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Technology-enabled great leap in deciphering plant genomes

Nature Plants volume 10, pages 551–566 (2024)Cite this article

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Abstract

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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Fig. 1: Overview of published plant genomes.
Fig. 2: Phylogeny of sequenced plant genomes and associated quality metrics for each taxonomic order.
Fig. 3: Utilization of sequencing platforms and the predominant software employed in assembling plant genomes over time.
Fig. 4: An overview of the N3 database.

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Data availability

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.

Code availability

The primary code used in this study is provided at https://github.com/Darlene1997/Statistic-of-sequenced-plant-genome-assemlies.

References

  1. Zhang, T. et al. Complex genome assembly based on long-read sequencing. Brief. Bioinform. 23, bbac305 (2022).

    Article  PubMed  Google Scholar 

  2. Edwards, D., Batley, J. & Snowdon, R. J. Accessing complex crop genomes with next-generation sequencing. Theor. Appl. Genet. 126, 1–11 (2013).

    Article  CAS  PubMed  Google Scholar 

  3. Marks, R. A., Hotaling, S., Frandsen, P. B. & VanBuren, R. Representation and participation across 20 years of plant genome sequencing. Nat. Plants 7, 1571–1578 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. The Arabidopsis Genome Initiative. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408, 796–815 (2000).

    Article  Google Scholar 

  5. Sun, Y., Shang, L., Zhu, Q.-H., Fan, L. & Guo, L. Twenty years of plant genome sequencing: achievements and challenges. Trends Plant Sci. 27, 391–401 (2022).

    Article  CAS  PubMed  Google Scholar 

  6. Morozova, O. & Marra, M. A. Applications of next-generation sequencing technologies in functional genomics. Genomics 92, 255–264 (2008).

    Article  CAS  PubMed  Google Scholar 

  7. Lo, Y. T. & Shaw, P. C. Application of next-generation sequencing for the identification of herbal products. Biotechnol. Adv. 37, 107450 (2019).

    Article  CAS  PubMed  Google Scholar 

  8. Mardis, E. R. Next-generation DNA sequencing methods. Annu. Rev. Genomics Hum. Genet. 9, 387–402 (2008).

    Article  CAS  PubMed  Google Scholar 

  9. Hu, T., Chitnis, N., Monos, D. & Dinh, A. Next-generation sequencing technologies: an overview. Hum. Immunol. 82, 801–811 (2021).

    Article  CAS  PubMed  Google Scholar 

  10. Weirather, J. L. et al. Comprehensive comparison of Pacific Biosciences and Oxford Nanopore Technologies and their applications to transcriptome analysis. F1000Res. 6, 100 (2017).

    Article  PubMed  PubMed Central  Google Scholar 

  11. Lang, D. et al. Comparison of the two up-to-date sequencing technologies for genome assembly: HiFi reads of Pacific Biosciences Sequel II system and ultralong reads of Oxford Nanopore. GigaScience 9, giaa123 (2020).

    Article  PubMed  PubMed Central  Google Scholar 

  12. Van Dijk, E. L. et al. Genomics in the long-read sequencing era. Trends Genet. 39, 649–671 (2023).

    Article  PubMed  Google Scholar 

  13. Warburton, P. E. & Sebra, R. P. Long-read DNA sequencing: recent advances and remaining challenges. Annu. Rev. Genomics Hum. Genet. 24, 109–132 (2023).

    Article  CAS  PubMed  Google Scholar 

  14. Laver, T. et al. Assessing the performance of the Oxford Nanopore Technologies MinION. Biomol. Detect. Quantif. 3, 1–8 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Award-winning Sequel II system sets a new standard for long-read sequencing. PacBio https://www.pacb.com/blog/award-winning-sequel-ii-system/ (2019).

  16. Nurk, S. et al. The complete sequence of a human genome. Science 376, 44–53 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Yue, J. et al. Telomere-to-telomere and gap-free reference genome assembly of the kiwifruit Actinidia chinensis. Hortic. Res. 10, uhac264 (2023).

    Article  PubMed  Google Scholar 

  18. Shirasawa, K. et al. An improved reference genome for Trifolium subterraneum L. provides insight into molecular diversity and intra-specific phylogeny. Front. Plant Sci. 14, 1103857 (2023).

