressed genes during the callus development of Eucalyptus and qRT-PCR experiment to validate the gene expression patterns. CONCLUSIONS This is the first time to globally study the gene profiles during the callus development of Eucalyptus. The results will improve our understanding of gene regulation and molecular mechanisms in the callus maturation and shoot regeneration.
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Affiliation(s)
- Ye Zhang
- Guangxi Key Laboratory of Superior Timber Trees Resource Cultivation, Guangxi Forestry Research Institute, 23 Yongwu Road, Nanning, 530002 Guangxi China
| | - Junji Li
- Guangxi Key Laboratory of Superior Timber Trees Resource Cultivation, Guangxi Forestry Research Institute, 23 Yongwu Road, Nanning, 530002 Guangxi China
| | - Changrong Li
- Guangxi Key Laboratory of Superior Timber Trees Resource Cultivation, Guangxi Forestry Research Institute, 23 Yongwu Road, Nanning, 530002 Guangxi China
| | - Shengkan Chen
- Guangxi Key Laboratory of Superior Timber Trees Resource Cultivation, Guangxi Forestry Research Institute, 23 Yongwu Road, Nanning, 530002 Guangxi China
| | - Qinglan Tang
- Guangxi Key Laboratory of Superior Timber Trees Resource Cultivation, Guangxi Forestry Research Institute, 23 Yongwu Road, Nanning, 530002 Guangxi China
| | - Yufei Xiao
- Guangxi Key Laboratory of Superior Timber Trees Resource Cultivation, Guangxi Forestry Research Institute, 23 Yongwu Road, Nanning, 530002 Guangxi China
| | - Lianxiang Zhong
- Guangxi Key Laboratory of Superior Timber Trees Resource Cultivation, Guangxi Forestry Research Institute, 23 Yongwu Road, Nanning, 530002 Guangxi China
| | - Yingying Chen
- Guangxi Key Laboratory of Superior Timber Trees Resource Cultivation, Guangxi Forestry Research Institute, 23 Yongwu Road, Nanning, 530002 Guangxi China
| | - Bowen Chen
- Guangxi Key Laboratory of Superior Timber Trees Resource Cultivation, Guangxi Forestry Research Institute, 23 Yongwu Road, Nanning, 530002 Guangxi China
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Ai Y, Li Z, Sun WH, Chen J, Zhang D, Ma L, Zhang QH, Chen MK, Zheng QD, Liu JF, Jiang YT, Li BJ, Liu X, Xu XY, Yu X, Zheng Y, Liao XY, Zhou Z, Wang JY, Wang ZW, Xie TX, Ma SH, Zhou J, Ke YJ, Zhou YZ, Lu HC, Liu KW, Yang FX, Zhu GF, Huang L, Peng DH, Chen SP, Lan S, Van de Peer Y, Liu ZJ. The Cymbidium genome reveals the evolution of unique morphological traits. HORTICULTURE RESEARCH 2021; 8:255. [PMID: 34848682 PMCID: PMC8633000 DOI: 10.1038/s41438-021-00683-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 06/22/2021] [Accepted: 07/30/2021] [Indexed: 05/04/2023]
Abstract
The marvelously diverse Orchidaceae constitutes the largest family of angiosperms. The genus Cymbidium in Orchidaceae is well known for its unique vegetation, floral morphology, and flower scent traits. Here, a chromosome-scale assembly of the genome of Cymbidium ensifolium (Jianlan) is presented. Comparative genomic analysis showed that C. ensifolium has experienced two whole-genome duplication (WGD) events, the most recent of which was shared by all orchids, while the older event was the τ event shared by most monocots. The results of MADS-box genes analysis provided support for establishing a unique gene model of orchid flower development regulation, and flower shape mutations in C. ensifolium were shown to be associated with the abnormal expression of MADS-box genes. The most abundant floral scent components identified included methyl jasmonate, acacia alcohol and linalool, and the genes involved in the floral scent component network of C. ensifolium were determined. Furthermore, the decreased expression of photosynthesis-antennae and photosynthesis metabolic pathway genes in leaves was shown to result in colorful striped leaves, while the increased expression of MADS-box genes in leaves led to perianth-like leaves. Our results provide fundamental insights into orchid evolution and diversification.
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Affiliation(s)
- Ye Ai
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zhen Li
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium
- VIB Center for Plant Systems Biology, Gent, Belgium
| | - Wei-Hong Sun
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Juan Chen
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Diyang Zhang
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Liang Ma
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Qing-Hua Zhang
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Ming-Kun Chen
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Qing-Dong Zheng
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
| | | | - Yu-Ting Jiang
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Bai-Jun Li
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Xuedie Liu
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xin-Yu Xu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xia Yu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yu Zheng
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xing-Yu Liao
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zhuang Zhou
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jie-Yu Wang
- Key Laboratory of Plant Resource Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | | | - Tai-Xiang Xie
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Shan-Hu Ma
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jie Zhou
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yu-Jie Ke
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yu-Zhen Zhou
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Hsiang-Chia Lu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Ke-Wei Liu
- Tsinghua-Berkeley Shenzhen Institute (TBSI), Center for Biotechnology and Biomedicine and Shenzhen Key Laboratory of Gene and Antibody Therapy, State Key Laboratory of Chemical Oncogenomics, State Key Laboratory of Health Sciences and Technology, Institute of Biopharmaceutical and Health Engineering (iBHE), Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
| | - Feng-Xi Yang
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Gen-Fa Zhu
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Laiqiang Huang
- Tsinghua-Berkeley Shenzhen Institute (TBSI), Center for Biotechnology and Biomedicine and Shenzhen Key Laboratory of Gene and Antibody Therapy, State Key Laboratory of Chemical Oncogenomics, State Key Laboratory of Health Sciences and Technology, Institute of Biopharmaceutical and Health Engineering (iBHE), Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
| | - Dong-Hui Peng
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Shi-Pin Chen
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Siren Lan
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium.
- VIB Center for Plant Systems Biology, Gent, Belgium.
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa.
- College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, China.
| | - Zhong-Jian Liu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China.
- Henry Fok College of Biology and Agriculture, Shaoguan University, Shaoguan, China.
- Institute of Vegetable and Flowers, Shandong Academy of Agricultural Sciences, Jinan, China.
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26
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Lu Y, Wang J, Chen B, Mo S, Lian L, Luo Y, Ding D, Ding Y, Cao Q, Li Y, Li Y, Liu G, Hou Q, Cheng T, Wei J, Zhang Y, Chen G, Song C, Hu Q, Sun S, Fan G, Wang Y, Liu Z, Song B, Zhu JK, Li H, Jiang L. A donor-DNA-free CRISPR/Cas-based approach to gene knock-up in rice. NATURE PLANTS 2021; 7:1445-1452. [PMID: 34782773 DOI: 10.1038/s41477-021-01019-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 10/10/2021] [Indexed: 06/13/2023]
Abstract
Structural variations (SVs), such as inversion and duplication, contribute to important agronomic traits in crops1. Pan-genome studies revealed that SVs were a crucial and ubiquitous force driving genetic diversification2-4. Although genome editing can effectively create SVs in plants and animals5-8, the potential of designed SVs in breeding has been overlooked. Here, we show that new genes and traits can be created in rice by designed large-scale genomic inversion or duplication using CRISPR/Cas9. A 911 kb inversion on chromosome 1 resulted in a designed promoter swap between CP12 and PPO1, and a 338 kb duplication between HPPD and Ubiquitin2 on chromosome 2 created a novel gene cassette at the joint, promoterUbiquitin2::HPPD. Since the original CP12 and Ubiquitin2 genes were highly expressed in leaves, the expression of PPO1 and HPPD in edited plants with homozygous SV alleles was increased by tens of folds and conferred sufficient herbicide resistance in field trials without adverse effects on other important agronomic traits. CRISPR/Cas-based genome editing for gene knock-ups has been generally considered very difficult without inserting donor DNA as regulatory elements. Our study challenges this notion by providing a donor-DNA-free strategy, thus greatly expanding the utility of CRISPR/Cas in plant and animal improvements.
