Changes in Genomes and Karyotypes during Speciation and Progressive Evolution of Plants

Мұқаба

Дәйексөз келтіру

Толық мәтін

Ашық рұқсат Ашық рұқсат
Рұқсат жабық Рұқсат берілді
Рұқсат жабық Тек жазылушылар үшін

Аннотация

Interspecies hybridization and polyploidy play a major role in the processes of speciation and progressive evolution in plants. There are three possible ways of transforming hybrid genomes, which is somehow related to speciation in plants: 1). Introgression – the hybrid genome is stabilized by backcrossing with parental species without polyploidization – this is how such species as the Finnish spruce Picea ×fennica arose. 2). Genome polyploidization – the hybrid genome becomes stable while retaining doubled sets of chromosomes of the parent species. It can be called a “good” (eu-) polyploid. Most genomes/karyotypes of numerous polyploid polyploid plant species are in the eupolypoloid state. This is a fast and effective way of speciation, but speciation at an already mastered level of evolutionary complexity. 3). Dysploidy and secondary diploidization of the genome – intensive genomic rearrangements occur in the hybrid and polyploid genome and karyotype. A significant part of the duplicated copies is pseudogenized or deleted. The number of chromosomes in the haploid genome is radically reduced, often to a level close to the primary diploid chromosome numbers “2x”. Different individuals of a species that have embarked on the path of stochastic “fractionation” of the genome and dysploidy, retain different sets of unique and multiplied during WGD protein-coding genes, transposons, short interfering and long non-coding RNAs. In this case, intraspecific genomic and epigenetic polymorphism increases radically, that provides rich material for natural selection. Diploidization of genomes and karyotypes makes combinations of gene alleles and neogens, previously buffered in the polyploid state, available for testing by natural selection. Massive gene losses during genome fractionation can have a most unexpected effect on the phenotype, which often takes neotenous forms. Some neotenic morphotypes with diploidized and fractionated postpolyploid genomes, “hopeful monsters”, have such an original combination of gene families and morphological features that gives their carriers a chance to become the founder of a new large taxon, tribe, family, class.

Авторлар туралы

A. Rodionov

Komarov Botanical Institute of the Russian Academy of Sciences

Email: avrodionov@mail.ru
Saint Petersburg, Russia

Әдебиет тізімі

  1. Burki F., Roger A.J., Brown M.W., Simpson A.G. The new tree of eukaryotes // Trends Ecol. Evol. 2020. V. 35. P. 43–55. https://doi.org/10.1016/j.tree.2019.08.008
  2. Koonin E.V. The origin and early evolution of eukaryotes in the light of phylogenomics // Genome Biol. 2010. V. 11. P. 1–12. https://doi.org/10.1186/gb-2010-11-5-209
  3. Раутиан М.С., Шнеер В.С., Родионов А.В. Полифилия носителей хлоропластов: где располагаются растения на древе жизни? // Turczaninowia. 2019. Т. 22. № 2. С. 121–132. https://doi.org/10.14258/turczaninowia.22.2.7
  4. Cerón-Romero M.A., Fonseca M.M., De Oliveira Martins L. et al. Phylogenomic analyses of 2,786 genes in 158 lineages support a root of the eukaryotic tree of life between Opisthokonts and all other lineages // Genome Biol. Evol. 2022. V. 14. https://doi.org/10.1093/gbe/evac119