    Article  PubMed  PubMed Central  Google Scholar 

  19. McLay, T. G. B. et al. A genome resource for Acacia, Australia’s largest plant genus. PLoS ONE 17, e0274267 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Alabi, N. et al. Genome report: a draft genome of Alliaria petiolata (garlic mustard) as a model system for invasion genetics. G3 11, jkab339 (2021).

  21. Luo, R. et al. SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. GigaScience 1, 18 (2012).

    Article  PubMed  PubMed Central  Google Scholar 

  22. Zheng, P. et al. Comparative analyses of American and Asian lotus genomes reveal insights into petal color, carpel thermogenesis and domestication. Plant J. 110, 1498–1515 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Xiao, C.-L. et al. MECAT: fast mapping, error correction, and de novo assembly for single-molecule sequencing reads. Nat. Methods 14, 1072–1074 (2017).

    Article  CAS  PubMed  Google Scholar 

  24. Zhang, B. et al. The chromosome-scale assembly of endive (Cichorium endivia) genome provides insights into the sesquiterpenoid biosynthesis. Genomics 114, 110400 (2022).

    Article  CAS  PubMed  Google Scholar 

  25. Hale, I. et al. Genomic resources to guide improvement of the shea tree. Front. Plant Sci. 12, 720670 (2021).

    Article  PubMed  PubMed Central  Google Scholar 

  26. Cheng, H., Concepcion, G. T., Feng, X., Zhang, H. & Li, H. Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm. Nat. Methods 18, 170–175 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Snyder, M. W., Adey, A., Kitzman, J. O. & Shendure, J. Haplotype-resolved genome sequencing: experimental methods and applications. Nat. Rev. Genet. 16, 344–358 (2015).

    Article  CAS  PubMed  Google Scholar 

  28. Guk, J., Jang, M., Choi, J., Lee, Y. M. & Kim, S. De novo phasing resolves haplotype sequences in complex plant genomes. Plant Biotechnol. J. 20, 1031–1041 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Tettelin, H. et al. Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial ‘pan-genome’. Proc. Natl Acad. Sci. USA 102, 13950–13955 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Li, Y. et al. De novo assembly of soybean wild relatives for pan-genome analysis of diversity and agronomic traits. Nat. Biotechnol. 32, 1045–1052 (2014).

    Article  CAS  PubMed  Google Scholar 

  31. Jiao, W.-B. & Schneeberger, K. Chromosome-level assemblies of multiple Arabidopsis genomes reveal hotspots of rearrangements with altered evolutionary dynamics. Nat. Commun. 11, 989 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Jayakodi, M. et al. The barley pan-genome reveals the hidden legacy of mutation breeding. Nature 588, 284–289 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Montenegro, J. D. et al. The pangenome of hexaploid bread wheat. Plant J. 90, 1007–1013 (2017).

    Article  CAS  PubMed  Google Scholar 

  34. Li, J. et al. Cotton pan-genome retrieves the lost sequences and genes during domestication and selection. Genome Biol. 22, 119 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Gao, L. et al. The tomato pan-genome uncovers new genes and a rare allele regulating fruit flavor. Nat. Genet. 51, 1044–1051 (2019).

    Article  CAS  PubMed  Google Scholar 

  36. Tang, D. et al. Genome evolution and diversity of wild and cultivated potatoes. Nature 606, 535–541 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Song, J.-M. et al. Eight high-quality genomes reveal pan-genome architecture and ecotype differentiation of Brassica napus. Nat. Plants 6, 34–45 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Qin, P. et al. Pan-genome analysis of 33 genetically diverse rice accessions reveals hidden genomic variations. Cell 184, 3542–3558 (2021).

    Article  CAS  PubMed  Google Scholar 

  39. Wu, D. et al. A syntelog-based pan-genome provides insights into rice domestication and de-domestication. Genome Biol. 24, 179 (2023).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Hufford, M. B. et al. De novo assembly, annotation and comparative analysis of 26 diverse maize genomes. Science 373, 655–662 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. Wang, B. et al. De novo genome assembly and analyses of 12 founder inbred lines provide insights into maize heterosis. Nat. Genet. 55, 312–323 (2023).