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Affiliation(s)
- Yu Lu
- Department of Plant Biosecurity, Key Laboratory of Pest Monitoring and Green Management, Ministry of Agriculture and Rural Affairs, College of Plant Protection, China Agricultural University, Beijing, China
| | - Jiyao Wang
- Qingdao Kingagroot Compounds Co. Ltd, Qingdao, China
| | - Bo Chen
- Qingdao Kingagroot Compounds Co. Ltd, Qingdao, China
| | - Sudong Mo
- Qingdao Kingagroot Compounds Co. Ltd, Qingdao, China
| | - Lei Lian
- Qingdao Kingagroot Compounds Co. Ltd, Qingdao, China
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for Research and Development of Fine Chemicals, Guizhou University, Guiyang, China
| | - Yanmin Luo
- Qingdao Kingagroot Compounds Co. Ltd, Qingdao, China
| | - Dehui Ding
- Qingdao Kingagroot Compounds Co. Ltd, Qingdao, China
| | - Yanhua Ding
- Qingdao Kingagroot Compounds Co. Ltd, Qingdao, China
| | - Qing Cao
- Qingdao Kingagroot Compounds Co. Ltd, Qingdao, China
| | - Yucai Li
- Qingdao Kingagroot Compounds Co. Ltd, Qingdao, China
| | - Yong Li
- Qingdao Kingagroot Compounds Co. Ltd, Qingdao, China
| | - Guizhi Liu
- Qingdao Kingagroot Compounds Co. Ltd, Qingdao, China
| | - Qiqi Hou
- Qingdao Kingagroot Compounds Co. Ltd, Qingdao, China
| | | | - Junting Wei
- Qingdao Kingagroot Compounds Co. Ltd, Qingdao, China
| | - Yanrong Zhang
- Qingdao Kingagroot Compounds Co. Ltd, Qingdao, China
| | - Guangwu Chen
- Qingdao Kingagroot Compounds Co. Ltd, Qingdao, China
| | - Chao Song
- Qingdao Kingagroot Compounds Co. Ltd, Qingdao, China
| | - Qiang Hu
- Qingdao Kingagroot Compounds Co. Ltd, Qingdao, China
| | - Shuai Sun
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- BGI-Qingdao, BGI-Shenzhen, Qingdao, China
| | | | - Yating Wang
- Department of Plant Biosecurity, Key Laboratory of Pest Monitoring and Green Management, Ministry of Agriculture and Rural Affairs, College of Plant Protection, China Agricultural University, Beijing, China
| | - Zhiting Liu
- Department of Plant Biosecurity, Key Laboratory of Pest Monitoring and Green Management, Ministry of Agriculture and Rural Affairs, College of Plant Protection, China Agricultural University, Beijing, China
| | - Baoan Song
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for Research and Development of Fine Chemicals, Guizhou University, Guiyang, China.
| | - Jian-Kang Zhu
- Shanghai Center for Plant Stress Biology and Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China.
| | - Huarong Li
- Qingdao Kingagroot Compounds Co. Ltd, Qingdao, China.
| | - Linjian Jiang
- Department of Plant Biosecurity, Key Laboratory of Pest Monitoring and Green Management, Ministry of Agriculture and Rural Affairs, College of Plant Protection, China Agricultural University, Beijing, China.
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27
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Ramakodi MP. A comprehensive evaluation of single-end sequencing data analyses for environmental microbiome research. Arch Microbiol 2021; 203:6295-6302. [PMID: 34654941 DOI: 10.1007/s00203-021-02597-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 09/17/2021] [Accepted: 09/28/2021] [Indexed: 01/04/2023]
Abstract
Illumina sequencing platforms have been widely used for amplicon-based environmental microbiome research. Analyses of amplicon data of environmental samples, generated from Illumina MiSeq platform illustrate the reverse (R2) reads in the PE datasets to have low quality towards the 3' end of the reads which affect the sequencing depth of samples and ultimately impact the sample size which may possibly lead to an altered outcome. This study evaluates the usefulness of single-end (SE) sequencing data in microbiome research when the Illumina MiSeq PE dataset shows significantly high number of low-quality reverse reads. In this study, the amplicon data (V1V3, V3V4, V4V5 and V6V8) from 128 environmental (soil) samples, downloaded from SRA, demonstrate the efficiency of single-end (SE) sequencing data analyses in microbiome research. The SE datasets were found to infer the core microbiome structure as comparable to the PE dataset. Conspicuously, the forward (R1) datasets inferred a higher number of taxa as compared to PE datasets for most of the amplicon regions, except V3V4. Thus, analyses of SE sequencing data, especially R1 reads, in environmental microbiome studies could ameliorate the problems arising on sample size of the study due to low quality reverse reads in the dataset. However, care must be taken while interpreting the microbiome structure as few taxa observed in the PE datasets were absent in the SE datasets. In conclusion, this study demonstrates the availability of choices in analyzing the amplicon data without having the need to remove samples with low quality reverse reads.
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Affiliation(s)
- Meganathan P Ramakodi
- CSIR-National Environmental Engineering Research Institute (NEERI), Hyderabad Zonal Centre, IICT Campus, Tarnaka, Hyderabad, Telangana, 500007, India.
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28
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Ullah F, Rauf W, Khan K, Khan S, Bell KM, de Oliveira VC, Tariq M, Bakhshalizadeh S, Touraine P, Katsanis N, Sinclair A, He S, Tucker EJ, Baig SM, Davis EE. A recessive variant in TFAM causes mtDNA depletion associated with primary ovarian insufficiency, seizures, intellectual disability and hearing loss. Hum Genet 2021; 140:1733-1751. [PMID: 34647195 DOI: 10.1007/s00439-021-02380-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 09/30/2021] [Indexed: 12/25/2022]
Abstract
Mitochondrial disorders are collectively common, genetically heterogeneous disorders in both pediatric and adult populations. They are caused by molecular defects in oxidative phosphorylation, failure of essential bioenergetic supply to mitochondria, and apoptosis. Here, we present three affected individuals from a consanguineous family of Pakistani origin with variable seizures and intellectual disability. Both females display primary ovarian insufficiency (POI), while the male shows abnormal sex hormone levels. We performed whole exome sequencing and identified a recessive missense variant c.694C > T, p.Arg232Cys in TFAM that segregates with disease. TFAM (mitochondrial transcription factor A) is a component of the mitochondrial replisome machinery that maintains mtDNA transcription and replication. In primary dermal fibroblasts, we show depletion of mtDNA and significantly altered mitochondrial function and morphology. Moreover, we observed reduced nucleoid numbers with significant changes in nucleoid size or shape in fibroblasts from an affected individual compared to controls. We also investigated the effect of tfam impairment in zebrafish; homozygous tfam mutants carrying an in-frame c.141_149 deletion recapitulate the mtDNA depletion and ovarian dysgenesis phenotypes observed in affected humans. Together, our genetic and functional data confirm that TFAM plays a pivotal role in gonad development and expands the repertoire of mitochondrial disease phenotypes.
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Affiliation(s)
- Farid Ullah
- National Institute for Biotechnology and Genetic Engineering (NIBGE-C), Faisalabad, Pakistan.,Pakistan Institute of Engineering and Applied Sciences (PIEAS), Islamabad, Pakistan.,Stanley Manne Children's Research Institute, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, USA
| | - Waqar Rauf
- National Institute for Biotechnology and Genetic Engineering (NIBGE-C), Faisalabad, Pakistan.,Pakistan Institute of Engineering and Applied Sciences (PIEAS), Islamabad, Pakistan
| | - Kamal Khan
- Stanley Manne Children's Research Institute, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, USA
| | - Sheraz Khan
- National Institute for Biotechnology and Genetic Engineering (NIBGE-C), Faisalabad, Pakistan.,Pakistan Institute of Engineering and Applied Sciences (PIEAS), Islamabad, Pakistan.,Stanley Manne Children's Research Institute, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, USA
| | - Katrina M Bell
- Department of Pediatrics, University of Melbourne, Melbourne, Australia.,Bioinformatics, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Australia
| | - Vanessa Cristina de Oliveira
- Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of São Paulo, Pirassununga, São Paulo, Brazil
| | - Muhammad Tariq
- National Institute for Biotechnology and Genetic Engineering (NIBGE-C), Faisalabad, Pakistan.,Pakistan Institute of Engineering and Applied Sciences (PIEAS), Islamabad, Pakistan
| | - Shabnam Bakhshalizadeh
- Department of Pediatrics, University of Melbourne, Melbourne, Australia.,Reproductive Development, MurdochChildren's Research Institute, Royal Children's Hospital, Melbourne, Australia
| | - Philippe Touraine
- Department of Endocrinology and Reproductive Medicine, Center for Rare Endocrine and Gynecological Diseases, Sorbonne Université Pitié Salpétrière Hospital, Paris, France
| | - Nicholas Katsanis
- Stanley Manne Children's Research Institute, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, USA.,Rescindo Therapeutics, Cary, NC, USA
| | - Andrew Sinclair
- Department of Pediatrics, University of Melbourne, Melbourne, Australia.,Reproductive Development, MurdochChildren's Research Institute, Royal Children's Hospital, Melbourne, Australia
| | | | - Elena J Tucker
- Department of Pediatrics, University of Melbourne, Melbourne, Australia.,Reproductive Development, MurdochChildren's Research Institute, Royal Children's Hospital, Melbourne, Australia
| | - Shahid M Baig
- National Institute for Biotechnology and Genetic Engineering (NIBGE-C), Faisalabad, Pakistan.,Pakistan Institute of Engineering and Applied Sciences (PIEAS), Islamabad, Pakistan.,Pakistan Science Foundation, Constitution Avenue, Islamabad, Pakistan.,Department of Biological and Biomedical Sciences, Aga Khan University, Karachi, Pakistan
| | - Erica E Davis
- Stanley Manne Children's Research Institute, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, USA. .,Department of Pediatrics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA. .,Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
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29
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Punzón-Jiménez P, Labarta E. The impact of the female genital tract microbiome in women health and reproduction: a review. J Assist Reprod Genet 2021; 38:2519-2541. [PMID: 34110573 PMCID: PMC8581090 DOI: 10.1007/s10815-021-02247-5] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Accepted: 05/25/2021] [Indexed: 12/17/2022] Open
Abstract
PURPOSE The aim of this review is to gather the available research focusing on female genital tract (FGT) microbiome. Research question focuses in decipher which is the role of FGT microbiota in eubiosis, assisted reproduction techniques (ARTs), and gynaecological disorders, and how microbiome could be utilised to improve reproduction outcomes and to treat fertility issues. METHODS PubMed was searched for articles in English from January 2004 to April 2021 for "genital tract microbiota and reproduction", "endometrial microbiome", "microbiome and reproduction" and "microbiota and infertility". Manual search of the references within the resulting articles was performed. RESULTS Current knowledge confirms predominance of Lactobacillus species, both in vagina and endometrium, whereas higher variability of species is both found in fallopian tubes and ovaries. Microbial signature linked to different disorders such endometriosis, bacterial vaginosis, and gynaecological cancers are described. Broadly, low variability of species and Lactobacillus abundance within the FGT is associated with better reproductive and ART outcomes. CONCLUSION Further research regarding FGT microbiome configuration needs to be done in order to establish a more precise link between microbiota and eubiosis or dysbiosis. Detection of bacterial species related with poor reproductive outcomes, infertility or gynaecological diseases could shape new tools for their diagnosis and treatment, as well as resources to assess the pregnancy prognosis based on endometrial microbiota. Data available suggest future research protocols should be standardised, and it needs to include the interplay among microbiome, virome and mycobiome, and the effect of antibiotics or probiotics on the microbiome shifts.
