Хронология секвенирования полных геномов растений
01.07.2025
Авторы:
Название:
Хронология секвенирования полных геномов растений
Страницы:
8 – 16
Начало эры секвенирования полных ядерных геномов высших растений совпало с началом нового тысячелетия, и за прошедшие четверть века достигнут большой прогресс в плане количества секвенированных геномов растений, которых насчитывается уже более 5 тысяч, принадлежащих приблизительно 2 тысячам видов. Однако подавляющее большинство секвенированных геномов представляют собой квазигеномы с консенсусными нуклеотидными последовательностями начала века, в виде мозаичной композитной сборки участков парных хромосом. При этом достигнутый не так давно уровень по-хромосомной сборки геномов, в том числе T2T (от теломеры до теломеры), несущей больше генетической информации, распределенной по отдельным хромосомам, включая теломеры и центромеры, тем не менее, сохраняет их мозаичный характер. Десятилетие назад для растений появились первые результаты по геномным последовательностям с фазированной сборкой гаплотипов, представляющие собой новый уровень знаний о геномах, в гораздо большей степени позволяющей проследить связь генотипа с фенотипом. Но подобных геномов собрано пока не так много. Со временем стало ясно, что один референсный геном для любого вида никак не соответствует огромному разнообразию полиморфизма ДНК, и тогда на сцену вышел пангеном вида, а вслед за ним и супер-пангеном рода. Однако пангеномов, супер-пангеномов составлено тоже пока не так много, но при этом уже есть таковые, опирающиеся на знания фазированных диплоидных геномов растений разных уровней плоидности, прошедших функциональную диплоидизацию. В данной статье представлено эволюционное развитие полногеномных исследований в виде улучшаемых сборок нуклеотидных последовательностей, особенностью которого является упоминание только тех геномов растений, которые соответствовали достигнутому уровню сборки в каждый отрезок времени, но при достижении нового порога «качества» генома приводятся лишь только геномы очередных уровней сборок, а геномы прежних уровней, которые продолжают секвенировать и дальше, уже игнорируются.
- Arabidopsis Genome Initiative. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature. 2000. V.408(6814). P.796-815. doi:10.1038/35048692 2. Bernal-Gallardo JJ, de Folter S. Plant genome information facilitates plant functional genomics. Planta. 2024. V.259(5). 117. doi:10.1007/s00425-024-04397-z 3. Sun Y, Shang L, Zhu QH et al. Twenty years of plant genome sequencing: achievements and challenges. Trends Plant Sci. 2022. V.27(4). P.391-401. doi:10.1016/j.tplants.2021.10.006 4. Xie L, Gong X, Yang K et al. Technology-enabled great leap in deciphering plant genomes. Nat Plants. 2024. V.10(4). P.551-566. doi:10.1038/s41477-024-01655-6 5. Yu J, Hu S, Wang J. et al. A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science. 2002. V.296(5565). P.79-92. doi:10.1126/science.1068037 6. Goff SA, Ricke D, Lan TH et al. A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science. 2002. V.296(5565). P.92-100. doi:10.1126/science.1068275 7. Tuskan GA, Difazio S, Jansson S. et al. The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science. 2006. V.313(5793). P.1596-1604. doi:10.1126/science.1128691 8. Jaillon O, Aury JM, Noel B. et al. The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature. 2007. V.449(7161). P.463-467. doi:10.1038/nature06148 9. Ming R, Hou S, Feng Y et al. The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus). Nature. 