    Article  CAS  PubMed  Google Scholar 

  42. Li, W. et al. SMRT sequencing of the Oryza rufipogon genome reveals the genomic basis of rice adaptation. Commun. Biol. 3, 167 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  43. Shen, J. et al. A haplotype‐resolved genome for Rhododendron × pulchrum and the expression analysis of heat shock genes. J. Syst. Evol. https://doi.org/10.1111/jse.13007 (2023).

  44. Zhuang, Y. et al. Phylogenomics of the genus Glycine sheds light on polyploid evolution and life-strategy transition. Nat. Plants 8, 233–244 (2022).

    Article  CAS  PubMed  Google Scholar 

  45. Kelly, L. J. et al. Convergent molecular evolution among ash species resistant to the emerald ash borer. Nat. Ecol. Evol. 4, 1116–1128 (2020).

    Article  PubMed  PubMed Central  Google Scholar 

  46. Wang, M. et al. Genomic innovation and regulatory rewiring during evolution of the cotton genus Gossypium. Nat. Genet. 54, 1959–1971 (2022).

    Article  CAS  PubMed  Google Scholar 

  47. Li, N. et al. Super-pangenome analyses highlight genomic diversity and structural variation across wild and cultivated tomato species. Nat. Genet. 55, 852–860 (2023).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  48. Yang, T. et al. Improved pea reference genome and pan-genome highlight genomic features and evolutionary characteristics. Nat. Genet. 54, 1553–1563 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  49. Mamidi, S. et al. A genome resource for green millet Setaria viridis enables discovery of agronomically valuable loci. Nat. Biotechnol. 38, 1203–1210 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  50. Zhou, Y. et al. Graph pangenome captures missing heritability and empowers tomato breeding. Nature 606, 527–534 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  51. Meleshko, D., Yang, R., Marks, P., Williams, S. & Hajirasouliha, I. Efficient detection and assembly of non-reference DNA sequences with synthetic long reads. Nucleic Acids Res. 50, e108 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  52. Zhang, F. et al. Long-read sequencing of 111 rice genomes reveals significantly larger pan-genomes. Genome Res. 32, 853–863 (2022).

    PubMed  PubMed Central  Google Scholar 

  53. Shi, J., Tian, Z., Lai, J. & Huang, X. Plant pan-genomics and its applications. Mol. Plant 16, 168–186 (2023).

    Article  CAS  PubMed  Google Scholar 

  54. He, Q. et al. A graph-based genome and pan-genome variation of the model plant Setaria. Nat. Genet. 55, 1232–1242 (2023).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  55. Cardinale, B. J. et al. Biodiversity loss and its impact on humanity. Nature 486, 59–67 (2012).

    Article  CAS  PubMed  Google Scholar 

  56. Wang, L., Zhao, Z., Shomurodov, K. & Tian, C. Address the Aral Sea crisis with cooperation. Science 380, 1114 (2023).

    Article  CAS  PubMed  Google Scholar 

  57. He, J. et al. A chromosome-level genome assembly of Artocarpus nanchuanensis (Moraceae), an extremely endangered fruit tree. GigaScience 11, giac042 (2022).

    Article  PubMed  PubMed Central  Google Scholar 

  58. Chen, J. et al. A complete telomere-to-telomere assembly of the maize genome. Nat. Genet. 55, 1221–1231 (2023).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  59. Zhang, H. et al. High-quality maple genome reveals duplication-facilitated leaf color diversity. Plant Sci. 338, 111917 (2024).

    Article  CAS  PubMed  Google Scholar 

  60. Yao, G. et al. Gapless genome assembly of Fusarium verticillioides, a filamentous fungus threatening plant and human health. Sci. Data 10, 229 (2023).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  61. Formenti, G. et al. Merfin: improved variant filtering, assembly evaluation and polishing via k-mer validation. Nat. Methods 19, 696–704 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  62. Rhie, A., Walenz, B. P., Koren, S. & Phillippy, A. M. Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies. Genome Biol. 21, 245 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  63. Nurk, S. et al. HiCanu: accurate assembly of segmental duplications, satellites and allelic variants from high-fidelity long reads. Genome Res. 30, 1291–1305 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  64. Song, J.-M. et al. Two gap-free reference genomes and a global view of the centromere architecture in rice. Mol. Plant 14, 1757–1767 (2021).