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Affiliation(s)
- Paula Punzón-Jiménez
- IVI Global Education, Edificio Bipolo, Hospital Universitario La Fe, Fernando Abril Martorell 106, Torre A, Planta 1ª, 46026, Valencia, Spain.
- Department of Pediatrics, Obstetrics and Gynaecology, Universitat de València, Av. Blasco Ibáñez, 15, 46010, Valencia, Spain.
| | - Elena Labarta
- IVIRMA Valencia, Plaza de la Policía Local, 3, 46015, Valencia, Spain
- IVI Foundation - IIS La Fe, Fernando Abril Martorell 106, Torre A, Planta 1ª, 46026, Valencia, Spain
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30
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Wang B, Wang L, Wang A, Miao Y. Next-generation sequencing of the mitochondrial genome of Thamnaconus septentrionalis Gunther, 1877 (Aluteridae: Thamnaconus) specimen collected in China. Mitochondrial DNA B Resour 2021; 6:2198-2199. [PMID: 34263049 PMCID: PMC8259841 DOI: 10.1080/23802359.2021.1945501] [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] [Indexed: 11/02/2022] Open
Abstract
In this article, the complete 16,439 bp mitochondrial genome of Thamnaconus septentrionalis was determined from a specimen collected in China. It contains 13 protein-coding genes, 22 transfer RNA genes, 1 D-loop region, 2 rRNA genes, the base composition of A 27.74%, G 17.09%, T 26.04%, and C 29.13%, resulting in a G + C content of 46.22%. Phylogenetic analysis showed that Thamnaconus septentrionalis was the nearest sister to Thamnaconus modestus. These presented data will be significant for evolution relationships study among fish species.
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Affiliation(s)
- Bin Wang
- Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Lei Wang
- Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, School of Life Sciences, South China Normal University, Guangzhou, China
- Institute of Modern Aquaculture Science and Engineering, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Anli Wang
- Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Yutao Miao
- Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, School of Life Sciences, South China Normal University, Guangzhou, China
- Institute of Modern Aquaculture Science and Engineering, School of Life Sciences, South China Normal University, Guangzhou, China
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31
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Diverse heterochromatin-associated proteins repress distinct classes of genes and repetitive elements. Nat Cell Biol 2021; 23:905-914. [PMID: 34354237 PMCID: PMC9248069 DOI: 10.1038/s41556-021-00725-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 06/30/2021] [Indexed: 12/28/2022]
Abstract
Heterochromatin, typically marked by histone H3 trimethylation at lysine 9 (H3K9me3) or lysine 27 (H3K27me3), represses different protein-coding genes in different cells, as well as repetitive elements. The basis for locus specificity is unclear. Previously, we identified 172 proteins that are embedded in sonication-resistant heterochromatin (srHC) harbouring H3K9me3. Here, we investigate in humans how 97 of the H3K9me3-srHC proteins repress heterochromatic genes. We reveal four groups of srHC proteins that each repress many common genes and repeat elements. Two groups repress H3K9me3-embedded genes with different extents of flanking srHC, one group is specific for srHC genes with H3K9me3 and H3K27me3, and one group is specific for genes with srHC as the primary feature. We find that the enhancer of rudimentary homologue (ERH) is conserved from Schizosaccharomyces pombe in repressing meiotic genes and, in humans, now represses other lineage-specific genes and repeat elements. The study greatly expands our understanding of H3K9me3-based gene repression in vertebrates.
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32
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Wang R, Yang Y, Jing Y, Segar ST, Zhang Y, Wang G, Chen J, Liu QF, Chen S, Chen Y, Cruaud A, Ding YY, Dunn DW, Gao Q, Gilmartin PM, Jiang K, Kjellberg F, Li HQ, Li YY, Liu JQ, Liu M, Machado CA, Ming R, Rasplus JY, Tong X, Wen P, Yang HM, Yang JJ, Yin Y, Zhang XT, Zhang YY, Yu H, Yue Z, Compton SG, Chen XY. Molecular mechanisms of mutualistic and antagonistic interactions in a plant-pollinator association. Nat Ecol Evol 2021; 5:974-986. [PMID: 34002050 DOI: 10.1038/s41559-021-01469-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 04/20/2021] [Indexed: 02/06/2023]
Abstract
Many insects metamorphose from antagonistic larvae into mutualistic adult pollinators, with reciprocal adaptation leading to specialized insect-plant associations. It remains unknown how such interactions are established at molecular level. Here we assemble high-quality genomes of a fig species, Ficus pumila var. pumila, and its specific pollinating wasp, Wiebesia pumilae. We combine multi-omics with validation experiments to reveal molecular mechanisms underlying this specialized interaction. In the plant, we identify the specific compound attracting pollinators and validate the function of several key genes regulating its biosynthesis. In the pollinator, we find a highly reduced number of odorant-binding protein genes and an odorant-binding protein mainly binding the attractant. During antagonistic interaction, we find similar chemical profiles and turnovers throughout the development of galled ovules and seeds, and a significant contraction of detoxification-related gene families in the pollinator. Our study identifies some key genes bridging coevolved mutualists, establishing expectations for more diffuse insect-pollinator systems.
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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.,Shanghai Institute of Pollution Control and Ecological Security, Shanghai, 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
| | - Yi Jing
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Simon T Segar
- Agriculture and Environment Department, Harper Adams University, Newport, UK
| | - Yu Zhang
- 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
| | - Gang Wang
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, China
| | - Jin Chen
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, 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
| | - Yan Chen
- Ecological Security and Protection Key Laboratory of Sichuan Province, Mianyang Normal University, Mianyang, 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
| | - Derek W Dunn
- College of Life Sciences, Northwest University, Xi'an, China
| | - Qiang Gao
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Philip M Gilmartin
- Department of Biological and Marine Science, University of Hull, Hull, UK
| | - 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
| | - Finn Kjellberg
- CEFE, CNRS, University of Montpellier, Paul Valéry University Montpellier, EPHE, IRD, Montpellier, France
| | - Hong-Qing Li
- School of Life 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
| | - Jian-Quan Liu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Min Liu
- School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Carlos A Machado
- Department of Biology, University of Maryland, College Park, MD, USA
| | - Ray Ming
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | | | - 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
| | - Ping Wen
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, China
| | | | - Jing-Jun 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
| | - Ye Yin
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Xing-Tan Zhang
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Corps, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, 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, China
| | - Hui Yu
- Key Laboratory of Plant Resource Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China. .,School of Life Sciences, Qufu Normal University, Qufu, China.
| | - Zhen Yue
- BGI Genomics, BGI-Shenzhen, Shenzhen, 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 Institute of Pollution Control and Ecological Security, Shanghai, China.