  5. Dobzhansky T. Genetics of the Еvolutionary Process. N.Y., London: Columbia Univ. Press, 1970. 505 p.
  6. Grant V. Plant Speciation. N.Y., London: Columbia Univ. Press, 1971. 435 p.
  7. Folk R.A., Soltis P.S., Soltis D.E., Guralnick R. New prospects in the detection and comparative analysis of hybridization in the tree of life // Am. J. Bot. 2018. V. 105. P. 364–375. https://doi.org/10.1002/ajb2.1018
  8. Stull G.W., Pham K.K., Soltis P.S., Soltis D.E. Deep reticulation: Тhe long legacy of hybridization in vascular plant evolution // Plant J. 2023. V. 114. P. 743–766. https://doi.org/10.1111/tpj.16142
  9. Whitney K.D., Ahern J.R., Campbell L.G. et al. Patterns of hybridization in plants // Perspect. Plant Ecol. Evol. Syst. 2010. V. 12. P. 175–182. https://doi.org/10.1016/j.ppees.2010.02.002
  10. Шнеер В.С., Пунина Е.О., Домашкина В.В., Родионов А.В. Криптогибриды у растений – подводная часть айсберга // Ботан. журнал. 2023. Т. 108. № 12. С. 1037–1053. https://doi.org/10.31857/S0006813623120098
  11. Van de Peer Y., Mizrachi E., Marchal K. The evolutionary significance of polyploidy // Nat. Rev. Genet. 2017. V. 18. P. 411–424. https://doi.org/10.1038/nrg.2017.26
  12. Eaton D.A., Hipp A.L., González-Rodríguez A., Cavender-Bares J. Historical introgression among the American live oaks and the comparative nature of tests for introgression // Evolution. 2015. V. 69. P. 2587–2601. https://doi.org/10.1111/evo.12758
  13. Leroy T., Louvet J.M., Lalanne C. et al. Adaptive introgression as a driver of local adaptation to climate in European white oaks // New Phytol. 2020. V. 226. P. 1171–1182. https://doi.org/10.1111/nph.16095
  14. Орлова Л.В., Егоров А.А. К систематике и географическому распространению ели финской (Picea fennica (Regel) Kom., Pinaceae) // Новости сист. высш. растений. 2010. Вып. 42. С. 5–23.
  15. Agafonov A.V., Shabanova E.V., Emtseva M.V. et al. Phylogenetic and taxonomic relationships between morphotypes related to Elymus caninus (Poaceae) based on sequence of a nuclear gene GBSS1 (waxy) and sexual hybridization // J. Syst. Evol. 2024. V. 62. P. 520–533. https://doi.org/10.1111/jse.13006
  16. Родионов А.В. Межвидовая гибридизация и полиплоидия в эволюции растений // Вавил. журн. генетики и селекции. 2013. Т. 17. № 4 (2). С. 916–929.
  17. Anderson E. Introgressive hybridization. N.Y., London: Hafner Publ. Comp., 1968. 109 p.
  18. Rieseberg L.H., Willis J.H. Plant speciation // Science. 2007. V. 317. P. 910–914. https://doi.org/10.1126/science.1137729
  19. Soltis P.S., Soltis D.E. The role of hybridization in plant speciation // Annu. Rev. Plant Biol. 2009. V. 60. P. 561–588. https://doi.org/10.1146/annurev.arplant.043008.092039
  20. Родионов А.В. Эуполиплоидия как способ видообразования у растений // Генетика. 2023. Т. 59. № 5. С. 493–506. https://doi.org/0.31857/S0016675823050119
  21. Wood T.E., Takebayashi N., Barker M.S. et al. The frequency of polyploid speciation in vascular plants // PNAS USA. 2009. V. 106. P. 13875–13879. https://doi.org/10.1073/pnas.0811575106
  22. Mandakova T., Lysak M.A. Post-polyploid diploidization and diversification through dysploid changes // Curr. Opin. Plant Biol. 2018. V. 42. P. 55–65. https://doi.org/10.1016/j.pbi.2018.03.001
  23. Li Z., McKibben M.T., Finch G.S. et al. Patterns and processes of diploidization in land plants // Annu. Rev. Plant Biol. 2021. V. 72. P. 387–410. https://doi.org/10.1146/annurev-arplant-050718-100344
  24. Scarrow M., Wang Y., Sun G. Molecular regulatory mechanisms underlying the adaptability of polyploid plants // Biol. Rev. 2021. V. 96. P. 394–407. https://doi.org/10.1111/brv.12661
  25. He X., Qi Z., Liu Z. et al. Pangenome analysis reveals transposon-driven genome evolution in cotton // BMC Biol. 2024. V. 22. P. 92. https://doi.org/10.1186/s12915-024-01893-2
  26. Decena M.Á., Sancho R., Inda L.A. et al. Expansions and contractions of repetitive DNA elements reveal contrasting evolutionary responses to the polyploid genome shock hypothesis in Brachypodium model grasses // Front. Plant Sci. 2024. V. 15. https://doi.org/10.3389/fpls.2024.1419255
  27. Teng J., Wang J., Zhang L. et al. Paleopolyploidies and genomic fractionation in major eudicot clades // Front. Plant Sci. 2022. V. 13. https://doi.org/10.3389/fpls.2022.883140
  28. Bomblies K. Learning to tango with four (or more): The molecular basis of adaptation to polyploid meiosis // Plant Reprod. 2023. V. 36. P. 107–124. https://doi.org/10.1007/s00497-022-00448-1
  29. Родионов А.В., Шнеер В.С., Гнутиков А.А. и др. Диалектика видов: от исходного единообразия, через максимально возможное разнообразие к конечному единообразию // Ботан. журнал. 2020. Т. 105. № 9. С. 835–853 https://doi.org/10.31857/S0006813620070091
  30. Favarger C. Sur l’emploi des nombres chromosomiques en geographie botanique historique // Ber. Geobot. Inst. Rubel. 1961. V. 32. P. 119–146.