2008. V.452(7190). P.991-996. doi:10.1038/nature06856 10. Sato S, Nakamura Y, Kaneko T et al. Genome structure of the legume, Lotus japonicus. DNA Res. 2008. V.15(4). P.227-239. doi:10.1093/dnares/dsn008 11. Schnable PS, Ware D, Fulton RS et al. The B73 maize genome: complexity, diversity, and dynamics. Science. 2009. V.326(5956). P.1112-1125. doi:10.1126/science.1178534 12. Huang S, Li R, Zhang Z, Li L. et al. The genome of the cucumber, Cucumis sativus L. Nat Genet. 2009. V.41(12). P.1275-1281. doi:10.1038/ng.475 13. Paterson AH, Bowers JE, Bruggmann R et al. The Sorghum bicolor genome and the diversification of grasses. Nature. 2009. V.457(7229). P.551-556. doi:10.1038/nature07723 14. Schmutz J, Cannon SB, Schlueter J et al. Genome sequence of the palaeopolyploid soybean. Nature. 2010. V.463(7278). P.178-183. doi:10.1038/nature08670 15. Chan AP, Crabtree J, Zhao Q et al. Draft genome sequence of the oilseed species Ricinus communis. Nat Biotechnol. 2010. V.28(9). P.951-956. doi:10.1038/nbt.1674 16. Velasco R, Zharkikh A, Affourtit J et al. The genome of the domesticated apple (Malus × domestica Borkh.). Nat Genet. 2010. V.42(10). P.833-839. doi:10.1038/ng.654 17. Lai J, Li R, Xu X et. al. Genome-wide patterns of genetic variation among elite maize inbred lines. Nat Genet. 2010. V.42(11). P.1027-1030. doi:10.1038/ng.684 18. Lam H.M., Xu X., Liu X. et al. Resequencing of 31 wild and cultivated soybean genomes identifies patterns of genetic diversity and selection. Nat Genet. 2010. V.42. P.1053–1059. doi:10.1038/ng.715 19. Cao J, Schneeberger K, Ossowski S et al. Whole-genome sequencing of multiple Arabidopsis thaliana populations. Nat Genet. 2011. V.43(10). P.956-963. doi:10.1038/ng.911 20. Lin K, Zhang N, Severing EI et al. Beyond genomic variation--comparison and functional annotation of three Brassica rapa genomes: a turnip, a rapid cycling and a Chinese cabbage. BMC Genomics. 2014. V.15(1). 250. doi:10.1186/1471-2164-15-250 21. Li YH, Zhou G, Ma J et al. De novo assembly of soybean wild relatives for pan-genome analysis of diversity and agronomic traits. Nat Biotechnol. 2014. V.32(10). P.1045-1052. doi:10.1038/nbt.2979 22. Schatz MC, Maron LG, Stein JC et al. Whole genome de novo assemblies of three divergent strains of rice, Oryza sativa, document novel gene space of aus and indica. Genome Biol. 2014. V.15(11). 506. doi:10.1186/PREACCEPT-2784872521277375 23. Lu F, Romay MC, Glaubitz JC et al. High-resolution genetic mapping of maize pan-genome sequence anchors. Nat Commun. 2015. V.6. 6914. doi:10.1038/ncomms7914 24. Golicz AA, Bayer PE, Barker GC et al. The pangenome of an agronomically important crop plant Brassica oleracea. Nat Commun. 2016. V.7. 13390. doi:10.1038/ncomms13390 25. Chin CS, Peluso P, Sedlazeck FJ. et al. Phased diploid genome assembly with single-molecule real-time sequencing. Nat. Methods. 2016. V.13(12). P.1050-1054. doi:10.1038/nmeth.4035 26. Yang J, Moeinzadeh MH, Kuhl H. et al. Haplotype-resolved sweet potato genome traces back its hexaploidization history. Nat Plants. 2017. V.3(9). P.696-703. doi:10.1038/s41477-017-0002-z 27. Hulse-Kemp AM, Maheshwari S, Stoffel K. et al. Reference quality assembly of the 3.5-Gb genome of Capsicum annuum from a single linked-read library. Hortic Res. 2018. V.5. 4. doi:10.1038/s41438-017-0011-0 28. Reuscher S, Furuta T, Bessho-Uehara K et al. Assembling the genome of the African wild rice Oryza longistaminata by exploiting synteny in closely related Oryza species. Commun Biol. 2018. V.1. 