    Article  CAS  PubMed  Google Scholar 

  65. Tatusova, T. et al. NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res. 44, 6614–6624 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  66. Bolger, M. E., Arsova, B. & Usadel, B. Plant genome and transcriptome annotations: from misconceptions to simple solutions. Brief. Bioinform. 19, 437–449 (2017).

    PubMed Central  Google Scholar 

  67. Winsor, G. L. et al. Enhanced annotations and features for comparing thousands of Pseudomonas genomes in the Pseudomonas genome database. Nucleic Acids Res. 44, D646–D653 (2016).

    Article  CAS  PubMed  Google Scholar 

  68. Amborella Genome Project et al. The Amborella genome and the evolution of flowering plants. Science 342, 1241089 (2013).

    Article  Google Scholar 

  69. Zhang, L. et al. The water lily genome and the early evolution of flowering plants. Nature 577, 79–84 (2020).

    Article  CAS  PubMed  Google Scholar 

  70. Li, F.-W. et al. Anthoceros genomes illuminate the origin of land plants and the unique biology of hornworts. Nat. Plants 6, 259–272 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  71. Westwood, J. H. Plant biology: genome reveals secrets of the alien within. Curr. Biol. 31, R241–R243 (2021).

    Article  CAS  PubMed  Google Scholar 

  72. Cai, L. et al. Deeply altered genome architecture in the endoparasitic flowering plant Sapria himalayana Griff. (Rafflesiaceae). Curr. Biol. 31, 1002–1011 (2021).

    Article  CAS  PubMed  Google Scholar 

  73. He, Z. et al. Evolution of coastal forests based on a full set of mangrove genomes. Nat. Ecol. Evol. 6, 738–749 (2022).

    Article  PubMed  Google Scholar 

  74. Thudi, M. et al. Genomic resources in plant breeding for sustainable agriculture. J. Plant Physiol. 257, 153351 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  75. Bailey-Serres, J. et al. Genetic strategies for improving crop yields. Nature 575, 109–118 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  76. Grassini, P., Eskridge, K. M. & Cassman, K. G. Distinguishing between yield advances and yield plateaus in historical crop production trends. Nat. Commun. 4, 2918 (2013).

    Article  PubMed  Google Scholar 

  77. McCouch, S. et al. Feeding the future. Nature 499, 23–24 (2013).

    Article  CAS  PubMed  Google Scholar 

  78. Swarup, S. et al. Genetic diversity is indispensable for plant breeding to improve crops. Crop Sci. 61, 839–852 (2021).

    Article  Google Scholar 

  79. Bohra, A. et al. Reap the crop wild relatives for breeding future crops. Trends Biotechnol. 40, 412–431 (2022).

    Article  CAS  PubMed  Google Scholar 

  80. DeHaan, L. et al. Roadmap for accelerated domestication of an emerging perennial grain crop. Trends Plant Sci. 25, 525–537 (2020).

    Article  CAS  PubMed  Google Scholar 

  81. Eshed, Y. & Lippman, Z. B. Revolutions in agriculture chart a course for targeted breeding of old and new crops. Science 366, eaax0025 (2019).

    Article  CAS  PubMed  Google Scholar 

  82. Curtin, S., Qi, Y., Peres, L. E. P., Fernie, A. R. & Zsögön, A. Pathways to de novo domestication of crop wild relatives. Plant Physiol. 188, 1746–1756 (2022).

    Article  CAS  PubMed  Google Scholar 

  83. Yu, H. et al. A route to de novo domestication of wild allotetraploid rice. Cell 184, 1156–1170 (2021).

    Article  CAS  PubMed  Google Scholar 

  84. Pennisi, E. New technologies boost genome quality. Science 357, 10–11 (2017).

    Article  CAS  PubMed  Google Scholar 

  85. Wang, Y., Zhao, Y., Bollas, A., Wang, Y. & Au, K. F. Nanopore sequencing technology, bioinformatics and applications. Nat. Biotechnol. 39, 1348–1365 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  86. Baid, G. et al. DeepConsensus improves the accuracy of sequences with a gap-aware sequence transformer. Nat. Biotechnol. 41, 232–238 (2023).

    CAS  PubMed  Google Scholar 

  87. Koren, S. et al. Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Res. 27, 722–736 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  88. Oddes, S., Zelig, A. & Kaplan, N. Three invariant Hi-C interaction patterns: applications to genome assembly. Methods 142, 89–99 (2018).