  31. Mandakova T., Joly S., Krzywinski M. et al. Fast diploidization in close mesopolyploid relatives of Arabidopsis // Plant Cell. 2010. V. 22. P. 2277–2290. https://doi.org/10.1105/tpc.110.074526
  32. Родионов А.В., Носов Н.Н., Ким Е.С. и др. Происхождение полиплоидных геномов мятликов (Poa L.) и феномен потока генов между Северной Пацификой и субантарктическими островами // Генетика. 2010. Т. 46. № 12. С. 1598–1608.
  33. Пробатова Н.С. Хромосомные числа в семействе Poaceae и их значение для систематики, филогении и фитогеографии (на примере злаков Дальнего Востока России) // Комаровские чтения. Вып. 55. Владивосток, 2007. С. 9–103.
  34. Guerra M. Chromosome numbers in plant cytotaxonomy: Сoncepts and implications // Cytogenet. Genome Res. 2008. V. 120. P. 339–350. https://doi.org/10.1159/000121083
  35. Pecrix Y., Rallo G., Folzer H. et al. Polyploidization mechanisms: Тemperature environment can induce diploid gamete formation in Rosa sp. // J. Exp. Bot. 2011. V. 62. P. 3587–3597. https://doi.org/10.1093/jxb/err052
  36. Prentis P.J., Wilson J.R., Dormontt E.E. et al. Adaptive evolution in invasive species // Trends Plant Sci. 2008. V. 13. P. 288–294. https://doi.org/10.1016/j.tplants.2008.03.004
  37. Meudt H.M., Albach D.C., Tanentzap A.J. et al. Polyploidy on islands: Its emergence and importance for diversification // Front. Plant Sci. 2021. V. 12. https://doi.org/10.3389/fpls.2021.637214
  38. Rice A., Šmarda P., Novosolov M. et al. The global biogeography of polyploid plants // Nature Ecol. Evol. 2019. V. 3. P. 265–273. https://doi.org/10.1038/s41559-018-0787-9
  39. Carman J.G. Asynchronous expression of duplicate genes in angiosperm may cause apomixis, bispory, tetraspory, and polyembryony // Biol. J. Linn. Soc. 1997. V. 61. P. 51–94. https://doi.org/10.1111/j.1095-8312.1997.tb01778.x
  40. Winterfeld G., Schneider J., Perner K., Roser M. Polyploidy and hybridization as main factors of speciation: Complex reticulate evolution within the grass genus Helictochloa // Cytogen. Genome Res. 2014. V. 142. P. 204–225. https://doi.org/10.1159/000361002
  41. Suissa J.S., Kinosian S.P., Schafran P.W. et al. Homoploid hybrids, allopolyploids, and high ploidy levels characterize the evolutionary history of a western North American quillwort (Isoetes) complex // Mol. Phylogenet. Evol. 2022. V. 166. https://doi.org/10.1016/j.ympev.2021.107332
  42. Шнеер В.С., Пунина Е.О., Родионов А.В. Внутривидовые различия в плоидности у покрытосеменных и их таксономическая интерпретация // Ботан. журнал. 2018. Т. 103. № 5. С. 555–585. https://doi.org/10.1134/S0006813618050010
  43. Sutherland B.L., Galloway L.F. Postzygotic isolation varies by ploidy level within a polyploid complex // New Phytol. 2017. V. 213. P. 404–412. https://doi.org/10.1111/nph.14116
  44. Цвелев Н.Н. Вид как один из таксонов // Бюлл. МОИП. Отд. биол. 1995. Т. 100. Вып. 5. С. 62–68.
  45. Камелин Р.В. Особенности видообразования у цветковых растений // Тр. Зоол. ин-та РАН. 2009. Т. 313. Прил. 1. С. 141–149.
  46. Гребельный С.Д. Много ли на свете клональных видов. Ч. 2. Клонирование в природе, его роль в формировании разнообразия фауны и флоры // Зоол. беспозвоночных. 2006. Т. 3. № 1. С. 77–109.
