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Rong J, Zheng Y, Zhang Z, Zhang J, Gu Y, Hua T, Zhao M, Fan L, Deng Z, Pan Y, Li B, Chen L, He T, Chen L, Ye J, Zhang H, Gu L. De novo Whole-Genome Assembly of the 10-Gigabase Fokienia Hodginsii Genome to Reveal Differential Epigenetic Events Between Callus and Xylem. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2402644. [PMID: 39229940 DOI: 10.1002/advs.202402644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 07/29/2024] [Indexed: 09/05/2024]
Abstract
Fokienia hodginsii (F. hodginsii), belonging to the genus Fokienia of the Cupressaceae. F. hodginsii has significant application value due to its wood properties and great research value in evolutionary studies as a gymnosperm. However, the genome of F. hodginsii remains unknown due to the large size of gymnosperms genome. Pacific Bioscience sequencing, Hi-C mapping, whole-genome Bisulfite Sequencing (BS-Seq), long-read isoform sequencing (Iso-Seq), direct RNA sequencing (DRS), quantitative proteomics, and metabonomics analysis are employed to facilitate genome assembly, gene annotation, and investigation into epigenetic mechanisms. In this study, the 10G F. hodginsii genome is assembled into 11 chromosomes. Furthermore, 50 521 protein-coding genes are annotated and determined that 65% of F. hodginsii genome comprises repetitive sequences. It is discovered that transposable element (TE)-including introns is associated with higher expression. The DNA methylome of F. hodginsii reveals that xylem has a higher DNA methylation level compared to callus. Moreover, DRS reveals the significant alterations in RNA full-length ratio, which potentially associated with poly(A) length (PAL) and alternative polyadenylation (APA). Finally, the morphology measurement and metabonomics analysis revealed the difference of 14 cultivars. In summary, the genomes and epigenetics datasets provide a molecular basis for callus formation in the gymnosperm family.
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Affiliation(s)
- Jundong Rong
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yushan Zheng
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Zeyu Zhang
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, School of Future Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Jun Zhang
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, School of Future Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yuying Gu
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, School of Future Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Tian Hua
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, School of Future Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Mengna Zhao
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, School of Future Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Lili Fan
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Zhiwen Deng
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yanmei Pan
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Bingjun Li
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Liguang Chen
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Tianyou He
- College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Lingyan Chen
- College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Jing Ye
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Hangxiao Zhang
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, School of Future Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Lianfeng Gu
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, School of Future Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
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Chen J, Peng L, Zhou C, Li L, Ge Q, Shi C, Guo W, Guo T, Jiang L, Zhang Z, Fan G, Zhang W, Kristiansen K, Jia Y. Datasets of fungal diversity and pseudo-chromosomal genomes of mangrove rhizosphere soil in China. Sci Data 2024; 11:901. [PMID: 39164251 PMCID: PMC11336097 DOI: 10.1038/s41597-024-03748-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Accepted: 08/06/2024] [Indexed: 08/22/2024] Open
Abstract
With climate change and anthropic influence on the coastal ecosystems, mangrove ecosystems are disappearing at an alarming rate. Accordingly, it becomes important to track, study, record and store the mangrove microbial community considering their ecological importance and potential for biotechnological applications. Here, we provide information on mangrove fungal community composition and diversity in mangrove ecosystems with different plant species and from various locations differing in relation to anthropic influences. We describe twelve newly assembled genomes, including four chromosomal-level genomes of fungal isolates from the mangrove ecosystems coupled with functional annotations. We envisage that these data will be of value for future studies including comparative genome analysis and large-scale temporal and/or spatial research to elucidate the potential mechanisms by which mangrove fungal communities assemble and evolve. We further anticipate that the genomes represent valuable resources for bioprospecting related to industrial or clinical uses.
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Affiliation(s)
- Jianwei Chen
- BGI Research, Qingdao, 266555, China
- Qingdao Key Laboratory of Marine Genomics, and Qingdao-Europe Advanced Institute for Life Sciences, BGI Research, Qingdao, 266555, China
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Universitetsparken 13, 2100, Copenhagen, Denmark
| | - Ling Peng
- BGI Research, Qingdao, 266555, China
| | - Changhao Zhou
- BGI Research, Qingdao, 266555, China
- Qingdao Key Laboratory of Marine Genomics, and Qingdao-Europe Advanced Institute for Life Sciences, BGI Research, Qingdao, 266555, China
| | | | - Qijin Ge
- BGI Research, Qingdao, 266555, China
| | | | | | | | - Ling Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing, 211816, China
| | - Zhidong Zhang
- Xinjiang Key Laboratory of Special Environmental Microbiology, Institute of Applied Microbiology, Xinjiang Academy of Agricultural Sciences, Urumqi, 830091, China
| | - Guangyi Fan
- BGI Research, Qingdao, 266555, China
- Qingdao Key Laboratory of Marine Genomics, and Qingdao-Europe Advanced Institute for Life Sciences, BGI Research, Qingdao, 266555, China
- BGI Research, Shenzhen, 518083, China
| | | | - Karsten Kristiansen
- Qingdao Key Laboratory of Marine Genomics, and Qingdao-Europe Advanced Institute for Life Sciences, BGI Research, Qingdao, 266555, China.