    Article  CAS  PubMed  Google Scholar 

  89. Ouchi, S., Kajitani, R. & Itoh, T. GreenHill: a de novo chromosome-level scaffolding and phasing tool using Hi-C. Genome Biol. 24, 162 (2023).

    Article  PubMed  PubMed Central  Google Scholar 

  90. Istace, B. et al. Sequencing and chromosome-scale assembly of plant genomes, Brassica rapa as a use case. Biology 10, 732 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  91. Hon, T. et al. Highly accurate long-read HiFi sequencing data for five complex genomes. Sci. Data 7, 399 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  92. Nguyen, L. T., Jung, H., Ma, J., Andersen, S. & Ross, E. Long-read Pore-C shows the 3D structure of the cattle genome. Anim. Prod. Sci. 63, 972–982 (2023).

    Article  CAS  Google Scholar 

  93. Ulahannan, N. et al. Nanopore sequencing of DNA concatemers reveals higher-order features of chromatin structure. Preprint at http://biorxiv.org/lookup/doi/10.1101/833590 (2019).

  94. Hung, T. H. et al. Range-wide differential adaptation and genomic offset in critically endangered Asian rosewoods. Proc. Natl Acad. Sci. USA 120, e2301603120 (2023).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  95. Wang, X., Wu, X., Hong, N. & Jin, W. Progress in single-cell multimodal sequencing and multi-omics data integration. Biophys. Rev. https://doi.org/10.1007/s12551-023-01092-3 (2023).

    Article  PubMed  Google Scholar 

  96. Grün, D. & van Oudenaarden, A. Design and analysis of single-cell sequencing experiments. Cell 163, 799–810 (2015).

    Article  PubMed  Google Scholar 

  97. Elmentaite, R., Domínguez Conde, C., Yang, L. & Teichmann, S. A. Single-cell atlases: shared and tissue-specific cell types across human organs. Nat. Rev. Genet. 23, 395–410 (2022).

    Article  CAS  PubMed  Google Scholar 

  98. Vandereyken, K., Sifrim, A., Thienpont, B. & Voet, T. Methods and applications for single-cell and spatial multi-omics. Nat. Rev. Genet. 24, 494–515 (2023).

    Article  CAS  PubMed  Google Scholar 

  99. Fan, X. et al. SMOOTH-seq: single-cell genome sequencing of human cells on a third-generation sequencing platform. Genome Biol. 22, 195 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  100. Zheng, W. et al. High-throughput, single-microbe genomics with strain resolution, applied to a human gut microbiome. Science 376, eabm1483 (2022).

    Article  CAS  PubMed  Google Scholar 

  101. Bankevich, A. et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J. Comput. Biol. 19, 455–477 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  102. Stuart, T. et al. Comprehensive integration of single-cell data. Cell 177, 1888–1902 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  103. Baysoy, A., Bai, Z., Satija, R. & Fan, R. The technological landscape and applications of single-cell multi-omics. Nat. Rev. Mol. Cell Biol. 24, 695–713 (2023).

    Article  CAS  PubMed  Google Scholar 

  104. Glick, L. & Mayrose, I. Panoramic: a package for constructing eukaryotic pan‐genomes. Mol. Ecol. Res. 21, 1393–1403 (2021).

  105. Kang, M. et al. The pan-genome and local adaptation of Arabidopsis thaliana. Nat. Commun. 14, 6259 (2023).

  106. Cai, X. et al. Impacts of allopolyploidization and structural variation on intraspecific diversification in Brassica rapa. Genome Biol. 22, 166 (2021).

  107. Cui, X. et al. BnaOmics: a comprehensive platform combining pan-genome and multi-omics data from Brassica napus. Plant Commun. 4, 100609 (2023).

  108. Chen, S. et al. Gene mining and genomics-assisted breeding empowered by the pangenome of tea plant Camellia sinensis. Nat. Plants 9, 1986–1999 (2023)

  109. Liu, F. et al. Genomes of cultivated and wild Capsicum species provide insights into pepper domestication and population differentiation. Nat. Commun. 14, 5487 (2023).