  47. Hojsgaard D., Pellino M., Sharbel T.F., Hörandl E. Resolving genome evolution patterns in asexual plants // Next Generation Sequencing in Plant Systematics / Eds Hörandl E., Appelhans M.S. Königstein: Koeltz Sci. Books, 2015. P. 119–153. https://doi.org/10.14630/ 000005
  48. Soltis P.S., Soltis D.E. Ancient WGD events as drivers of key innovations in angiosperms // Curr. Opin. Plant Biol. 2016. V. 30. P. 159–165. https://doi.org/10.1016/j.pbi.2016.03.015
  49. Landis J.B., Soltis D.E., Li Z. et al. Impact of whole – genome duplication events on diversification rates in angiosperms // Amer. J. Bot. 2018. V. 105. P. 348–363. https://doi.org/10.1002/ajb2.1060
  50. Schranz M.E., Mohammadin S., Edger P.P. Ancient whole genome duplications, novelty and diversification: the WGD radiation lag-time model // Curr. Opin. Plant Biol. 2012. V. 15. P. 147–153. https://doi.org/10.1016/j.pbi.2012.03.011
  51. Ma P.F., Liu Y.L., Jin G.H. et al. The Pharus latifolius genome bridges the gap of early grass evolution // Plant Cell. 2021. V. 33. P. 846–864. https://doi.org/10.1093/plcell/koab015
  52. Huang J., Xu W., Zhai J. et al. Nuclear phylogeny and insights into whole-genome duplications and reproductive development of Solanaceae plants // Plant Commun. 2023. V. 4. https://doi.org/10.1016/j.xplc.2023.100595
  53. Mayrose I., Zhan S.H., Rothfels C.J. et al. Recently formed polyploid plants diversify at lower rates // Science. 2011. V. 333. P. 1257–1267. https://doi.org/10.1126/science.1207205
  54. Clark J.W. Genome evolution in plants and the origins of innovation // New Phytol. 2023. V. 240. P. 2204–2209. https://doi.org/10.1111/nph.19242
  55. Patel N., Budke J.M., Bainard J. Distinct patterns of genome size evolution in each bryophyte lineage are not correlated with whole genome duplication // Ann. Bot. 2025. https://doi.org/10.1093/aob/mcaf012
  56. Skaptsov M.V., Vaganov A.V., Kechaykin A.A. et al. The cytotypes variability of the complex Selaginella sanguinolenta s. L. // Turczaninowia. 2020. V. 23. № 2. P. 5–14. https://doi.org/10.14258/turczaninowia.23.2.1
  57. Liang Z., Schnable J.C. Functional divergence between subgenomes and gene pairs after whole genome duplications // Mol. Plant. 2018. V. 11. P. 388–397. https://doi.org/10.1016/j.molp.2017.12.010
  58. Carta A., Bedini G., Peruzzi L. A deep dive into the ancestral chromosome number and genome size of flowering plants // New Phytol. 2020. V. 228. P. 1097–1106. https://doi.org/10.1111/nph.16668
  59. Li Z., Kinosian S.P., Zhan S., Barker M.S. Ancient polyploidy and low rate of chromosome loss explain the high chromosome numbers of homosporous ferns // bioRxiv. 2024. https://doi.org/10.1101/2024.09.23.614530
  60. Klekowski E.J. Jr., Baker H.G. Evolutionary significance of polyploidy in the Pteridophyta // Science. 1966. V. 153. P. 305–307. https://doi.org/10.1126/science.153.3733.305
  61. Zhong Y., Liu Y., Wu W. et al. Genomic insights into genetic diploidization in the homosporous fern Adiantum nelumboides // Gen. Biol. Evol. 2022. V. 14. https://doi.org/10.1093/gbe/evac127
  62. Levin D.A., Wilson A.C. Rates of evolution in seed plants: Net increase in diversity of chromosome numbers and species numbers through time // PNAS USA. 1976. V. 73. https://doi.org/10.1073/pnas.73.6.2086
  63. Laurie D.A., Bennett M.D. The timing of chromosome elimination in hexaploid wheat × maize crosses // Genome. 1989. V. 32. P. 953–961. https://doi.org/10.1139/g89-537
  64. Evtushenko E.V., Lipikhina Y.A., Stepochkin P.I., Vershinin A.V. Cytogenetic and molecular characteristics of rye genome in octoploid Triticale (× Triticosecale Wittmack) // Comp. Cytogen. 2019. V. 13. № 4. P. 423–434. https://doi.org/10.3897/ CompCytogen.v13i4.39576
  65. Rutledge S.D., Cimini D. Consequences of aneuploidy in sickness and in health // Curr. Opin. Cell. Biol. 2016. V. 40. P. 41–46. https://doi.org/10.1016/j.ceb.2016.02.003
  66. Gaeta R.T., Pires J.C., Iniguez-Luy F. et al. Genomic changes in resynthesized Brassica napus and their effect on gene expression and phenotype // Plant Cell. 2007. V. 19. P. 3403–3417. https://doi.org/10.1105/tpc.107.054346
  67. Lim K.Y., Soltis D.E., Soltis P.S. et al. Rapid chromosome evolution in recently formed polyploids in Tragopogon (Asteraceae) // PloS One. 2008. V. 3. https://doi.org/10.1371/journal.pone.0003353
