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| Improved pea reference genome and pan-genome highlight genomic features and evolutionary characteristics | |
Yang, Tao; Liu, Rong; Luo, Yingfeng1; Hu, Songnian1,13; Wang, Dong1; Wang, Chenyu; Pandey, Manish K.; Ge, Song4,13 ; Xu, Quanle5; Li, Nana2,12; Li, Guan; Huang, Yuning; Saxena, Rachit K.; Ji, Yishan; Li, Mengwei; Yan, Xin; He, Yuhua6; Liu, Yujiao7,8; Wang, Xuejun9; Xiang, Chao10; Varshney, Rajeev K.; Ding, Hanfeng2,12; Gao, Shenghan1; Zong, Xuxiao
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| 2022 | |
| 发表期刊 | NATURE GENETICS
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| ISSN | 1061-4036 |
| 卷号 | 54期号:10页码:1553+ |
| 摘要 | Complete and accurate reference genomes and annotations provide fundamental resources for functional genomics and crop breeding. Here we report a de novo assembly and annotation of a pea cultivar ZW6 with contig N50 of 8.98 Mb, which features a 243-fold increase in contig length and evident improvements in the continuity and quality of sequence in complex repeat regions compared with the existing one. Genome diversity of 118 cultivated and wild pea demonstrated that Pisum abyssinicum is a separate species different from P. fulvum and P. sativum within Pisum. Quantitative trait locus analyses uncovered two known Mendel's genes related to stem length (Le/le) and seed shape (R/r) as well as some candidate genes for pod form studied by Mendel. A pan-genome of 116 pea accessions was constructed, and pan-genes preferred in P. abyssinicum and P. fulvum showed distinct functional enrichment, indicating the potential value of them as pea breeding resources in the future. A high-quality genome assembly of pea cultivar ZW6 and pan-genome analyses provide insights into pea genome evolution and domestication as well as genomic resources for pea improvement. |
| 学科领域 | Genetics & Heredity |
| DOI | 10.1038/s41588-022-01172-2 |
| 收录类别 | SCI |
| 语种 | 英语 |
| WOS关键词 | STRUCTURAL VARIANTS ; DOMESTICATION ; ALIGNMENT ; GENETICS ; PREDICTION ; DISCOVERY ; ACCURATE ; PROVIDES ; PLANT ; WILD |
| WOS研究方向 | Science Citation Index Expanded (SCI-EXPANDED) |
| WOS记录号 | WOS:000856613600004 |
| 出版者 | NATURE PORTFOLIO |
| 文献子类 | Article |
| 出版地 | BERLIN |
| EISSN | 1546-1718 |
| 资助机构 | National Key R&D Program of China [2018YFD1000701/2018YFD1000700] ; Youth Innovation Promotion Association of Chinese Academy of Science [2017140] ; Agricultural Variety Improvement Project of Shandong Province [2019LZGC017] ; China Agriculture Research System of MOF and MARA-Food Legumes [CARS08] ; National Natural Science Foundation of China [31801428] ; Subject Team of Science and Technology Innovation Project of Shandong Academy of Agricultural Sciences [CXGC2018E15] ; Crop Germplasm Resources Protection [2130135] ; Industry Team of Science and Technology Innovation Project of Shandong Academy of Agricultural Sciences [CXGC2016A02] ; Coarse Cereals Innovation Team of Modern Agricultural Industry Technology System of Shandong Province [SDAIT-15-01] ; Agricultural Science and Technology Innovation Program (ASTIP) in CAAS ; Youth Research Fund of Shandong Academy of Agricultural Sciences [2016YQN19] ; Food Futures Institute of the Murdoch University, Australia |
| 作者邮箱 | rajeev.varshney@murdoch.edu.au ; dinghf2019@sina.com ; gaoshh@im.ac.cn ; zongxuxiao@caas.cn |
| 作品OA属性 | Green Published, hybrid |
| 引用统计 | |
| 文献类型 | 期刊论文 |
| 条目标识符 | http://ir.ibcas.ac.cn/handle/2S10CLM1/28716 |
| 专题 | 系统与进化植物学国家重点实验室 |
| 作者单位 | 1.Chinese Acad Agr Sci, Natl Key Facil Crop Gene Resources & Genet Improv, Inst Crop Sci, Beijing, Peoples R China 2.Chinese Acad Sci, Inst Microbiol, State Key Lab Microbial Resources, Beijing, Peoples R China 3.Shandong Acad Agr Sci, Shandong Prov Key Lab Crop Genet Improvement Ecol, Inst Crop Germplasm Resources, Jinan, Peoples R China 4.Pandey, Manish K.; Saxena, Rachit K.; Varshney, Rajeev K.] Int Crops Res Inst Semi Arid Trop, Ctr Excellence Genom & Syst Biol, Hyderabad, India 5.Chinese Acad Sci, Inst Bot, State Key Lab Systemat & Evolutionary Bot, Beijing, Peoples R China 6.Northwest A&F Univ, Coll Life Sci, Yangling, Shaanxi, Peoples R China 7.Yunnan Acad Agr Sci, Inst Grain Crops, Kunming, Yunnan, Peoples R China 8.Qinghai Univ, State Key Lab Plateau Ecol & Agr, Xining, Peoples R China 9.Qinghai Acad Agr & Forestry Sci, Xining, Peoples R China 10.Jiangsu Yanjiang Inst Agr Sci, Nantong, Peoples R China 11.Sichuan Acad Agr Sci, Crop Res Inst, Chengdu, Peoples R China 12.Varshney, Rajeev K.] Murdoch Univ, Murdochs Ctr Crop & Food Innovat, WA State Agr Biotechnol Ctr, Food Futures Inst, Murdoch, WA, Australia 13.Shandong Normal Univ, Coll Life Sci, Jinan, Peoples R China 14.Univ Chinese Acad Sci, Beijing, Peoples R China |
| 推荐引用方式 GB/T 7714 | Yang, Tao,Liu, Rong,Luo, Yingfeng,et al. Improved pea reference genome and pan-genome highlight genomic features and evolutionary characteristics[J]. NATURE GENETICS,2022,54(10):1553+. |
| APA | Yang, Tao.,Liu, Rong.,Luo, Yingfeng.,Hu, Songnian.,Wang, Dong.,...&Zong, Xuxiao.(2022).Improved pea reference genome and pan-genome highlight genomic features and evolutionary characteristics.NATURE GENETICS,54(10),1553+. |
| MLA | Yang, Tao,et al."Improved pea reference genome and pan-genome highlight genomic features and evolutionary characteristics".NATURE GENETICS 54.10(2022):1553+. |
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| Yang-2022-Improved p（5518KB） | 期刊论文 | 出版稿 | 开放获取 | CC BY-NC-SA | 浏览 请求全文 | |
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