  110. Wu, S. et al. A Citrullus genus super‐pangenome reveals extensive variations in wild and cultivated watermelons and sheds light on watermelon evolution and domestication. Plant Biotechnol. J. 21, 1926–1928 (2023).

  111. Gao, Y. et al. Citrus genomic resources unravel putative genetic determinants of Huanglongbing pathogenicity. iScience 26, 106024 (2023).

  112. Huang, Y. et al. Pangenome analysis provides insight into the evolution of the orange subfamily and a key gene for citric acid accumulation in citrus fruits. Nat. Genet. 55, 1964–1975 (2023).

  113. Oren, E. et al. Pan‐genome and multi‐parental framework for high‐resolution trait dissection in melon (Cucumis melo). Plant J. 112, 1525–1542 (2022).

  114. Li, H. et al. Graph-based pan-genome reveals structural and sequence variations related to agronomic traits and domestication in cucumber. Nat. Commun. 13, 682 (2022).

  115. Chu, J. S.-C. et al. Eight soybean reference genome resources from varying latitudes and agronomic traits. Sci. Data 8, 164 (2021).

  116. Wang, T. et al. Pan-genome analysis of 13 Malus accessions reveals structural and sequence variations associated with fruit traits. Nat. Commun. 14, 7377 (2023).

  117. Shang, L. et al. A super pan-genomic landscape of rice. Cell Res. 32, 878–896 (2022).

  118. Chen, J. et al. Pangenome analysis reveals genomic variations associated with domestication traits in broomcorn millet. Nat. Genet. 55, 2243–2254 (2023).

  119. Yan, H. et al. Pangenomic analysis identifies structural variation associated with heat tolerance in pearl millet. Nat. Genet. 55, 507–518 (2023).

  120. Zhang, X. et al. Pan-genome of Raphanus highlights genetic variation and introgression among domesticated, wild, and weedy radishes. Mol. Plant 14, 2032–2055 (2021)

  121. Karetnikov, D. I. et al. Analysis of genome structure and its variations in potato cultivars grown in Russia. IJMS 24, 5713 (2023).

  122. Bozan, I. et al. Pangenome analyses reveal impact of transposable elements and ploidy on the evolution of potato species. Proc. Natl Acad. Sci. USA 120, e2211117120 (2023).

  123. Tao, Y. et al. Extensive variation within the pan-genome of cultivated and wild sorghum. Nat. Plants 7, 766–773 (2021).

  124. Liang, Q. et al. A view of the pan‐genome of domesticated cowpea (Vigna unguiculata [L.] Walp.). Plant Genome https://doi.org/10.1002/tpg2.20319 (2023).

  125. Cochetel, N. et al. A super-pangenome of the North American wild grape species. Genome Biol. 24, 290 (2023).

  126. Huff, M. et al. Long-read, chromosome-scale assembly of Vitis rotundifolia cv. Carlos and its unique resistance to Xylella fastidiosa subsp. fastidiosa. BMC Genomics 24, 409 (2023).

  127. Hou, X., Wang, D., Cheng, Z., Wang, Y. & Jiao, Y. A near-complete assembly of an Arabidopsis thaliana genome. Mol. Plant 15, 1247–1250 (2022).

  128. Zhang, Y. et al. The telomere‐to‐telomere gap‐free genome of four rice parents reveals SV and PAV patterns in hybrid rice breeding. Plant Biotechnol. J. 20, 1642–1644 (2022).

  129. Yang, X. et al. The gap-free potato genome assembly reveals large tandem gene clusters of agronomical importance in highly repeated genomic regions. Mol. Plant 16, 314–317 (2023).

  130. Han, X. et al. Two haplotype-resolved, gap-free genome assemblies for Actinidia latifolia and Actinidia chinensis shed light on the regulatory mechanisms of vitamin C and sucrose metabolism in kiwifruit. Mol. Plant 16, 452–470 (2023).

  131. Zhang, L. et al. A near‐complete genome assembly of Brassica rapa provides new insights into the evolution of centromeres. Plant Biotechnol. J. 21, 1022–1032 (2023).

  132. Zheng, H. et al. A near-complete genome assembly of the allotetrapolyploid Cenchrus fungigraminus (JUJUNCAO) provides insights into its evolution and C4 photosynthesis. Plant Commun. 4, 100633 (2023).