  68. Zhang A., Li N., Gong L. et al. Global analysis of gene expression in response to whole-chromosome aneuploidy in hexaploid wheat // Plant Physiol. 2017. V. 175. P. 828–847. https://doi.org/10.1104/pp.17.00819
  69. Panchy N., Lehti-Shiu M., Shiu S.H. Evolution of gene duplication in plants // Plant Physiol. 2016. V. 171. № 4. P. 2294–2316. https://doi.org/10.1104/pp.16.00523
  70. D’Hont A., Denoeud F., Aury J.M. et al. The banana (Musa acuminata) genome and the evolution of monocotyledonous plants // Nature. 2012. V. 488. P. 213–217. https://doi.org/10.1038/nature11241
  71. International Wheat Genome Sequencing Consortium. Shifting the limits in wheat research and breeding using a fully annotated reference genome // Science. 2018. V. 361. https://doi.org/10.1126/science.aar7191
  72. Chalhoub B., Denoeud F., Liu S. et al. Early allopolyploid evolution in the post-neolithic Brassica napus oilseed genome // Science. 2014. V. 345. P. 950–953. https://doi.org/10.1126/science.1253435
  73. Yoo M.J., Szadkowski E., Wendel J.F. Homoeolog expression bias and expression level dominance in allopolyploid cotton // Heredity. 2013. V. 110. P. 171–180. https://doi.org/10.1038/hdy.2012.94
  74. Родионов А.В., Амосова А.В., Крайнова Л.М. и др. Феномен высокой частоты мутаций в генах 35S рРНК С-субгенома у полиплоидных видов Avena L. // Генетика. 2020. Т. 56. № 6. С. 657–666. https://doi.org/10.31857/S0016675820060090
  75. Wang X., Morton J.A., Pellicer J. et al. Genome downsizing after polyploidy: Mechanisms, rates and selection pressures // Plant J. 2021. V. 107. P. 1003–1015. https://doi.org/10.1111/tpj.15363
  76. Xiong Z., Gaeta R.T., Pires J.C. Homoeologous shuffling and chromosome compensation maintain genome balance in resynthesized allopolyploid Brassica napus // PNAS USA. 2011. V. 108. P. 7908–7913. https://doi.org/10.1073/pnas.1014138108
  77. Buggs R.J., Chamala S., Wu W. et al. Rapid, repeated, and clustered loss of duplicate genes in allopolyploid plant populations of independent origin // Curr. Biol. 2012. V. 22. P. 248–252. https://doi.org/10.1016/j.cub.2011.12.027
  78. Bayer P.E., Scheben A., Golicz A.A. et al. Modelling of gene loss propensity in the pangenomes of three Brassica species suggests different mechanisms between polyploids and diploids // Plant Biotechnol. J. 2021. V. 19. P. 2488–2500. https://doi.org/10.1111/pbi.13674
  79. Lien S., Koop B.F., Sandve S.R. et al. The Atlantic salmon genome provides insights into rediploidization // Nature. 2016. V. 533. P. 200–205. https://doi.org/10.1038/nature17164
  80. Li Y.H., 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. P. 1045–1052. https://doi.org/10.1038/nbt.2979
  81. Golicz A.A., Bayer P.E., Barker G.C. et al. The pangenome of an agronomically important crop plant Brassica oleracea // Nat. Commun. 2016. V. 7. https://doi.org/0.1038/ncomms13390
  82. Gordon S.P., Contreras-Moreira B., Woods D.P. et al. Extensive gene content variation in the Brachypodium distachyon pan-genome correlates with population structure // Nat. Commun. 2017. V. 8. P. 2184. https://doi.org/10.1038/s41467-017-02292-8
  83. Montenegro J.D., Golicz A.A., Bayer P.E. et al. The pangenome of hexaploid bread wheat // Plant J. 2017. V. 90. P. 1007–1013. https://doi.org/10.1111/tpj.13515
  84. Seetharam A.S., Yu Y., Belanger S. et al. The Streptochaeta genome and the evolution of the grasses // Front. Plant Sci. 2021. V. 12. https://doi.org/10.3389/fpls.2021.710383
  85. Ma P.F., Liu Y.L., Jin G.H. et al. The Pharus latifolius genome bridges the gap of early grass evolution // Plant Cell. 2021. V. 33. P. 846–864. https://doi.org/10.1093/plcell/koab015
  86. Harris B.J., Harrison C.J., Hetherington A.M., Williams T.A. Phylogenomic evidence for the monophyly of bryophytes and the reductive evolution of stomata // Curr. Biol. 2020. V. 30. P. 2001–2012. https://doi.org/10.1016/j.cub.2020.03.048
  87. Renzaglia K.S., Browning W.B., Merced A. With over 60 independent losses, stomata are expendable in mosses // Front. Plant Sci. 2020. V. 11. https://doi.org/10.3389/fpls.2020.00567
  88. Ma X., Vanneste S., Chang J. et al. Seagrass genomes reveal a hexaploid ancestry facilitating adaptation to the marine environment // BioRxiv. 2023. https://doi.org/10.1101/2023.03.05.531170.