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33
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Edgecombe J, Urban L, Todd EV, Gemmell NJ. Might Gene Duplication and Neofunctionalization Contribute to the Sexual Lability Observed in Fish? Sex Dev 2021; 15:122-133. [PMID: 34167118 DOI: 10.1159/000515425] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 02/24/2021] [Indexed: 11/19/2022] Open
Abstract
Sex determination and differentiation varies widely across vertebrates, but is most dramatically diverse in fishes. Among fishes sex reversal and sex change are observed in 41 teleost families spanning 7 orders. These sex-changing fish perhaps highlight better than any other system that sex determination is not the narrow and fixed construct we once thought, but a plastic trait that is better viewed as a reaction norm. However, while this stunning transformation is increasingly understood, a fundamental question arises, which is why some fish species have retained this inherent plasticity in sexual fate, while others have not? Here, we explore our current understanding of sex change in fish, some of the factors that permit and constrain sex reversal, and posit that gene duplication and neofunctionalization contribute to the sexual lability observed in fish.
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Affiliation(s)
- Jonika Edgecombe
- Department of Anatomy, University of Otago, Dunedin, New Zealand
| | - Lara Urban
- Department of Anatomy, University of Otago, Dunedin, New Zealand
| | - Erica V Todd
- School of Life and Environmental Sciences, Deakin University, Queenscliff, Victoria, Australia
| | - Neil J Gemmell
- Department of Anatomy, University of Otago, Dunedin, New Zealand
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34
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Pang XM, Tian D, Zhang T, Liao LS, Li CX, Luo XM, Feng JX, Zhao S. G protein γ subunit modulates expression of plant-biomass-degrading enzyme genes and mycelial-development-related genes in Penicillium oxalicum. Appl Microbiol Biotechnol 2021; 105:4675-4691. [PMID: 34076714 DOI: 10.1007/s00253-021-11370-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 05/05/2021] [Accepted: 05/26/2021] [Indexed: 01/24/2023]
Abstract
Heterotrimeric-G-protein-mediated signaling pathways modulate the expression of the essential genes in many fundamental cellular processes in fungi at the transcription level. However, these processes remain unclear in Penicillium oxalicum. In this study, we generated knockout and knockout-complemented strains of gng-1 (POX07071) encoding the Gγ protein and found that GNG-1 modulated the expression of genes encoding plant-biomass-degrading enzymes (PBDEs) and sporulation-related activators. Interestingly, GNG-1 affected expression of the cxrB that encodes a known transcription factor required for the expression of major cellulase and xylanase genes. Constitutive overexpression of cxrB in ∆gng-1 circumvented the dependence of PBDE production on GNG-1. Further evidence indicated that CxrB indirectly regulated the transcription levels of key amylase genes by controlling the expression of the regulatory gene amyR. These data extended the diversity of Gγ protein functions and provided new insight into the signal transduction and regulation of PBDE gene expression in filamentous fungi. KEY POINTS: • GNG-1 modulates the expression of PBDE genes and sporulation-related genes. • GNG-1 controls expression of the key regulatory gene cxrB. • Overexpression of cxrB circumvents dependence of PBDE production on GNG-1.
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Affiliation(s)
- Xiao-Ming Pang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, Guangxi, 530004, People's Republic of China
| | - Di Tian
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, Guangxi, 530004, People's Republic of China
| | - Ting Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, Guangxi, 530004, People's Republic of China
| | - Lu-Sheng Liao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, Guangxi, 530004, People's Republic of China
| | - Cheng-Xi Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, Guangxi, 530004, People's Republic of China
| | - Xue-Mei Luo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, Guangxi, 530004, People's Republic of China
| | - Jia-Xun Feng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, Guangxi, 530004, People's Republic of China
| | - Shuai Zhao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, Guangxi, 530004, People's Republic of China.
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Zhu KC, Zhang N, Liu BS, Guo L, Guo HY, Jiang SG, Zhang DC. A chromosome-level genome assembly of the yellowfin seabream (Acanthopagrus latus; Hottuyn, 1782) provides insights into its osmoregulation and sex reversal. Genomics 2021; 113:1617-1627. [PMID: 33839268 DOI: 10.1016/j.ygeno.2021.04.017] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 12/14/2020] [Accepted: 04/05/2021] [Indexed: 12/15/2022]
Abstract
The yellowfin seabream Acanthopagrus latus is the economically most important Sparidae fish in the northern South China Sea. As euryhaline fish, they are perfect model for investigating osmoregulatory mechanisms in teleosts. Moreover, the reproductive biology of hermaphrodites has long been intriguing; however, little information is known about the molecular pathways underlying their sex change. Here, we report a chromosome level reference genome of A. latus generated by employing the PacBio single molecule sequencing technique (SMRT) and high-throughput chromosome conformation capture (Hi-C) technologies. The draft genome of yellowfin seabream was 806 Mb, with 732 Mb scaffolds anchored on 24 chromosomes. The contig N50 and scaffold N50 were 2.6 Mb and 30.17 Mb, respectively. The assembly is of high integrity and includes 92.23% universal single-copy orthologues based on benchmarking universal single-copy orthologs (BUSCO) analysis. A total of 19,631 protein-coding genes were functionally annotated in the reference genome. Moreover, ARRDC3 and GSTA gene families which related to osmoregulation underwent an extensive expansion in two euryhaline sparids fish genomes compared to other teleost genomes. Moreover, integrating sex-specific transcriptome analyses, several genes related to the transforming growth factor beta (TGF-β) signalling pathway involved in sex differentiation and development. This genomic resource will not only be valuable for studying the osmoregulatory mechanisms in estuarine fish and sex determination in hermaphrodite vertebrate species, but also provide useful genomic tools for facilitating breeding of the yellowfin seabream.
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Affiliation(s)
- Ke-Cheng Zhu
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, Guangdong Province, PR China; Tropical Aquaculture Research and Development Center, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Sanya 572018, China
| | - Nan Zhang
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, Guangdong Province, PR China; Southern Marine Science and Engineering Guangdong Laboratory(Guangzhou), 511458, Guangzhou, Guangdong Province, PR China; Tropical Aquaculture Research and Development Center, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Sanya 572018, China
| | - Bao-Suo Liu
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, Guangdong Province, PR China; Tropical Aquaculture Research and Development Center, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Sanya 572018, China
| | - Liang Guo
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, Guangdong Province, PR China; Southern Marine Science and Engineering Guangdong Laboratory(Guangzhou), 511458, Guangzhou, Guangdong Province, PR China; Tropical Aquaculture Research and Development Center, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Sanya 572018, China
| | - Hua-Yang Guo
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, Guangdong Province, PR China; Tropical Aquaculture Research and Development Center, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Sanya 572018, China
| | - Shi-Gui Jiang
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, Guangdong Province, PR China; Southern Marine Science and Engineering Guangdong Laboratory(Guangzhou), 511458, Guangzhou, Guangdong Province, PR China; Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry, Guangzhou, Guangdong Province, PR China; Sanya Tropical Fisheries Research Institute, Sanya, Hainan Province, China
| | - Dian-Chang Zhang
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, Guangdong Province, PR China; Southern Marine Science and Engineering Guangdong Laboratory(Guangzhou), 511458, Guangzhou, Guangdong Province, PR China; Tropical Aquaculture Research and Development Center, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Sanya 572018, China; Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry, Guangzhou, Guangdong Province, PR China; Sanya Tropical Fisheries Research Institute, Sanya, Hainan Province, China.
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Liu D, Zhang X, Zheng T, Shi Q, Cui Y, Wang Y, Liu L. Optimisation and evaluation of the random forest model in the efficacy prediction of chemoradiotherapy for advanced cervical cancer based on radiomics signature from high-resolution T2 weighted images. Arch Gynecol Obstet 2021; 303:811-820. [PMID: 33394142 PMCID: PMC7960581 DOI: 10.1007/s00404-020-05908-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 11/17/2020] [Indexed: 12/28/2022]
Abstract
PURPOSE Our objective was to establish a random forest model and to evaluate its predictive capability of the treatment effect of neoadjuvant chemotherapy-radiation therapy. METHODS This retrospective study included 82 patients with locally advanced cervical cancer who underwent scanning from March 2013 to May 2018. The random forest model was established and optimised based on the open source toolkit scikit-learn. Byoptimising of the number of decision trees in the random forest, the criteria for selecting the final partition index and the minimum number of samples partitioned by each node, the performance of random forest in the prediction of the treatment effect of neoadjuvant chemotherapy-radiation therapy on advanced cervical cancer (> IIb) was evaluated. RESULTS The number of decision trees in the random forests influenced the model performance. When the number of decision trees was set to 10, 25, 40, 55, 70, 85 and 100, the performance of random forest model exhibited an increasing trend first and then a decreasing one. The criteria for the selection of final partition index showed significant effects on the generation of decision trees. The Gini index demonstrated a better effect compared with information gain index. The area under the receiver operating curve for Gini index attained a value of 0.917. CONCLUSION The random forest model showed potential in predicting the treatment effect of neoadjuvant chemotherapy-radiation therapy based on high-resolution T2WIs for advanced cervical cancer (> IIb).