  133. Payne, Z. L., Penny, G. M., Turner, T. N. & Dutcher, S. K. A gap-free genome assembly of Chlamydomonas reinhardtii and detection of translocations induced by CRISPR-mediated mutagenesis. Plant Commun. 4, 100493 (2023).

  134. Deng, Y. et al. A telomere-to-telomere gap-free reference genome of watermelon and its mutation library provide important resources for gene discovery and breeding. Mol. Plant 15, 1268–1284 (2022).

  135. Wang, Y.-H. et al. Telomere-to-telomere carrot (Daucus carota) genome assembly reveals carotenoid characteristics. Hortic. Res. 10, uhad103 (2023).

  136. Wang, T. et al. A complete gap-free diploid genome in Saccharum complex and the genomic footprints of evolution in the highly polyploid Saccharum genus. Nat. Plants 9, 554–571 (2023).

  137. Zhou, Y. et al. The telomere-to-telomere genome of Fragaria vesca reveals the genomic evolution of Fragaria and the origin of cultivated octoploid strawberry. Hortic. Res. 10, uhad027 (2023).

  138. Xu, M. et al. A novel genome sequence of Jasminum sambac helps uncover the molecular mechanism underlying the accumulation of jasmonates. J. Exp. Bot. 74, 1275–1290 (2023).

  139. Fu, A. et al. Telomere-to-telomere genome assembly of bitter melon (Momordica charantia L. var. abbreviata Ser.) reveals fruit development, composition and ripening genetic characteristics. Hortic. Res. 10, uhac228 (2023).

  140. Ma, B. et al. The gap-free genome of mulberry elucidates the architecture and evolution of polycentric chromosomes. Hortic. Res. 10, uhad111 (2023).

  141. Belser, C. et al. Telomere-to-telomere gapless chromosomes of banana using nanopore sequencing. Commun. Biol. 4, 1047 (2021).

  142. Li, F. et al. Gap-free genome assembly and comparative analysis reveal the evolution and anthocyanin accumulation mechanism of Rhodomyrtus tomentosa. Hortic. Res. 10, uhad005 (2023).

  143. Tang, M. et al. A near-complete genome assembly of Thalia dealbata Fraser (Marantaceae). Front. Plant Sci. 14, 1183361 (2023).

    Article  PubMed  PubMed Central  Google Scholar 

  144. Shi, X. et al. The complete reference genome for grapevine (Vitis vinifera L.) genetics and breeding. Hortic. Res. 10, uhad061 (2023).

  145. Huang, Y. et al. A complete reference genome for the soybean cv. Jack. Plant Commun. 5, 100765 (2024).

  146. Lan, L. et al. The haplotype-resolved telomere-to-telomere carnation (Dianthus caryophyllus) genome reveals the correlation between genome architecture and gene expression. Hortic. Res. 11, uhad244 (2024).

  147. Wei, M. et al. Telomere-to-telomere genome assembly of melon (Cucumis melo L. var. inodorus) provides a high-quality reference for meta-QTL analysis of important traits. Hortic. Res. 10, uhad189 (2023).

  148. Sun, M. et al. Telomere-to-telomere pear (Pyrus pyrifolia) reference genome reveals segmental and whole genome duplication driving genome evolution. Hortic. Res. 10, uhad201 (2023).

  149. Zhang, A. et al. A telomere-to-telomere genome assembly of Zhonghuang 13, a widely-grown soybean variety from the original center of Glycine max. Crop J. 12, 142–153 (2024).

  150. Liao, Z. et al. A telomere-to-telomere reference genome of ficus (Ficus hispida) provides new insights into sex determination. Hortic. Res. 11, uhad257 (2024).

  151. Pei, T. et al. Gap-free genome assembly and CYP450 gene family analysis reveal the biosynthesis of anthocyanins in Scutellaria baicalensis. Hortic. Res. 10, uhad235 (2023).

  152. Wang, X. et al. Telomere-to-telomere and gap-free genome assembly of a susceptible grapevine species (Thompson Seedless) to facilitate grape functional genomics. Hortic. Res. 11, uhad260 (2024).

  153. Wang, Z. et al. Insights into the superrosids phylogeny and flavonoid synthesis from the telomere-to-telomere gap-free genome assembly of Penthorum chinense Pursh. Hortic. Res. 11, uhad274 (2024).