  89. Michael T.P., Ernst E., Hartwick N. et al. Genome and time-of-day transcriptome of Wolffia australiana link morphological minimization with gene loss and less growth control // Genome Res. 2021. V. 31. P. 225–238. https://doi.org/10.1101/gr.266429.120
  90. Domazet-Lošo M., Široki T., Šimičević K., Domazet-Lošo T. Macroevolutionary dynamics of gene family gain and loss along multicellular eukaryotic lineages // Nat. Commun. 2024. V. 15. P. 2663. https://doi.org/10.1038/s41467-024-47017-w
  91. Goldschmidt R. Some aspects of evolution // Science. 1933. V. 78. P. 539–547. https://doi.org/10.1126/science.78.2033.539
  92. Van Steenis C.G.G.J. Plant speciation in Malesia, with special reference to the theory of non-adaptive saltatory evolution // Biol. J. Linn. Soc. 1969. V. 1. P. 97–133. https://doi.org/10.1111/j.1095-8312.1969.tb01815.x
  93. Тахтаджян А.Л. Макроэволюционные процессы в истории растительного мира // Ботан. журнал. 1983. Т. 68. № 12. С. 1593–1603.
  94. Кольцов Н.К. Организация клетки. М., Л.: Гос. изд-во биол. и мед. лит-ры, 1936. C. 520.
  95. Van Steenis C.G.G.J. Autonomous evolution in plants. Differences in plant and animal evolution // Gard. Bull. Singapore. 1977. V. 29. P. 103–126.
  96. Guo H., Jiao Y., Tan X. et al. Gene duplication and genetic innovation in cereal genomes // Genome Res. 2019. V. 29. P. 261–269. https://doi.org/10.1101/gr.237511.118
  97. Freeling M. Bias in plant gene content following different sorts of duplication: Тandem, whole-genome, segmental, or by transposition // Annu. Rev. Plant Biol. 2009. V. 60. P. 433–453. https://doi.org/10.1146/annurev.arplant.043008.092122
  98. Kuzmin E., Taylor J.S., Boone C. Retention of duplicated genes in evolution // Trends Genet. 2021. V. 38. P. 59–72. https://doi.org/10.1016/j.tig.2021.06.016
  99. Lallemand T., Leduc M., Landes C. et al. An overview of duplicated gene detection methods: Why the duplication mechanism has to be accounted for in their choice // Genes. 2020. V. 11. https://doi.org/10.3390/genes11091046
  100. Vollger M.R., Guitart X., Dishuck P.C. et al. Segmental duplications and their variation in a complete human genome // Science. 2022. V. 376. https://doi.org/10.1126/science.abj6965
  101. Busche M., Pucker B., Viehover P. et al. Genome sequencing of Musa acuminata Dwarf Cavendish reveals a duplication of a large segment of chromosome 2 // G3 (Bethesda). 2020. V. 10. P. 37–42. https://doi.org/10.1534/g3.119.400847
  102. Shimizu N. Gene amplification and the extrachromosomal circular DNA // Genes. 2021. V. 12. https://doi.org/10.3390/genes12101533
  103. Koo D.H., Molin W.T., Saski C.A. et al. Extrachromosomal circular DNA-based amplification and transmission of herbicide resistance in crop weed Amaranthus palmeri // PNAS USA. 2018. V. 115. P. 3332–3337. https://doi.org/10.1073/pnas.1719354115
  104. Ain Q., Schmeer C., Wengerodt D. et al. Extrachromosomal circular DNA: Сurrent knowledge and implications for CNS aging and neurodegeneration // Int. J. Mol. Sci. 2020. V. 21. https://doi.org/10.3390/ijms21072477
  105. Kono T.J., Brohammer A.B., McGaugh S.E., Hirsch C.N. Tandem duplicate genes in maize are abundant and date to two distinct periods of time // G3 (Bethesda). 2018. V. 8. P. 3049–3058. https://doi.org/10.1534/g3.118.200580
  106. Blanc G., Wolfe K.H. Functional divergence of duplicated genes formed by polyploidy during Arabidopsis evolution // Plant Cell. 2004. V. 16. P. 1679–1691. https://doi.org/10.1105/tpc.021410
  107. Yu J., Wang J., Lin W. et al. The genomes ofOryza sativa: A history of duplications // PLoS Biol. 2005. V. 3. https://doi.org/10.1371/journal.pbio.0030038