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Affiliation(s)
- Defeng Liu
- Department of Magnetic Resonance Imaging, Qinhuangdao Municipal No. 1 Hospital, Qinhuangdao, People's Republic of China
| | - Xiaohang Zhang
- State Grid Information & Telecommunication Group Co., Ltd., Beijing, People's Republic of China
| | - Tao Zheng
- Department of Magnetic Resonance Imaging, Qinhuangdao Municipal No. 1 Hospital, Qinhuangdao, People's Republic of China
| | - Qinglei Shi
- Scientific Clinical Specialist, Siemens Ltd., Beijing, People's Republic of China
| | - Yujie Cui
- Department of Magnetic Resonance Imaging, Qinhuangdao Municipal No. 1 Hospital, Qinhuangdao, People's Republic of China
| | - Yongji Wang
- Cooperative Innovation Center, Institute of Software, Chinese Academy of Sciences, Beijing, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, People's Republic of China
- State Key Laboratory of Computer Science (Institute of Software, The Chinese Academy of Sciences), Beijing, People's Republic of China
| | - Lanxiang Liu
- Department of Magnetic Resonance Imaging, Qinhuangdao Municipal No. 1 Hospital, Qinhuangdao, People's Republic of China.
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Xing Y, Yang X, Chen H, Zhu S, Xu J, Chen Y, Zeng J, Chen F, Johnson MR, Jiang H, Wang WJ. Impact of storage conditions on peripheral leukocytes transcriptome. Mol Biol Rep 2021; 48:1151-1159. [PMID: 33565022 DOI: 10.1007/s11033-021-06194-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 01/28/2021] [Indexed: 12/13/2022]
Abstract
Leukocytes reflect the physiological and pathological states of each individual, and transcriptomic data of leukocytes have been used to reflect health conditions. Since the overall impact of ex vivo conditions on the leukocyte transcriptome before RNA stabilization remains unclear, we evaluated the influence of temporary storage conditions on the leukocyte transcriptome through RNA sequencing. We collected peripheral blood with EDTA tubes, which were processed immediately or stored either at 4 °C or room temperature (RT, 18-22 °C) for 2 h, 6 h and 24 h. Total cellular RNA was extracted from 42 leukocyte samples after red blood cells lysis for subsequent RNA sequencing. We applied weighted gene co-expression network analysis to construct co-expression networks of mRNA and lncRNA among the samples, and then performed gene ontology (GO) term enrichment to explore possible biological processes affected by storage conditions. Storage conditions change the gene expression of peripheral leukocytes. Comparing with fresh leukocytes, storage for 24 h at 4 °C and RT affected 1515 (1.51%) and 10,823 (10.82%) genes, respectively. Pathway enrichment analysis identified nucleosome assembly enriched in up-regulated genes at both conditions. When blood was stored at RT for 24 h, genes involved in apoptotic signaling pathway, negative regulation of cell cycle and lymphocyte activation were upregulated, while the relative proportion of neutrophils was significantly decreased. Temporary storage conditions profoundly affect the gene expression profiles of leukocytes and might further change cell viability and state. Storage of blood samples at 4 °C within 6 h largely maintains their original transcriptome.
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Affiliation(s)
- Yanru Xing
- School of Future Technology, University of Chinese Academy of Sciences, Beijing, China
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Xi Yang
- BGI-Shenzhen, Shenzhen, 518083, China
- ShenZhen Engineering Laboratory for Innovative Molecular Diagnostic, BGI-Shenzhen, Shenzhen, 518083, China
| | | | - Sujun Zhu
- Obstetrics Department, Shenzhen Maternity and Child Healthcare Hospital, Shenzhen, Guangdong, China
| | - Jinjin Xu
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Yuan Chen
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Juan Zeng
- Obstetrics Department, Shenzhen Maternity and Child Healthcare Hospital, Shenzhen, Guangdong, China
| | - Fang Chen
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Mark Richard Johnson
- Academic Obstetric Department, Imperial College London, Chelsea & Westminster Hospital campus, London, UK
| | - Hui Jiang
- School of Future Technology, University of Chinese Academy of Sciences, Beijing, China
- Guangdong Enterprise Key Laboratory of Human Disease Genomics, Shenzhen Key Laboratory of Genomics, BGI-Shenzhen, Shenzhen, 518083, China
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Wu R, Li H, Li R, Peng D, Wang N, Shen X, Sun H. Identification and sequencing of 59 highly polymorphic microhaplotypes for analysis of DNA mixtures. Int J Legal Med 2021; 135:1137-1149. [PMID: 33502549 DOI: 10.1007/s00414-020-02483-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Accepted: 12/09/2020] [Indexed: 12/30/2022]
Abstract
Mixture detection remains one of the major challenges within a forensic science context. In recent years, microhaplotypes were proposed to have great potential in mixture detection, although many of them are not as polymorphic as widely used short tandem repeat (STR) markers. In this study, 59 new highly polymorphic microhaplotypes were identified and sequenced with the NextSeq 500 Sequencer. Based on the whole 1000 Genomes Project dataset, the average effective number of alleles (Ae) of the 59 microhaplotypes was 5.44, and the Ae values of 36 of these microhaplotypes were > 5.00. Their genetic variations in 187 Han Chinese individuals were evaluated. The average allele coverage ratio (ACR) of heterozygotes across all loci was 0.96 ± 0.05. The number of observed alleles varied from 4 to 23, with an average of 8.8 alleles per microhaplotype locus. The average observed heterozygosity (Ho) of 59 loci was 0.77 ± 0.05, and the Ho values of 15 of these loci were > 0.80. All loci showed high polymorphisms with a discrimination power (DP) ranging from 0.80 to 0.97, and the average DP was 0.92 ± 0.03. The analysis of simulated mixtures demonstrated that the microhaplotypes reported here were highly polymorphic and performed well in forensic DNA mixture analysis. This study not only demonstrated the applicability of microhaplotypes in mixture analysis but also provided new choices for highly polymorphic microhaplotypes because after adding the markers identified here, the number of microhaplotypes with Ae values of > 4.00 will increase from ~ 50 to ~ 110.
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Affiliation(s)
- Riga Wu
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, No. 74 Zhongshan Road II, Guangzhou, 510080, Guangdong, People's Republic of China
- Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou, 510080, People's Republic of China
| | - Haixia Li
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, No. 74 Zhongshan Road II, Guangzhou, 510080, Guangdong, People's Republic of China
| | - Ran Li
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, No. 74 Zhongshan Road II, Guangzhou, 510080, Guangdong, People's Republic of China
| | - Dan Peng
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, No. 74 Zhongshan Road II, Guangzhou, 510080, Guangdong, People's Republic of China
| | - Nana Wang
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, No. 74 Zhongshan Road II, Guangzhou, 510080, Guangdong, People's Republic of China
| | - Xuefeng Shen
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, No. 74 Zhongshan Road II, Guangzhou, 510080, Guangdong, People's Republic of China
| | - Hongyu Sun
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, No. 74 Zhongshan Road II, Guangzhou, 510080, Guangdong, People's Republic of China.
- Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou, 510080, People's Republic of China.
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Li SH, Gu LS, Qu XY, Zhang T, Li CX, Mai RM, Liao LS, Zhang FF, Luo XM, Zhao S, Feng JX. Involvement of phospholipase PLA 2 in production of cellulase and xylanase by Penicillium oxalicum. Appl Microbiol Biotechnol 2021; 105:679-694. [PMID: 33394158 DOI: 10.1007/s00253-020-11065-1] [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: 07/03/2020] [Revised: 12/07/2020] [Accepted: 12/15/2020] [Indexed: 10/22/2022]
Abstract
Phospholipases play vital roles in immune and inflammatory responses in mammals and plants; however, knowledge of phospholipase functions in fungi is limited. In this study, we investigated the effects of deleting predicted phospholipase genes on cellulase and xylanase production, and morphological phenotype, in Penicillium oxalicum. Individual deletion of nine of the ten predicted phospholipase genes resulted in alteration of cellulase and xylanase production, and the morphological phenotypes, to various degrees. The mutant ∆POX07277 lost 22.5 to 82.8% of cellulase (i.e., filter paper cellulase, carboxymethylcellulase, and p-nitrophenyl-β-cellobiosidase) and xylanase production, whereas p-nitrophenyl-β-glucopyranosidase production increased by 5.8-127.8 fold. POX07277 (P. oxalicum gene No. 07277) was predicted to encode phospholipase A2 and was found to negatively affect the sporulation of P. oxalicum. Comparative transcriptomic and quantitative reverse transcription-PCR analysis indicated that POX07277 dynamically affected the expression of cellulase and xylanase genes and the regulatory genes for fungal sporulation, under micro-crystalline cellulose induction. POX07277 was required for the expression of the known regulatory gene PoxCxrB (cellulolytic and xylanolytic regulator B in P. oxalicum), which is involved in cellulase and xylanase gene expression in P. oxalicum. Conversely, POX07277 expression was regulated by PoxCxrB. These findings will aid the understanding of phospholipase functions and provide novel insights into the mechanism of fungal cellulase and xylanase gene expression. KEY POINTS : • The roles of phospholipases were investigated in Penicillium oxalicum. • POX07277 (PLA2) is required for the expression of cellulase and xylanase genes. • PoxCxrB dynamically regulated POX07277 expression.