  154. He, Q. et al. A complete reference genome assembly for foxtail millet and Setaria-db, a comprehensive database for Setaria. Mol. Plant 17, 219–222 (2024).

  155. Wang, X. et al. A near-complete genome sequence of einkorn wheat provides insight into the evolution of wheat A subgenomes. Plant Commun. https://doi.org/10.1016/j.xplc.2023.100768 (2023).

  156. Song, Y. et al. Phased gap-free genome assembly of octoploid cultivated strawberry illustrates the genetic and epigenetic divergence among subgenomes. Hortic. Res. 11, uhad252 (2024).

  157. Xu, X.-D. et al. Telomere-to-telomere assembly of cassava genome reveals the evolution of cassava and divergence of allelic expression. Hortic. Res. 10, uhad200 (2023).

  158. Wang, L. et al. A telomere-to-telomere gap-free assembly of soybean genome. Mol. Plant 16, 1711–1714 (2023).

  159. Yang, Y. et al. A near‐complete assembly of asparagus bean provides insights into anthocyanin accumulation in pods. Plant Biotechnol. J. 21, 2473–2489 (2023).

  160. Zhang, C. et al. The T2T genome assembly of soybean cultivar ZH13 and its epigenetic landscapes. Mol. Plant 16, 1715–1718 (2023).

  161. Yang, M. et al. Insights into the evolution and spatial chromosome architecture of jujube from an updated gapless genome assembly. Plant Commun. 4, 100662 (2023).

  162. Zeng, T. et al. The telomere-to-telomere gap-free reference genome of wild blueberry (Vaccinium duclouxii) provides its high soluble sugar and anthocyanin accumulation. Hortic. Res. 10, uhad209 (2023).

  163. Luo, H. et al. Telomere-to-telomere genome of the allotetraploid legume Sesbania cannabina reveals transposon-driven subgenome divergence and mechanisms of alkaline stress tolerance. Sci. China Life Sci. 67, 149–160 (2024).

  164. Huang, H.-R. et al. Telomere-to-telomere haplotype-resolved reference genome reveals subgenome divergence and disease resistance in triploid Cavendish banana. Hortic. Res. 10, uhad153 (2023).

  165. He, S. et al. A telomere-to-telomere reference genome provides genetic insight into the pentacyclic triterpenoid biosynthesis in Chaenomeles speciosa. Hortic. Res. 10, uhad183 (2023).

  166. Liu, X. et al. The phased telomere-to-telomere reference genome of Musa acuminata, a main contributor to banana cultivars. Sci. Data 10, 631 (2023).

  167. Chang, Y., Zhang, R., Ma, Y. & Sun, W. A haplotype-resolved genome assembly of Rhododendron vialii based on PacBio HiFi reads and Hi-C data. Sci. Data 10, 451 (2023).

  168. Shen, F., Xu, S., Shen, Q., Bi, C. & Lysak, M. A. The allotetraploid horseradish genome provides insights into subgenome diversification and formation of critical traits. Nat. Commun. 14, 4102 (2023).

  169. Li, G. et al. The haplotype-resolved T2T reference genome highlights structural variation underlying agronomic traits of melon. Hortic. Res. 10, uhad182 (2023).

  170. Shang, L. et al. A complete assembly of the rice Nipponbare reference genome. Mol. Plant 16, 1232–1236 (2023).

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Acknowledgements

This study was supported by the Department of Science and Technology of Zhejiang and Hainan Province (ZDYF2022XDNY271 and 2022C02032).

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  1. These authors contributed equally: Lingjuan Xie, Xiaojiao Gong.

Authors and Affiliations

  1. 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

  2. Hainan Institute of Zhejiang University, Yazhou Bay, Shanya, China

    Lingjuan Xie, Leti Shen & Longjiang Fan

  3. CSIRO Agriculture and Food, Black Mountain Laboratories, Canberra, Australia

    Qian-Hao Zhu

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  1. Lingjuan Xie
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Contributions

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.

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Correspondence to Longjiang Fan.

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Xie, L., Gong, X., Yang, K. et al. Technology-enabled great leap in deciphering plant genomes. Nat. Plants 10, 551–566 (2024). https://doi.org/10.1038/s41477-024-01655-6

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