  108. Zhang L., Zhu X., Zhao Y. et al. Phylotranscriptomics resolves the phylo geny of Pooideae and uncovers factors for their adaptive evolution // Mol. Biol. Evol. 2022. V. 39. https://doi.org/10.1093/molbev/msac026
  109. Bent A.F., Mackey D. Elicitors, effectors, and R genes: The new paradigm and a lifetime supply of questions // Annu. Rev. Phytopathol. 2007. V. 45. P. 399–436. https://doi.org/10.1146/annurev.phyto.45.062806.094427
  110. Shao Z.Q., Xue J.Y., Wang Q. et al. Revisiting the origin of plant NBS-LRR genes // Trends Plant Sci. 2019. V. 24. P. 9–12. https://doi.org/10.1016/j.tplants.2018.10.015
  111. Wei H., Liu J., Guo Q. et al. Genomic organization and comparative phylogenic analysis of NBS-LRR resistance gene family in Solanum pimpinellifolium and Arabidopsis thaliana // Evol. Bioinformatics. 2020. V. 16. https://doi.org/10.1177/117693432091105
  112. Meyers B.C., Kozik A., Griego A. et al. Genome-wide analysis of NBS-LRR–encoding genes in Arabidopsis // Plant Cell. 2003. V. 15. P. 809–834. https://doi.org/10.1105/tpc.009308
  113. Yang S., Gu T., Pan C. et al. Genetic variation of NBS-LRR class resistance genes in rice lines // Theor. Appl. Genet. 2008. V. 116. P. 165–177. https://doi.org/10.1007/s00122-007-0656-4
  114. Goffova I., Fajkus J. The rDNA loci – intersections of replication, transcription, and repair pathways // Int. J. Mol. Sci. 2021. V. 22. https://doi.org/10.3390/ijms22031302
  115. Takahashi H. Sulfate transport systems in plants: Functional diversity and molecular mechanisms underlying regulatory coordination // J. Exp. Bot. 2019. V. 70. P. 4075–4087. https://doi.org/10.1093/jxb/erz132
  116. Eirin-Lopez J.M., Rebordinos L., Rooney A.P., Rozas J. The birth-and-death evolution of multigene families revisited // Genome Dyn. 2012. P. 170–196. https://doi.org/10.1159/000337119
  117. Yuan D., He X., Han X. et al. Comprehensive review and evaluation of computational methods for identifying FLT3-internal tandem duplication in acute myeloid leukaemia // Brief. Bioinform. 2021. V. 22. https://doi.org/10.1093/bib/bbab099
  118. Khan I.U., Rono J.K., Zhang B.Q. et al. Identification of novel rice (Oryza sativa) HPP and HIPP genes tolerant to heavy metal toxicity // Ecotoxicol. Environ. Saf. 2019. V. 175. P. 8–18. https://doi.org/10.1016/j.ecoenv.2019.03.040
  119. Force A., Lynch M., Pickett F.B. et al. Preservation of duplicate genes by complementary, degenerative mutations // Genetics. 1999. V. 151. P. 1531–1545. https://doi.org/10.1093/genetics/151.4.1531
  120. Rodgers-Melnick E., Mane S.P., Dharmawardhana P. et al. Contrasting patterns of evolution following whole genome versus tandem duplication events in Populus // Genome Res. 2012. V. 22. P. 95–105. https://doi.org/10.1101/gr.125146.111
  121. Wu F., Shi X., Lin X. et al. The ABC s of flower development: Mutational analysis of AP 1/FUL-like genes in rice provides evidence for a homeotic (A)-function in grasses // Plant J. 2017. V. 89. P. 310–324. https://doi.org/10.1111/tpj.13386
  122. Li W., Chen Y., Ye M. et al. Evolutionary history of the C-repeat binding factor/dehydration-responsive element-binding 1 (CBF/DREB1) protein family in 43 plant species and characterization of CBF/DREB1 proteins in Solanum tuberosum // BMC Evol. Biol. 2020. V. 20. P. 142. https://doi.org/10.1186/s12862-020-01710-8
  123. Guo J., Ren Y., Tang Z. et al. Characterization and expression profiling of the ICE-CBF-COR genes in wheat // PeerJ. 2019. V. 7. https://doi.org/10.7717/peerj.8190
  124. Ibarra-Laclette E., Lyons E., Hernandez-Guzman G. et al. Architecture and evolution of a minute plant genome // Nature. 2013. V. 498. P. 94–98. https://doi.org/10.1038/nature12132