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Universitetsparken 13, 2100, Copenhagen, Denmark.
- BGI Research, Shenzhen, 518083, China.
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Xia W, Wang S, Liu X, Chen Y, Lin C, Liu R, Liu H, Li J, Zhu J. Chromosome-level genome provides new insight into the overwintering process of Korla pear (Pyrus sinkiangensis Yu). BMC PLANT BIOLOGY 2024; 24:773. [PMID: 39138412 PMCID: PMC11323677 DOI: 10.1186/s12870-024-05490-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Accepted: 08/06/2024] [Indexed: 08/15/2024]
Abstract
Korla pear has a unique taste and aroma and is a breeding parent of numerous pear varieties. It is susceptible to Valsa mali var. pyri, which invades bark wounded by freezing injury. Its genetic relationships have not been fully defined and could offer insight into the mechanism for freezing tolerance and disease resistance. We generated a high-quality, chromosome-level genome assembly for Korla pear via the Illumina and PacBio circular consensus sequencing (CCS) platforms and high-throughput chromosome conformation capture (Hi-C). The Korla pear genome is ~ 496.63 Mb, and 99.18% of it is assembled to 17 chromosomes. Collinearity and phylogenetic analyses indicated that Korla might be derived from Pyrus pyrifolia and that it diverged ~ 3.9-4.6 Mya. During domestication, seven late embryogenesis abundant (LEA), two dehydrin (DHN), and 54 disease resistance genes were lost from Korla pear compared with P. betulifolia. Moreover, 21 LEA and 31 disease resistance genes were common to the Korla pear and P. betulifolia genomes but were upregulated under overwintering only in P. betulifolia because key cis elements were missing in Korla pear. Gene deletion and downregulation during domestication reduced freezing tolerance and disease resistance in Korla pear. These results could facilitate the breeding of novel pear varieties with high biotic and abiotic stress resistance.
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Affiliation(s)
- Wenwen Xia
- Key Laboratory of Agricultural Biotechnology, College of Life Science, Shihezi University, Shihezi, 832000, China
| | - Saisai Wang
- Key Laboratory of Agricultural Biotechnology, College of Life Science, Shihezi University, Shihezi, 832000, China
| | - Xiaoyan Liu
- Key Laboratory of Agricultural Biotechnology, College of Life Science, Shihezi University, Shihezi, 832000, China
| | - Yifei Chen
- Key Laboratory of Agricultural Biotechnology, College of Life Science, Shihezi University, Shihezi, 832000, China
| | - Caixia Lin
- Xinjiang Production and Construction Crops, Institute of Agricultural Sciences, Tiemenguan, 841007, China
| | - Ruina Liu
- Key Laboratory of Agricultural Biotechnology, College of Life Science, Shihezi University, Shihezi, 832000, China
| | - Hailiang Liu
- Key Laboratory of Agricultural Biotechnology, College of Life Science, Shihezi University, Shihezi, 832000, China
- Institute for Regenerative Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, 200123, China
| | - Jin Li
- Key Laboratory of Agricultural Biotechnology, College of Life Science, Shihezi University, Shihezi, 832000, China.
| | - Jianbo Zhu
- Key Laboratory of Agricultural Biotechnology, College of Life Science, Shihezi University, Shihezi, 832000, China.
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Wu F, Mai Y, Chen C, Xia R. SynGAP: a synteny-based toolkit for gene structure annotation polishing. Genome Biol 2024; 25:218. [PMID: 39138517 PMCID: PMC11323386 DOI: 10.1186/s13059-024-03359-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Accepted: 07/29/2024] [Indexed: 08/15/2024] Open
Abstract
Genome sequencing has become a routine task for biologists, but the challenge of gene structure annotation persists, impeding accurate genomic and genetic research. Here, we present a bioinformatics toolkit, SynGAP (Synteny-based Gene structure Annotation Polisher), which uses gene synteny information to accomplish precise and automated polishing of gene structure annotation of genomes. SynGAP offers exceptional capabilities in the improvement of gene structure annotation quality and the profiling of integrative gene synteny between species. Furthermore, an expression variation index is designed for comparative transcriptomics analysis to explore candidate genes responsible for the development of distinct traits observed in phylogenetically related species.
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Affiliation(s)
- Fengqi Wu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Horticulture, South China Agricultural University, Guangzhou, 510640, Guangdong, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510640, Guangdong, China
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, 510640, Guangdong, China
| | - Yingxiao Mai
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Horticulture, South China Agricultural University, Guangzhou, 510640, Guangdong, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510640, Guangdong, China
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, 510640, Guangdong, China
| | - Chengjie Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Horticulture, South China Agricultural University, Guangzhou, 510640, Guangdong, China.
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510640, Guangdong, China.