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Affiliation(s)
- Shi-Huan Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, 530004, Guangxi, People's Republic of China
| | - Li-Sha Gu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, 530004, Guangxi, People's Republic of China
| | - Xiao-Yi Qu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, 530004, Guangxi, People's Republic of China
| | - Ting Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, 530004, Guangxi, People's Republic of China
| | - Cheng-Xi Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, 530004, Guangxi, People's Republic of China
| | - Rong-Ming Mai
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, 530004, Guangxi, People's Republic of China
| | - Lu-Sheng Liao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, 530004, Guangxi, People's Republic of China
| | - Feng-Fei Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, 530004, Guangxi, People's Republic of China
| | - Xue-Mei Luo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, 530004, Guangxi, People's Republic of China
| | - Shuai Zhao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, 530004, Guangxi, People's Republic of China.
| | - Jia-Xun Feng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, 530004, Guangxi, People's Republic of China.
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Sun C, Cheng L, He K, Zhang S, Li F. Next-generation sequencing of the mitochondrial genome of Macculochella peeli (Percichthyoidei: Percichthyidae). MITOCHONDRIAL DNA PART B-RESOURCES 2020; 5:2222-2223. [PMID: 33366981 PMCID: PMC7510683 DOI: 10.1080/23802359.2020.1768953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 05/09/2020] [Indexed: 11/28/2022]
Abstract
The Maccullochella peeli belongs to family Maccullochella, and is distributed in Australia and South America (mainly Argentina and Chile). In this paper, the complete mitochondrial genome of M. peeli was determined using next-generation sequencing. The whole mitogenome is a typical circular DNA molecule of 16,442 bp and contains 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and a D-loop region, with the base composition of A 31.6%, G 14.3%, T 26.3%, and C 27.8%. Phylogenetic analysis showed that M. peeli was the nearest sister to Macquaria australasica. Our whole mitogenome presented here would be useful for further study of M. peeli.
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Affiliation(s)
- Chengfei Sun
- Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Linhui Cheng
- College of Animal Science and Techonology, Jiangxi Agricultural University, Nanchang, China
| | - Kun He
- College of Animal Science and Techonology, Jiangxi Agricultural University, Nanchang, China
| | - Shilin Zhang
- College of Animal Science and Techonology, Jiangxi Agricultural University, Nanchang, China
| | - Fugui Li
- College of Animal Science and Techonology, Jiangxi Agricultural University, Nanchang, China
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Sun C, Li J, Dong J, Niu Y, Hu J, Lian J, Li W, Li J, Tian Y, Shi Q, Ye X. Chromosome-level genome assembly for the largemouth bass Micropterus salmoides provides insights into adaptation to fresh and brackish water. Mol Ecol Resour 2020; 21:301-315. [PMID: 32985096 DOI: 10.1111/1755-0998.13256] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 08/19/2020] [Accepted: 08/24/2020] [Indexed: 12/16/2022]
Abstract
Largemouth bass (LMB; Micropterus salmoides) has been an economically important fish in North America, Europe, and China. This study obtained a chromosome-level genome assembly of LMB using PacBio and Hi-C sequencing. The final assembled genome is 964 Mb, with contig N50 and scaffold N50 values of 1.23 Mb and 36.48 Mb, respectively. Combining with RNA sequencing data, we annotated a total of 23,701 genes. Chromosomal assembly and syntenic analysis proved that, unlike most Perciformes with the popular haploid chromosome number of 24, LMB has only 23 chromosomes (Chr), among which the Chr1 seems to be resulted from a chromosomal fusion event. LMB is phylogenetically closely related to European seabass and spotted seabass, diverging 64.1 million years ago (mya) from the two seabass species. Eight gene families comprising 294 genes associated with ionic regulation were identified through positive selection, transcriptome and genome comparisons. These genes involved in iron facilitated diffusion (such as claudin, aquaporins, sodium channel protein and so on) and others related to ion active transport (such as sodium/potassium-transporting ATPase and sodium/calcium exchanger). The claudin gene family, which is critical for regulating cell tight junctions and osmotic homeostasis, showed a significant expansion in LMB with 27 family members and 68 copies for salinity adaptation. In summary, we reported the first high-quality LMB genome, and provided insights into the molecular mechanisms of LMB adaptation to fresh and brackish water. The chromosome-level LMB genome will also be a valuable genomic resource for in-depth biological and evolutionary studies, germplasm conservation and genetic breeding of LMB.
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Affiliation(s)
- Chengfei Sun
- Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Jia Li
- Shenzhen Key Laboratory of Marine Genomics, Guangdong Provincial Key Laboratory of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen, China
| | - Junjian Dong
- Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | | | - Jie Hu
- Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | | | - Wuhui Li
- Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Jiang Li
- Biozeron Shenzhen Inc., Shenzhen, China
| | - Yuanyuan Tian
- Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Qiong Shi
- Shenzhen Key Laboratory of Marine Genomics, Guangdong Provincial Key Laboratory of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen, China
| | - Xing Ye
- Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
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42
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Chung WY, Zhu Y, Mahamad Maifiah MH, Shivashekaregowda NKH, Wong EH, Abdul Rahim N. Novel antimicrobial development using genome-scale metabolic model of Gram-negative pathogens: a review. J Antibiot (Tokyo) 2020; 74:95-104. [PMID: 32901119 DOI: 10.1038/s41429-020-00366-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 08/04/2020] [Accepted: 08/08/2020] [Indexed: 12/13/2022]
Abstract
Antimicrobial resistance (AMR) threatens the effective prevention and treatment of a wide range of infections. Governments around the world are beginning to devote effort for innovative treatment development to treat these resistant bacteria. Systems biology methods have been applied extensively to provide valuable insights into metabolic processes at system level. Genome-scale metabolic models serve as platforms for constraint-based computational techniques which aid in novel drug discovery. Tools for automated reconstruction of metabolic models have been developed to support system level metabolic analysis. We discuss features of such software platforms for potential users to best fit their purpose of research. In this work, we focus to review the development of genome-scale metabolic models of Gram-negative pathogens and also metabolic network approach for identification of antimicrobial drugs targets.
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Affiliation(s)
- Wan Yean Chung
- School of Pharmacy, Taylor's University, 47500, Subang Jaya, Selangor, Malaysia
| | - Yan Zhu
- Biomedicine Discovery Institute, Infection and Immunity Program and Department of Microbiology, Monash University, Melbourne, 3800, VIC, Australia
| | - Mohd Hafidz Mahamad Maifiah
- International Institute for Halal Research and Training (INHART), International Islamic University Malaysia (IIUM), 53100, Jalan Gombak, Selangor, Malaysia
| | - Naveen Kumar Hawala Shivashekaregowda
- Center for Drug Discovery and Molecular Pharmacology (CDDMP), Faculty of Health and Medical Sciences, Taylor's University, 47500, Subang Jaya, Selangor, Malaysia
| | - Eng Hwa Wong
- School of Medicine, Taylor's University, 47500, Subang Jaya, Selangor, Malaysia.
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43
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Aberrant expression of a novel circular RNA in pancreatic cancer. J Hum Genet 2020; 66:181-191. [PMID: 32879441 DOI: 10.1038/s10038-020-00826-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 08/01/2020] [Accepted: 08/11/2020] [Indexed: 12/31/2022]
Abstract
Circular RNAs (circRNAs) are single-stranded, covalently closed RNA molecules that are produced from pre-mRNAs through a process known as back-splicing. Although circRNAs are expressed under specific conditions, current understanding of their comprehensive expression status is still limited. Here, we performed a large-scale circRNA profiling analysis in human pancreatic ductal adenocarcinoma (PDAC) tissues, using circular RNA-specific RNA sequencing. We identified more than 40,000 previously unknown circRNAs, some of which were upregulated in PDAC tissues, compared with normal pancreatic tissues. We determined the full-length sequence of a circRNA upregulated in PDAC, which was derived from two noncoding RNA loci on chromosome 12. The novel circRNA, named circPDAC RNA, was not expressed in normal human cells, but was expressed in PDAC and other carcinoma cells. While postulated biological functions, such as peptide production from the circPDAC RNA, were not detected, its aberrant expression was confirmed in other PDAC tissues and in serum from a PDAC patient. These results demonstrate that comprehensive studies are necessary to reveal the expression status of circRNAs and that the circPDAC RNA identified here might serve as a novel biomarker for cancers, including PDAC.
