Technology-enabled great leap in deciphering plant genomes – Nature.com
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Nature Plants (2024)
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Plant genomes provide essential and vital basic resources for studying many aspects of plant biology and applications (for example, breeding). From 2000 to 2020, 1,144 genomes of 782 plant species were sequenced. In the past three years (2021–2023), 2,373 genomes of 1,031 plant species, including 793 newly sequenced species, have been assembled, representing a great leap. The 2,373 newly assembled genomes, of which 63 are telomere-to-telomere assemblies and 921 have been generated in pan-genome projects, cover the major phylogenetic clades. Substantial advances in read length, throughput, accuracy and cost-effectiveness have notably simplified the achievement of high-quality assemblies. Moreover, the development of multiple software tools using different algorithms offers the opportunity to generate more complete and complex assemblies. A database named N3: plants, genomes, technologies has been developed to accommodate the metadata associated with the 3,517 genomes that have been sequenced from 1,575 plant species since 2000. We also provide an outlook for emerging opportunities in plant genome sequencing.
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Philipp E. Bayer, Agnieszka A. Golicz, … David Edwards
Rose A. Marks, Scott Hotaling, … Robert VanBuren
Hyunjin Koo, Gir-Won Lee, … Ah-Young Shin
All metadata associated with this study, including the accession numbers of all genome assemblies, the quality statistics of the assemblies and the technologies (sequencing platforms and assembly tools) used in generating the published plant genomes, are available in the N3 database (http://ibi.zju.edu.cn/N3database/index.php). Source data are provided with this paper.
The primary code used in this study is provided at https://github.com/Darlene1997/Statistic-of-sequenced-plant-genome-assemlies.
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This study was supported by the Department of Science and Technology of Zhejiang and Hainan Province (ZDYF2022XDNY271 and 2022C02032).
These authors contributed equally: Lingjuan Xie, Xiaojiao Gong.
Institute of Crop Sciences & Institute of Bioinformatics, Zhejiang University, Hangzhou, China
Lingjuan Xie, Xiaojiao Gong, Kun Yang, Yujie Huang, Shiyu Zhang, Yanqing Sun, Dongya Wu, Chuyu Ye & Longjiang Fan
Hainan Institute of Zhejiang University, Yazhou Bay, Shanya, China
Lingjuan Xie, Leti Shen & Longjiang Fan
CSIRO Agriculture and Food, Black Mountain Laboratories, Canberra, Australia
Qian-Hao Zhu
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L.F. conceived of the study and designed the project. X.G., L.X., K.Y., Y.H., S.Z. and L.S. collected and analysed data. L.X. and K.Y. constructed the database. L.X. and X.G. wrote the manuscript. L.F., D.W., Y.S. and C.Y. discussed the results. L.F. and Q.-H.Z. revised and approved the manuscript.
Correspondence to Longjiang Fan.
The authors declare no competing interests.
Nature Plants thanks the anonymous reviewers for their contribution(s) to the peer review of this work.
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Xie, L., Gong, X., Yang, K. et al. Technology-enabled great leap in deciphering plant genomes. Nat. Plants (2024). https://doi.org/10.1038/s41477-024-01655-6
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Plant genomes provide essential and vital basic resources for studying many aspects of plant biology and applications (for example, breeding). From 2000 to 2020, 1,144 genomes of 782 plant species were sequenced. In the past three years (2021–2023), 2,373 genomes of 1,031 plant species, including 793 newly sequenced species, have been assembled, representing a great leap. The 2,373 newly assembled genomes, of which 63 are telomere-to-telomere assemblies and 921 have been generated in pan-genome projects, cover the major phylogenetic clades. Substantial advances in read length, throughput, accuracy and cost-effectiveness have notably simplified the achievement of high-quality assemblies. Moreover, the development of multiple software tools using different algorithms offers the opportunity to generate more complete and complex assemblies. A database named N3: plants, genomes, technologies has been developed to accommodate the metadata associated with the 3,517 genomes that have been sequenced from 1,575 plant species since 2000. We also provide an outlook for emerging opportunities in plant genome sequencing.
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Philipp E. Bayer, Agnieszka A. Golicz, … David Edwards
Rose A. Marks, Scott Hotaling, … Robert VanBuren
Hyunjin Koo, Gir-Won Lee, … Ah-Young Shin
All metadata associated with this study, including the accession numbers of all genome assemblies, the quality statistics of the assemblies and the technologies (sequencing platforms and assembly tools) used in generating the published plant genomes, are available in the N3 database (http://ibi.zju.edu.cn/N3database/index.php). Source data are provided with this paper.
The primary code used in this study is provided at https://github.com/Darlene1997/Statistic-of-sequenced-plant-genome-assemlies.
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This study was supported by the Department of Science and Technology of Zhejiang and Hainan Province (ZDYF2022XDNY271 and 2022C02032).
These authors contributed equally: Lingjuan Xie, Xiaojiao Gong.
Institute of Crop Sciences & Institute of Bioinformatics, Zhejiang University, Hangzhou, China
Lingjuan Xie, Xiaojiao Gong, Kun Yang, Yujie Huang, Shiyu Zhang, Yanqing Sun, Dongya Wu, Chuyu Ye & Longjiang Fan
Hainan Institute of Zhejiang University, Yazhou Bay, Shanya, China
Lingjuan Xie, Leti Shen & Longjiang Fan
CSIRO Agriculture and Food, Black Mountain Laboratories, Canberra, Australia
Qian-Hao Zhu
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L.F. conceived of the study and designed the project. X.G., L.X., K.Y., Y.H., S.Z. and L.S. collected and analysed data. L.X. and K.Y. constructed the database. L.X. and X.G. wrote the manuscript. L.F., D.W., Y.S. and C.Y. discussed the results. L.F. and Q.-H.Z. revised and approved the manuscript.
Correspondence to Longjiang Fan.
The authors declare no competing interests.
Nature Plants thanks the anonymous reviewers for their contribution(s) to the peer review of this work.
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Xie, L., Gong, X., Yang, K. et al. Technology-enabled great leap in deciphering plant genomes. Nat. Plants (2024). https://doi.org/10.1038/s41477-024-01655-6
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