162. doi:10.1038/s42003-018-0171-y 29. Zhang J, Zhang X, Tang H et al. Allele-defined genome of the autopolyploid sugarcane Saccharum spontaneum L. Nat Genet. 2018. V.50(11). P.1565-1573. doi:10.1038/s41588-018-0237-2. 30. Colle M, Leisner C, Wai CM. et al. Haplotype-phased genome and evolution of phytonutrient pathways of tetraploid blueberry. Gigascience. 2019. V.8(3). giz012. doi:10.1093/gigascience/giz012 31. Minio A, Massonnet M, Figuerosa-Balderas R et al. Diploid Genome Assembly of the Wine Grape Carmenere. G3 (Bethesda). 2019. V.9(5). P.1331-1337. doi:10.1534/g3.119.400030 32. Kuon JE, Qi W, Schläpfer P et al. Haplotype-resolved genomes of geminivirus-resistant and geminivirus-susceptible African cassava cultivars. BMC Biol. 2019. V.17(1). 75. doi:10.1186/s12915-019-0697-6 33. Shirasawa K, Esumi T, Hirakawa H. et al. Phased genome sequence of an interspecific hybrid flowering cherry, 'Somei-Yoshino' (Cerasus × yedoensis). DNA Res. 2019. V.26(5). P.379-389. doi:10.1093/dnares/dsz016 34. Shi D, Wu J, Tang H et al. Single-pollen-cell sequencing for gamete-based phased diploid genome assembly in plants. Genome Res. 2019. V.29(11). P.1889-1899. doi:10.1101/gr.251033.119 35. Vondras AM, Minio A, Blanco-Ulate B. et al. The genomic diversification of grapevine clones. BMC Genomics. 2019. V.20(1). 972. doi:10.1186/s12864-019-6211-2 36. Chen H, Zeng Y, Yang Y et al. Allele-aware chromosome-level genome assembly and efficient transgene-free genome editing for the autotetraploid cultivated alfalfa. Nat Commun. 2020. V.11(1). 2494. doi:10.1038/s41467-020-16338-x 37. Wang J, Liu W, Zhu D et al. Chromosome-scale genome assembly of sweet cherry (Prunus avium L.) cv. Tieton obtained using long-read and Hi-C sequencing. Hortic Res. 2020. V.7(1). 122. doi:10.1038/s41438-020-00343-8 38. Sun X, Jiao C, Schwaninger H. et al. Phased diploid genome assemblies and pan-genomes provide insights into the genetic history of apple domestication. Nat Genet. 2020. V.52(12). P.1423-1432. doi:10.1038/s41588-020-00723-9 39. Campoy JA, Sun H, Goel M. et al. Gamete binning: chromosome-level and haplotype-resolved genome assembly enabled by high-throughput single-cell sequencing of gamete genomes. Genome Biol. 2020. V.21(1). 306. doi:10.1186/s13059-020-02235-5 40. Zhang W, Luo C, Scossa F et al. A phased genome based on single sperm sequencing reveals crossover pattern and complex relatedness in tea plants. Plant J. 2021. V.105(1). P.197-208. doi:10.1111/tpj.15051 41. Cochetel N, Minio A, Massonnet M. et al. Diploid chromosome-scale assembly of the Muscadinia rotundifolia genome supports chromosome fusion and disease resistance gene expansion during Vitis and Muscadinia divergence. G3 (Bethesda). 2021. V.11(4). jkab033. doi:10.1093/g3journal/jkab033 42. Lovell JT, Bentley NB, Bhattarai G et al. Four chromosome scale genomes and a pan-genome annotation to accelerate pecan tree breeding. Nat Commun. 2021. V.12(1). 4125. doi:10.1038/s41467-021-24328-w 43. Zhang X, Chen S, Shi L et al. Haplotype-resolved genome assembly provides insights into evolutionary history of the tea plant Camellia sinensis. Nat Genet. 2021. V.53(8). P.1250-1259. doi:10.1038/s41588-021-00895-y 44. Cheng SP, Jia KH, Liu H et al. Haplotype-resolved genome assembly and allele-specific gene expression in cultivated ginger. Hortic Res. 2021. V.8(1). 