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44
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Cao Y, Li L, Xu M, Feng Z, Sun X, Lu J, Xu Y, Du P, Wang T, Hu R, Ye Z, Shi L, Tang X, Yan L, Gao Z, Chen G, Zhang Y, Chen L, Ning G, Bi Y, Wang W. The ChinaMAP analytics of deep whole genome sequences in 10,588 individuals. Cell Res 2020; 30:717-731. [PMID: 32355288 PMCID: PMC7609296 DOI: 10.1038/s41422-020-0322-9] [Citation(s) in RCA: 129] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 04/09/2020] [Indexed: 12/12/2022] Open
Abstract
Metabolic diseases are the most common and rapidly growing health issues worldwide. The massive population-based human genetics is crucial for the precise prevention and intervention of metabolic disorders. The China Metabolic Analytics Project (ChinaMAP) is based on cohort studies across diverse regions and ethnic groups with metabolic phenotypic data in China. Here, we describe the centralized analysis of the deep whole genome sequencing data and the genetic bases of metabolic traits in 10,588 individuals from the ChinaMAP. The frequency spectrum of variants, population structure, pathogenic variants and novel genomic characteristics were analyzed. The individual genetic evaluations of Mendelian diseases, nutrition and drug metabolism, and traits of blood glucose and BMI were integrated. Our study establishes a large-scale and deep resource for the genetics of East Asians and provides opportunities for novel genetic discoveries of metabolic characteristics and disorders.
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Affiliation(s)
- Yanan Cao
- National Clinical Research Centre for Metabolic Diseases, State Key Laboratory of Medical Genomics, Shanghai Clinical Center for Endocrine and Metabolic Diseases, Shanghai Institute for Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- National Research Center for Translational Medicine, National Key Scientific Infrastructure for Translational Medicine (Shanghai), Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Lin Li
- National Clinical Research Centre for Metabolic Diseases, State Key Laboratory of Medical Genomics, Shanghai Clinical Center for Endocrine and Metabolic Diseases, Shanghai Institute for Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- National Research Center for Translational Medicine, National Key Scientific Infrastructure for Translational Medicine (Shanghai), Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Min Xu
- National Clinical Research Centre for Metabolic Diseases, State Key Laboratory of Medical Genomics, Shanghai Clinical Center for Endocrine and Metabolic Diseases, Shanghai Institute for Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Zhimin Feng
- National Clinical Research Centre for Metabolic Diseases, State Key Laboratory of Medical Genomics, Shanghai Clinical Center for Endocrine and Metabolic Diseases, Shanghai Institute for Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Xiaohui Sun
- National Clinical Research Centre for Metabolic Diseases, State Key Laboratory of Medical Genomics, Shanghai Clinical Center for Endocrine and Metabolic Diseases, Shanghai Institute for Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Jieli Lu
- National Clinical Research Centre for Metabolic Diseases, State Key Laboratory of Medical Genomics, Shanghai Clinical Center for Endocrine and Metabolic Diseases, Shanghai Institute for Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Yu Xu
- National Clinical Research Centre for Metabolic Diseases, State Key Laboratory of Medical Genomics, Shanghai Clinical Center for Endocrine and Metabolic Diseases, Shanghai Institute for Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Peina Du
- National Clinical Research Centre for Metabolic Diseases, State Key Laboratory of Medical Genomics, Shanghai Clinical Center for Endocrine and Metabolic Diseases, Shanghai Institute for Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Tiange Wang
- National Clinical Research Centre for Metabolic Diseases, State Key Laboratory of Medical Genomics, Shanghai Clinical Center for Endocrine and Metabolic Diseases, Shanghai Institute for Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Ruying Hu
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, 310006, Zhejiang, China
| | - Zhen Ye
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, 310006, Zhejiang, China
| | - Lixin Shi
- Affiliated Hospital of Guiyang Medical College, Guiyang, 550004, Guizhou, China
| | - Xulei Tang
- The First Hospital of Lanzhou University, Lanzhou, 730000, Gansu, China
| | - Li Yan
- Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, Guangdong, China
| | - Zhengnan Gao
- Dalian Municipal Central Hospital, Dalian, 116033, Liaoning, China
| | - Gang Chen
- Fujian Provincial Hospital, Fujian Medical University, Fuzhou, 350001, Fujian, China
| | - Yinfei Zhang
- Central Hospital of Shanghai Jiading District, Shanghai, 201800, China
| | - Lulu Chen
- Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, Hubei, China
| | - Guang Ning
- National Clinical Research Centre for Metabolic Diseases, State Key Laboratory of Medical Genomics, Shanghai Clinical Center for Endocrine and Metabolic Diseases, Shanghai Institute for Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Yufang Bi
- National Clinical Research Centre for Metabolic Diseases, State Key Laboratory of Medical Genomics, Shanghai Clinical Center for Endocrine and Metabolic Diseases, Shanghai Institute for Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Weiqing Wang
- National Clinical Research Centre for Metabolic Diseases, State Key Laboratory of Medical Genomics, Shanghai Clinical Center for Endocrine and Metabolic Diseases, Shanghai Institute for Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
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45
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Liu S, Wang Z, Wang H, Su Y, Wang T. Patterns and Rates of Plastid rps12 Gene Evolution Inferred in a Phylogenetic Context using Plastomic Data of Ferns. Sci Rep 2020; 10:9394. [PMID: 32523061 PMCID: PMC7287138 DOI: 10.1038/s41598-020-66219-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 05/14/2020] [Indexed: 12/14/2022] Open
Abstract
The trans-splicing rps12 gene of fern plastomes (plastid genomes) exhibits a unique structure owing to its variations in intragenic exon location and intron content, and thus, it provides an excellent model system for examining the effect of plastid gene structure on rates and patterns of molecular evolution. In this study, 16 complete fern plastome sequences were newly generated via the Illumina HiSeq sequencing platform. We reconstructed the phylogeny of ferns and inferred the patterns and rates of plastid rps12 gene evolution in a phylogenetic context by combining these plastome data with those of previously published fern species. We uncovered the diversity of fern plastome evolution by characterizing the structures of these genomes and obtained a highly supported phylogenetic framework for ferns. Furthermore, our results revealed molecular evolutionary patterns that were completely different from the patterns revealed in previous studies. There were significant differences in the patterns and rates of nucleotide substitutions in both intron-containing and intron-less rps12 alleles. Rate heterogeneity between single-copy (SC) and inverted repeat (IR) exons was evident. Unexpectedly, however, IR exons exhibited significantly higher synonymous substitution rates (dS) than SC exons, a pattern that contrasts the regional effect responsible for decreased rates of nucleotide substitutions in IRs. Our results reveal that structural changes in plastid genes have important effects on evolutionary rates, and we propose possible mechanisms to explain the variations in the nucleotide substitution rates of this unusual gene.
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Affiliation(s)
- Shanshan Liu
- School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Zhen Wang
- School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Hui Wang
- Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, 518004, China
| | - Yingjuan Su
- School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China. .,Research Institute of Sun Yat-sen University in Shenzhen, Shenzhen, 518057, China.
| | - Ting Wang
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China.
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46
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Chen J, Gao T, Chen M, Ou Q. Next-generation sequencing of the mitochondrial genome of Pangasius bocourti (Siluroidei: Pangasiidae). Mitochondrial DNA B Resour 2020. [DOI: 10.1080/23802359.2020.1749148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
Affiliation(s)
| | - Teng Gao
- Qingyuan Agricultural Science and Technology Extension Service Center, Qingyuan, China
| | - Mei Chen
- Foshan University, Foshon, China
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47
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Hu Y, Liu X, Yang J, Xiao K, Wang B, Du H. Development and characterization of a duplex PCR assay in Chinese sturgeon (Acipenser sinensis) for genetic analysis. Sci Rep 2020; 10:3451. [PMID: 32103060 PMCID: PMC7044248 DOI: 10.1038/s41598-020-60401-y] [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: 01/25/2019] [Accepted: 02/06/2020] [Indexed: 11/09/2022] Open
Abstract
Chinese sturgeon (Acipenser sinensis) has been listed as a critically endangered species on the IUCN Red List and is an endemic fish of China. Five sets of duplex polymerase chain reactions (PCR) assays were developed with 10 tetranucleotide microsatellites for Chinese sturgeon. The size of CS57, ZHX43, ZHX69, AS105, ZHX51, AS074, ZHX2, AS078, AS026 and AS073 products in 184 Chinese sturgeon individuals ranged from 257-305, 191-241, 251-285, 172-244, 236-260, 169-209, 194-234, 92-176, 165-257 and 120-164, respectively. The observed allele number of the 10 microsatellites ranged from 7 to 16, and the total number of alleles was 106. The number of alleles per individual in CS57, ZHX43, AS105, AS074, AS078 and AS026 was 1-4. The number of alleles per individual in ZHX69, ZHX51, ZHX2 and AS073 was 2-4. The mean number of alleles per locus per individual ranged from 2.01-3.76. The expected heterozygosity (HE), observed heterozygosity (HO), polymorphic information content (PIC) and Shannon-Weiner diversity index (H') ranged from 0.582 to 0.899, from 0.676 to 1, from 0.518 to 0.886 and from 1.034 to 2.34, respectively. Despite many advantages, the use of microsatellites as genetic analysis tools can be limited by the cost of the associated experiment. To solve this problem, this set of five duplex PCRs will provide tools that are more helpful, less expensive and less time consuming than others used for genetic analyses in Chinese sturgeon.