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, 510640, Guangdong, China.
| | - Rui Xia
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Horticulture, South China Agricultural University, Guangzhou, 510640, Guangdong, China.
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510640, Guangdong, China.
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, 510640, Guangdong, China.
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Chen BZ, Yang ZJ, Wang WB, Hao TT, Yu PB, Dong Y, Yu WB. Chromosome-level genome assembly and annotation of Flueggea virosa (Phyllanthaceae). Sci Data 2024; 11:875. [PMID: 39138223 PMCID: PMC11322648 DOI: 10.1038/s41597-024-03681-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2024] [Accepted: 07/25/2024] [Indexed: 08/15/2024] Open
Abstract
Flueggea virosa (Roxb. ex Willd.) Royle, an evergreen shrub and small tree in the Phyllanthaceae family, holds significant potential in garden landscaping and pharmacological applications. However, the lack of genomic data has hindered further scientific understanding of its horticultural and medicinal values. In this study, we have assembled a haplotype-resolved genome of F. virosa for the first time. The two haploid genomes, named haplotype A genome and haplotype B genome, are 487.33 Mb and 477.53 Mb in size, respectively, with contig N50 lengths of 31.45 Mb and 32.81 Mb. More than 99% of the assembled sequences were anchored to 13 pairs of pseudo-chromosomes. Furthermore, 21,587 and 21,533 protein-coding genes were predicted in haplotype A and haplotype B genomes, respectively. The availability of this chromosome-level genome fills the gap in genomic data for F. virosa and provides valuable resources for molecular studies of this species, supporting future research on speciation, functional genomics, and comparative genomics within the Phyllanthaceae family.
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Affiliation(s)
- Bao-Zheng Chen
- College of Food Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
- Yunnan Provincial Key Laboratory of Biological Big Data, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
| | - Zi-Jiang Yang
- Bioinformatics group, Wageningen University and Research, Wageningen, Netherlands
| | - Wei-Bin Wang
- Yunnan Provincial Key Laboratory of Biological Big Data, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
| | - Ting-Ting Hao
- Yunnan Provincial Key Laboratory of Biological Big Data, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
| | - Peng-Ban Yu
- Center for Integrative Conservation and Yunnan Key Laboratory for the Conservation of Tropical Rainforests and Asian Elephants, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan, 666303, China
| | - Yang Dong
- Yunnan Provincial Key Laboratory of Biological Big Data, Yunnan Agricultural University, Kunming, Yunnan, 650201, China.
| | - Wen-Bin Yu
- Center for Integrative Conservation and Yunnan Key Laboratory for the Conservation of Tropical Rainforests and Asian Elephants, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan, 666303, China.
- Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Mengla, Yunnan, 666303, China.
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Li M, Pu J, Jia C, Luo D, Zhou Q, Fang X, Nie B, Liu W, Nan Z, Searle IR, Fang L, Liu Z. The genome of Vicia sativa ssp. amphicarpa provides insights into the role of terpenoids in antimicrobial resistance within subterranean fruits. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024. [PMID: 39039964 DOI: 10.1111/tpj.16939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Revised: 07/03/2024] [Accepted: 07/10/2024] [Indexed: 07/24/2024]
Abstract
Vicia sativa ssp. amphicarpa is a unique forage crop capable of simultaneously producing fruits above and below ground, representing a typical amphicarpic plant. In this study, we sequenced and assembled seven pseudo-chromosomes of the genome of V. sativa ssp. amphicarpa (n = 7) yielding a genome size of 1.59 Gb, with a total annotation of 48 932 protein-coding genes. Long terminal repeat (LTR) elements constituted 62.28% of the genome, significantly contributing to the expansion of genome size. Phylogenetic analysis revealed that the divergence between V. sativa ssp. amphicarpa and V. sativa was around 0.88 million years ago (MYA). Comparative transcriptomic and metabolomic analysis of aerial and subterranean pod shells showed biosynthesis of terpenoids in the subterranean pod shells indicating a correlation between the antimicrobial activity of subterranean pod shells and the biosynthesis of terpenoids. Furthermore, functional validation indicates that overexpression of VsTPS5 and VsTPS16 enhances terpenoid biosynthesis for antibacterial activity. Metabolomic analysis suggests the involvement of terpenoids in the antimicrobial properties of subterranean pod shells. Deciphering the genome of V. sativa ssp. amphicarpa elucidated the molecular mechanisms behind the antimicrobial properties of subterranean fruits in amphicarpic plants, providing valuable insights for the study of amphicarpic plant biology.
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Affiliation(s)
- Mingyu Li
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China
| | - Jun Pu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China
| | - Chenglin Jia
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China
| | - Dong Luo
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China
| | - Qiang Zhou
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China
| | - Xiangling Fang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China
| | - Bin Nie
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China
| | - Wenxian Liu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China
| | - Zhibiao Nan
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China
| | - Iain Robert Searle
- School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, 5005, Australia
| | - Longfa Fang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China
| | - Zhipeng Liu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China
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