188. doi:10.1038/s41438-021-00599-8 45. Belser C, Baurens FC, Noel B et al. Telomere-to-telomere gapless chromosomes of banana using nanopore sequencing. Commun Biol. 2021. V.4(1). 1047. doi:10.1038/s42003-021-02559-3 46. Song JM, Xie WZ, Wang S et al. Two gap-free reference genomes and a global view of the centromere architecture in rice. Mol Plant. 2021. V.14(10). P.1757-1767. doi:10.1016/j.molp.2021.06.018 47. Shirasawa K, Ueta S, Murakami K et al. Chromosome-scale haplotype-phased genome assemblies of the male and female lines of wild asparagus (Asparagus kiusianus), a dioecious plant species. DNA Res. 2022. V.29(1). dsac002. doi:10.1093/dnares/dsac002 48. An X, Gao K, Chen Z et al. High quality haplotype-resolved genome assemblies of Populus tomentosa Carr., a stabilized interspecific hybrid species widespread in Asia. Mol Ecol Resour. 2022. V.22(2). P.786-802. doi:10.1111/1755-0998.13507 49. Bickhart DM, Koch LM, Smith TPL et al. Chromosome-scale assembly of the highly heterozygous genome of red clover (Trifolium pratense L.), an allogamous forage crop species. GigaByte. 2022. 2022. gigabyte42. doi:10.46471/gigabyte.42 50. Zhang Q, Li M, Chen X et al. Chromosome-Level Genome Assembly of Bupleurum chinense DC Provides Insights Into the Saikosaponin Biosynthesis. Front Genet. 2022. V.13. 878431. doi:10.3389/fgene.2022.878431 51. Zheng Y, Yang D, Rong J. et al. Allele-aware chromosome-scale assembly of the allopolyploid genome of hexaploid Ma bamboo (Dendrocalamus latiflorus Munro). J Integr Plant Biol. 2022. V.64(3). P.649-670. doi:10.1111/jipb.13217 52. Nath O, Fletcher SJ, Hayward A et al. A haplotype resolved chromosomal level avocado genome allows analysis of novel avocado genes. Hortic Res. 2022. V.9. uhac157. doi:10.1093/hr/uhac157 53. Hoopes G, Meng X, Hamilton JP et al. Phased, chromosome-scale genome assemblies of tetraploid potato reveal a complex genome, transcriptome, and predicted proteome landscape underpinning genetic diversity. Mol Plant. 2022. V.15(3). P.520-536. doi:10.1016/j.molp.2022.01.003 54. Shen Y, Li W, Zeng Y. et al. Chromosome-level and haplotype-resolved genome provides insight into the tetraploid hybrid origin of patchouli. Nat Commun. 2022. V.13(1). 3511. doi:10.1038/s41467-022-31121-w 55. An X, Gao K, Chen Z et al. High quality haplotype-resolved genome assemblies of Populus tomentosa Carr., a stabilized interspecific hybrid species widespread in Asia. Mol Ecol Resour. 2022. V.22(2). P.786-802. doi:10.1111/1755-0998.13507 56. Liao B, Shen X, Xiang L et al. Allele-aware chromosome-level genome assembly of Artemisia annua reveals the correlation between ADS expansion and artemisinin yield. Mol Plant. 2022. V.15(8). P.1310-1328. doi:10.1016/j.molp.2022.05.013 57. Jiang L, Lin M, Wang H et al. Haplotype-resolved genome assembly of Bletilla striata (Thunb.) Reichb. f. to elucidate medicinal value. Plant J. 2022. V.111(5). P.1340-1353. doi:10.1111/tpj.15892 58. Khan A, Carey SB, Serrano A et al. A phased, chromosome-scale genome of 'Honeycrisp' apple (Malus domestica). GigaByte. 2022. gigabyte69. doi:10.46471/gigabyte.69 59. Piet Q, Droc G, Marande W. et al. A chromosome-level, haplotype-phased Vanilla planifolia genome highlights the challenge of partial endoreplication for accurate whole-genome assembly. Plant Commun. 2022. V.3(5). 100330. doi:10.1016/j.xplc.2022.100330 60. Minio A, Cochetel N, Massonnet M. et al. HiFi chromosome-scale diploid assemblies of the grape rootstocks 110R, Kober 5BB, and 101-14 Mgt. Sci Data. 2022. V.9(1). 