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Affiliation(s)
- Yacheng Hu
- Chinese Sturgeon Research Institute, China Three Gorges Corporation, Yichang Hubei, 443100, China.,Hubei Key Laboratory of Three Gorges Project for Conservation of Fishes, Yichang Hubei, 443100, China
| | - Xueqing Liu
- Chinese Sturgeon Research Institute, China Three Gorges Corporation, Yichang Hubei, 443100, China.,Hubei Key Laboratory of Three Gorges Project for Conservation of Fishes, Yichang Hubei, 443100, China
| | - Jing Yang
- Chinese Sturgeon Research Institute, China Three Gorges Corporation, Yichang Hubei, 443100, China.,Hubei Key Laboratory of Three Gorges Project for Conservation of Fishes, Yichang Hubei, 443100, China
| | - Kan Xiao
- Chinese Sturgeon Research Institute, China Three Gorges Corporation, Yichang Hubei, 443100, China.,Hubei Key Laboratory of Three Gorges Project for Conservation of Fishes, Yichang Hubei, 443100, China
| | - Binzhong Wang
- Chinese Sturgeon Research Institute, China Three Gorges Corporation, Yichang Hubei, 443100, China.,Hubei Key Laboratory of Three Gorges Project for Conservation of Fishes, Yichang Hubei, 443100, China
| | - Hejun Du
- Chinese Sturgeon Research Institute, China Three Gorges Corporation, Yichang Hubei, 443100, China. .,Hubei Key Laboratory of Three Gorges Project for Conservation of Fishes, Yichang Hubei, 443100, China.
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48
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Natsidis P, Tsakogiannis A, Pavlidis P, Tsigenopoulos CS, Manousaki T. Phylogenomics investigation of sparids (Teleostei: Spariformes) using high-quality proteomes highlights the importance of taxon sampling. Commun Biol 2019; 2:400. [PMID: 31701028 PMCID: PMC6825128 DOI: 10.1038/s42003-019-0654-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 10/08/2019] [Indexed: 12/29/2022] Open
Abstract
Sparidae (Teleostei: Spariformes) are a family of fish constituted by approximately 150 species with high popularity and commercial value, such as porgies and seabreams. Although the phylogeny of this family has been investigated multiple times, its position among other teleost groups remains ambiguous. Most studies have used a single or few genes to decipher the phylogenetic relationships of sparids. Here, we conducted a thorough phylogenomic analysis using five recently available Sparidae gene-sets and 26 high-quality, genome-predicted teleost proteomes. Our analysis suggested that Tetraodontiformes (puffer fish, sunfish) are the closest relatives to sparids than all other groups used. By analytically comparing this result to our own previous contradicting finding, we show that this discordance is not due to different orthology assignment algorithms; on the contrary, we prove that it is caused by the increased taxon sampling of the present study, outlining the great importance of this aspect in phylogenomic analyses in general.
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Affiliation(s)
- Paschalis Natsidis
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Heraklion, Greece
- School of Medicine, University of Crete, Heraklion, Greece
| | - Alexandros Tsakogiannis
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Heraklion, Greece
| | - Pavlos Pavlidis
- Institute of Computer Science, Foundation for Research and Technology, Heraklion, Greece
| | - Costas S. Tsigenopoulos
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Heraklion, Greece
| | - Tereza Manousaki
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Heraklion, Greece
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49
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Zhang X, Zhang Z, Yu Z, Li J, Chen S, Sun R, Jia C, Zhu F, Meng Q, Xu S. Molecular cloning and expression pattern of IGFBP-2a in black porgy (Acanthopagrus schlegelii) and evolutionary analysis of IGFBP-2s in the species of Perciformes. FISH PHYSIOLOGY AND BIOCHEMISTRY 2019; 45:1731-1745. [PMID: 31418102 DOI: 10.1007/s10695-019-00665-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 05/24/2019] [Indexed: 06/10/2023]
Abstract
Insulin-like growth factor-binding protein-2 (IGFBP-2) plays a key role in regulating growth and development by its affinity with insulin-like growth factors (IGFs). In this study, we cloned the coding sequence (CDS) of IGFBP-2a from the black porgy (Acanthopagrus schlegelii) muscle and identified that the full-length CDS of IGFBP-2a was 882 bp. Real-time quantitative PCR revealed that IGFBP-2a was most abundant in the liver of the black porgy and backcross breed (F1♀×black porgy♂) but remained lower in each tested tissue in self-cross breed (F1♀×F1♂). In addition, the IGFBP-2a expression in the liver of three breeds showed a negative correlation with their growth rates, indicating that the IGFBP-2a played a growth-inhibiting role in the three breeds. We further identified 810 bp IGFBP-2b gene from the draft genome of black porgy. Finally, we examined the IGFBP-2a and IGFBP-2b genes by scanning the genomes of the species of Perciformes and found the IGFBP-2 gene duplication took place earlier than the divergence of perciform species. Interestingly, six positively selected sites were detected in both Perciformes IGFBP-2 genes, although both genes were identified to be under purifying selection. Specially, these positively selected sites were located in the functional domains, suggesting these sites played key roles in the growth of Perciformes. Our study partially explains the molecular basis for the prepotency in black porgy hybrids, which will provide guidance for their cultivation in the future.
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Affiliation(s)
- Xinyi Zhang
- Marine Fisheries Research Institute of Jiangsu Province, Nantong, 226007, China
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Zhiyong Zhang
- Marine Fisheries Research Institute of Jiangsu Province, Nantong, 226007, China
| | - Zhenpeng Yu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Jiayi Li
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Shuyin Chen
- Marine Fisheries Research Institute of Jiangsu Province, Nantong, 226007, China.
| | - Ruijian Sun
- Marine Fisheries Research Institute of Jiangsu Province, Nantong, 226007, China
| | - Chaofeng Jia
- Marine Fisheries Research Institute of Jiangsu Province, Nantong, 226007, China
| | - Fei Zhu
- Marine Fisheries Research Institute of Jiangsu Province, Nantong, 226007, China
| | - Qian Meng
- Marine Fisheries Research Institute of Jiangsu Province, Nantong, 226007, China
| | - Shixia Xu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China.
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50
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Bian C, Li J, Lin X, Chen X, Yi Y, You X, Zhang Y, Lv Y, Shi Q. Whole Genome Sequencing of the Blue Tilapia ( Oreochromis aureus) Provides a Valuable Genetic Resource for Biomedical Research on Tilapias. Mar Drugs 2019; 17:E386. [PMID: 31261751 PMCID: PMC6669741 DOI: 10.3390/md17070386] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 06/21/2019] [Accepted: 06/26/2019] [Indexed: 12/16/2022] Open
Abstract
Blue tilapia (Oreochromis aureus) has been an economically important fish in Asian countries. It can grow and reproduce in both freshwater and brackish water conditions, whereas it is also considered as a significant invasive species around the world. This species has been widely used as the hybridization parent(s) for tilapia breeding with a major aim to produce novel strains. However, available genomic resources are still limited for this important tilapia species. Here, we for the first time sequenced and assembled a draft genome for a seawater cultured blue tilapia (0.92 Gb), with 97.8% completeness and a scaffold N50 of 1.1 Mb, which suggests a relatively high quality of this genome assembly. We also predicted 23,117 protein-coding genes in the blue tilapia genome. Comparisons of predicted antimicrobial peptides between the blue tilapia and its close relative Nile tilapia proved that these immunological genes are highly similar with a genome-wide scattering distribution. As a valuable genetic resource, our blue tilapia genome assembly will benefit for biomedical researches and practical molecular breeding for high resistance to various diseases, which have been a critical problem in the aquaculture of tilapias.
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Affiliation(s)
- Chao Bian
- Center of Reproduction, Development and Aging, Faculty of Health Sciences, University of Macau, Taipa, Macau 999078, China
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China
| | - Jia Li
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China
| | - Xueqiang Lin
- BGI Marine-Hainan, BGI Marine, BGI, Wenchang 571327, China
| | - Xiyang Chen
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China
| | - Yunhai Yi
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China
| | - Xinxin You
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China
| | - Yiping Zhang
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China
| | - Yunyun Lv
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China
| | - Qiong Shi
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China.
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China.
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