  125. Lan T., Renner T., Ibarra-Laclette E. et al. Longread sequencing uncovers the adaptive topography of a carnivorous plant genome // PNAS USA. 2017. V. 114. P. E4435–E4441. https://doi.org/10.1073/pnas.1702072114
  126. Adamec L., Matušikova I., Pavlovič A. Recent ecophysiological, biochemical and evolutional insights into plant carnivory // Ann. Bot. 2021. V. 128. P. 241–259. https://doi.org/10.1093/aob/mcab071
  127. Palfalvi G., Hackl T., Terhoeven N. et al. Genomes of the Venus flytrap and close relatives unveil the roots of plant carnivory // Curr. Biol. 2020. V. 30. P. 2312–2320. https://doi.org/10.1016/j.cub.2020.04.051
  128. Gruzdev E.V., Kadnikov V.V., Beletsky A.V. et al. Plastid genomes of carnivorous plants Drosera rotundifolia and Nepenthes × ventrata reveal evolutionary patterns resembling those observed in parasitic plants // Int. J. Mol. Sci. 2019. V. 20. https://doi.org/10.3390/ijms20174107
  129. Arendsee Z.W., Li L., Wurtele E.S. Coming of age: orphan genes in plants // Trends Plant Sci. 2014. V. 19. P. 698–708. https://doi.org/10.1016/j.tplants.2014.07.003
  130. Yao C., Yan H., Zhang X., Wang R. A database for orphan genes in Poaceae // Exp. Ther. Med. 2017. V. 14. P. 2917–2924. https://doi.org/10.3892/etm.2017.4918
  131. Stein J.C., Yu Y., Copetti D. et al. Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza // Nat. Genet. 2018. V. 50. P. 285–296. https://doi.org/10.1038/s41588-018-0040-0
  132. Guo T., Yang J., Li D. et al. Integrating GWAS, QTL, mapping and RNA-seq to identify candidate genes for seed vigor in rice (Oryza sativa L.) // Mol. Breeding. 2019. V. 39. P. 1–16. https://doi.org/10.1007/s11032-019-0993-4
  133. Wang W., Zheng H., Fan C. et al. High rate of chimeric gene origination by retroposition in plant genomes // Plant Cell. 2006. V. 18. P. 1791–1802. https://doi.org/10.1105/tpc.106.041905
  134. Zhou Y., Zhang C., Zhang L. et al. Gene fusion as an important mechanism to generate new genes in the genus Oryza // Genome Biol. 2022. V. 23. P. 130. https://doi.org/10.1186/s13059-022-02696-w
  135. Jiang N., Feschotte C., Zhang X., Wessler S.R. Using rice to understand the origin and amplification of miniature inverted repeat transposable elements (MITEs) // Curr. Opin. Plant Biol. 2004. V. 7. P. 115–119. https://doi.org/10.1016/j.pbi.2004.01.004
  136. Li G., Zhang T., Yu Z. et al. An efficient oligo-FISH painting system for revealing chromosome rearrangements and polyploidization in Triticeae // Plant J. 2021. V. 105. P. 978–993. https://doi.org/10.1111/tpj.15081
  137. Huang Y., Chen J., Dong C. Species-specific partial gene duplication in Arabidopsis thaliana evolved novel phenotypic effects on morphological traits under strong positive selection // Plant Cell. 2022. V. 34. P. 802–817. https://doi.org/10.1093/plcell/koab291
  138. Chen X., Rechavi O. Plant and animal small RNA communications between cells and organisms // Nat. Rev. Mol. Cell. Biol. 2022. V. 23. P. 185–203. https://doi.org/10.1038/s41580-021-00425-y
  139. Zhao Z., Zang S., Zou W. et al. Long non-coding RNAs: New players in plants // Int. J. Mol. Sci. 2022. V. 23. https://doi.org/0.3390/ijms23169301
  140. Barber W.T., Zhang W., Win H. et al. Repeat associated small RNAs vary among parents and following hybridization in maize // PNAS USA. 2012. V. 109. P. 10444–10449. https://doi.org/10.1073/pnas.1202073109
  141. Wu L., Liu S., Qi H. et al. Research progress on plant long non-coding RNA // Plants. 2020. V. 9. https://doi.org/10.3390/plants9040408

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