660. doi:10.1038/s41597-022-01753-0 61. Yue J, Chen Q, Wang Y et al. Telomere-to-telomere and gap-free reference genome assembly of the kiwifruit Actinidia chinensis. Hortic Res. 2023. V.10(2). uhac264. doi:10.1093/hr/uhac264 62. Han X, Zhang Y, Zhang Q 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. 2023. V.16(2). P.452-470. doi:10.1016/j.molp.2022.12.022 63. Wang Y, Dong M, Wu Y et al. Telomere-to-telomere and haplotype-resolved genome of the kiwifruit Actinidia eriantha. Mol Hortic. 2023. V.3(1). 4. doi:10.1186/s43897-023-00052-5 64. Xu M, Gao Q, Jiang M et al. A novel genome sequence of Jasminum sambac helps uncover the molecular mechanism underlying the accumulation of jasmonates. J Exp Bot. 2023. V.74(4). P.1275-1290. doi:10.1093/jxb/erac464 65. Li G, Tang L, He Y et al. The haplotype-resolved T2T reference genome highlights structural variation underlying agronomic traits of melon. Hortic Res. 2023. V.10(10). uhad182. doi:10.1093/hr/uhad182 66. He S, Weng D, Zhang Y et al. A telomere-to-telomere reference genome provides genetic insight into the pentacyclic triterpenoid biosynthesis in Chaenomeles speciosa. Hortic Res. 2023. V.10(10). uhad183. doi:10.1093/hr/uhad183 67. Huang HR, Liu X, Arshad R et al. Telomere-to-telomere haplotype-resolved reference genome reveals subgenome divergence and disease resistance in triploid Cavendish banana. Hortic Res. 2023. V.10(9). uhad153. doi:10.1093/hr/uhad153 68. Liu X, Arshad R, Wang X. et al. The phased telomere-to-telomere reference genome of Musa acuminata, a main contributor to banana cultivars. Sci Data. 2023. V.10(1). 631. doi:10.1038/s41597-023-02546-9 69. Xu XD, Zhao RP, Xiao L et al. Telomere-to-telomere assembly of cassava genome reveals the evolution of cassava and divergence of allelic expression. Hortic Res. 2023. V.10(11). uhad200. doi:10.1093/hr/uhad200 70. Wang L, Li LL, Chen L. et al. Telomere-to-telomere and haplotype-resolved genome assembly of the Chinese cork oak (Quercus variabilis). Front Plant Sci. 2023. V.14. 1290913. doi:10.3389/fpls.2023.1290913 71. Lan L, Leng L, Liu W et al. The haplotype-resolved telomere-to-telomere carnation (Dianthus caryophyllus) genome reveals the correlation between genome architecture and gene expression. Hortic Res. 2023. V.11(1). uhad244. doi:10.1093/hr/uhad244 72. Li K, Chen R, Abudoukayoumu A et al. Haplotype-resolved T2T reference genomes for wild and domesticated accessions shed new insights into the domestication of jujube. Hortic Res. 2024. V.11(5). uhae071. doi:10.1093/hr/uhae071 73. Huang J, Zhang Y, Li Y et al. Haplotype-resolved gapless genome and chromosome segment substitution lines facilitate gene identification in wild rice. Nat Commun. 2024. V.15(1). 4573. doi:10.1038/s41467-024-48845-6 74. Qiao Q, Cao Q, Zhang R et al. Genomic analyses provide insights into sex differentiation of tetraploid strawberry (Fragaria moupinensis). Plant Biotechnol J. 2024. V.22(6). P.1552-1565. doi:10.1111/pbi.14286 75. Djari A, Madignier G, Di Valentin O et al. Haplotype-resolved genome assembly and implementation of VitExpress, an open interactive transcriptomic platform for grapevine. Proc Natl Acad Sci USA. 2024. V.121(23). e2403750121. doi:10.1073/pnas.2403750121 76. Wang Y, Li P, Zhu Y, Zhang F et al. Graph-Based Pangenome of Actinidia chinensis Reveals Structural Variations Mediating Fruit Degreening. Adv Sci (Weinh). 