Biomics

The beginning of the era of sequencing complete nuclear genomes of higher plants coincided with the beginning of the new millennium, and over the past quarter century, great progress has been made in terms of the number of sequenced plant genomes, of which there are already more than 5,000, belonging to approximately 2,000 species.. The same cannot be said about the quality of genome assembly, since the vast majority of currently sequenced genomes are essentially quasi-genomes with consensus nucleotide sequences as in the beginning of the century in the form of a mosaic assembly of sections of paired chromosomes. At the same time, the T2T (telomere-to-telomere) level of chromosome assembly achieved not so long ago, despite the fact that such genomes carry more genetic information distributed across individual chromosomes, including telomeres and centromeres, they retain a mosaic character. A decade ago, the first results on genomic sequences with phased assembly of haplotypes for plants appeared, representing a new level of knowledge about genomes, which makes it possible to trace the relationship between genotype and phenotype to a much greater extent. But so far, not many such genomes have been assembled. Over time, it became clear that one reference genome for any species does not correspond to the huge variety of DNA polymorphism, and then the pangenome of the species, followed by a super-pangenome of the genus appeared. However, not so many pangenomes or super-pangenomes have been composed yet, but there are already some based on the knowledge of phased diploid genomes of plants of different ploidy levels that have undergone functional diploidization. This article presents the evolutionary development of genome-wide research in the form of improved assemblies of nucleotide sequences, the feature of which is to mention only those plant genomes that corresponded to the achieved assembly level in each time period, but when a new threshold of "quality" of the genome is reached, only the genomes of the next assembly levels are given, and the genomes of previous levels that continue to be sequenced and further, they are already ignored.

genome, sequencing, assembly, quasigenome, T2T genome, pangenome, super-pangenome, phased genome, diploid genome, haplotype-resolved genome

1. 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