2024. V.11(28). e2400322. doi:10.1002/advs.202400322 77. Su Y, Yang X, Wang Y et al. Phased telomere-to-telomere reference genome and pangenome reveal an expansion of resistance genes during apple domestication. Plant Physiol. 2024. V.195(4). P.2799-2814. doi:10.1093/plphys/kiae258 78. Wang J, Xu D, Sang YL et al. A telomere-to-telomere gap-free reference genome of Chionanthus retusus provides insights into the molecular mechanism underlying petal shape changes. Hortic Res. 2024. V.11(12). uhae249. doi:10.1093/hr/uhae249 79. Ferguson S, Bar-Ness YD, Borevitz J, Jones A. A telomere-to-telomere Eucalyptus regnans genome: unveiling haplotype variance in structure and genes within one of the world's tallest trees. BMC Genomics. 2024. V.25(1). 913. doi:10.1186/s12864-024-10810-4 80. Hou Y, Gan J, Fan Z et al. Haplotype-based pangenomes reveal genetic variations and climate adaptations in moso bamboo populations. Nat Commun. 2024. V.15(1). 8085. doi:10.1038/s41467-024-52376-5 81. Feng J, Zhang W, Chen C et al. The pineapple reference genome: Telomere-to-telomere assembly, manually curated annotation, and comparative analysis. J Integr Plant Biol. 2024. V.66(10). P.2208-2225. doi:10.1111/jipb.13748 82. Li Q, Qiao X, Li L et al. Haplotype-resolved T2T genome assemblies and pangenome graph of pear reveal diverse patterns of allele-specific expression and the genomic basis of fruit quality traits. Plant Commun. 2024. V.5(10). 101000. doi:10.1016/j.xplc.2024.101000 83. Feng Y, Zhou J, Li D et al. The haplotype-resolved T2T genome assembly of the wild potato species Solanum commersonii provides molecular insights into its freezing tolerance. Plant Commun. 2024. V.5(10). 100980. doi:10.1016/j.xplc.2024.100980 84. Zhao L, Li Z, Jiang S et al. The Telomere-to-Telomere Genome of Jaboticaba Reveals the Genetic Basis of Fruit Color and Citric Acid Content. Int J Mol Sci. 2024. V.25(22). 11951. doi:10.3390/ijms252211951 85. Wang B, Zhang R, Sun W, Yang J. A nearly telomere-to-telomere diploid genome assembly of Firmiana kwangsiensis, a threatened species in China. Sci Data. 2024. V.11(1). 1394. doi:10.1038/s41597-024-04250-8 86. Guo M, Bi G, Wang H et al. Genomes of autotetraploid wild and cultivated Ziziphus mauritiana reveal polyploid evolution and crop domestication. Plant Physiol. 2024. V.196(4). P.2701-2720. doi:10.1093/plphys/kiae512 87. Mu W, Darian JC, Sung WK et al. The haplotype-resolved T2T genome for Bauhinia × blakeana sheds light on the genetic basis of flower heterosis. Gigascience. 2025. V.14. giaf044. doi:10.1093/gigascience/giaf044 88. Hu T, Duan L, Shangguan L et al. Haploid-Phased Chromosomal Telomere-to-Telomere Genome Assembly of Medicinal Plant Uncaria rhynchophylla Dissects Genetic Controls on the Biosynthesis of Bioactive Alkaloids. Plant Cell Environ. 2025. V.48(3). P.1932-1946. doi:10.1111/pce.15257 89. Liu Y, Chen Y, Ren Z et al. Two haplotype-resolved telomere-to-telomere genome assemblies of Xanthoceras sorbifolium. Sci Data. 2025. V.12(1). 791. doi:10.1038/s41597-025-05057-x 90. Matniyazov R.T., Kuluev A.R., Baymiev An.Kh. et al. T2T genomes of higher plants. Biomics. 2025. V.17(1). P. 65 - 76. DOI:10.31301/2221-6197.bmcs.2025-5 91. Kuluev B.R., Chemeris D.A., Gerashchenkov G.A. et al. Pangenomics of plants. Biomics. 2025. V.17(1). P. 42 - 64. DOI:10.31301/2221-6197.bmcs.2025-4 92. Baymiev Al.Kh., Chemeris D.A., Sakhabutdinova A.R. et al. In higher plants as an example, one can see that the era of sequencing of their diploid genomes is coming. Biomics. 2025. V.17(1). P. 17 – 41. DOI: 10.31301/2221-6197.bmcs.2025-3