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doi: 10.15389/agrobiology.2024.3.426eng

UDC: 573.4:575.1[631.52+636.082.12

 

ON GENOCENTRICITY AND GENOMOCENTRICITY IN BASIC LIVING SYSTEMS: MICROORGANISMS, PLANTS, ANIMALS (review)

V.I. Glazko, G.Yu. Kosovsky, T.T. Glazko

Afanas’ev Research Institute of Fur-Bearing Animal Breeding and Rabbit Breeding,6, ul. Trudovaya, pos. Rodniki, Ramenskii Region, Moscow Province, 140143 Russia, e-mail vigvalery@gmail.com, gkosovsky@mail.ru, tglazko@rambler.ru (✉ corresponding author)

ORCID:
Glazko V.I. orcid.org/0000-0003-4242-2239
Glazko T.T. orcid.org/0000-0002-0520-7022
Kosovsky G.Yu. orcid.org/0000-0003-1889-6063

Final revision received April 07, 2024
Accepted April 26, 2024

The development of genomics and pangenomics is becoming increasingly relevant for the development of new methods for solving traditional problems of control and directed influence on the variability of polygenic quantitative traits for the conservation and improvement of genetic resources of agricultural species. It is necessary to systematize data on the elements of the genome organization, on the levels of genes and regulatory genomic sequences, for realization of these purposes. This paper examines the functional “redundancy” of protein-coding genes (E.V. Koonin, 2000; G. Rancati et al., 2008; M. Isalan et al., 2008); species-specificity of the genetic bases of adaptation to environmental factors, even in species close in origin (B. Benjelloun et al., 2023). The different rates of evolution of genomic elements, namely the genes encoding proteins and non-coding DNA sequences involved in general, taxon-specific, and species-specific biological processes, are revealed: the higher specificity of genome elements, the higher polymorphism and the evolutionarily "younger" variability are, usually associated with the pressure of environmental factors (W. Yang wt al., 2022; J. Damas et al., 2022; M.J. Christmas et al., 2023). Mobile genetic elements (transposons) are discussed as a central source of regulatory elements at different levels of the organization of regulatory networks (L.F.K. Kuderna et al., 2024), data are provided on their involvement in the variability of various genes, mutations of which are involved in breeding work with agricultural species (P. Zhao et al., 2023; X.M. Zheng et al., 2019; R. Xiang et al., 2019). Approaches to the management of these elements are considered by applying methods of gene and genomic editing using not only information about such inserts, but also mechanisms that prevent the negative effects of their transcription and transpositions (G. Farmiloe et al., 2023). It is assumed that it is the regulatory elements and their control mechanisms that can be an effective target for the development of methods for managing genetic resources of agricultural species.

Keywords: domestication, microevolution, macroevolution, biological codes, regulatory elements, transposons, gene expression profiles, CRISPR systems.  

 

REFERENCES

  1. Bar-On Y.M., Phillips R., Milo R. The biomass distribution on Earth. Proc. Natl. Acad. Sci USA, 2018, 115(25): 6506-6511 CrossRef
  2. Diamond J. Evolution, consequences and future of plant and animal domestication. Nature, 2002, 418(6898): 700-7007 CrossRef
  3. FAO. Intergovernmental technical working group on animal genetic resources for food and agriculture. Status of animal genetic resources—2016. Ninth Session Rome, 6-8 July 2016. Available: https://openknowledge.fao.org/server/api/core/bitstreams/c1d6a4cd-b263-4d85-8bc3-ed16630ceb61/content. No date.
  4. Burgin C.J., Colella J.P., Kahn P.L., Upham N.S. How many species of mammals are there? J. Mammal., 2018, 99: 1-14 CrossRef
  5. Zoonomia Consortium. A comparative genomics multitool for scientific discovery and conservation. Nature, 2020, 587: 240-245 CrossRef
  6. Wang W., Mauleon R., Hu Z., Chebotarov D., Tai S., Wu Z., Li M., Zheng T., Fuentes R.R., Zhang F., Mansueto L., Copetti D., Sanciangco M., Palis K.C., Xu J., Sun C., Fu B., Zhang H., Gao Y., Zhao X., Shen F., Cui X., Yu H., Li Z., Chen M., Detras J., Zhou Y., Zhang X., Zhao Y., Kudrna D., Wang C., Li R., Jia B., Lu J., He X., Dong Z., Xu J., Li Y., Wang M., Shi J., Li J., Zhang D., Lee S., Hu W., Poliakov A., Dubchak I., Ulat V.J., Borja F.N., Mendoza J.R., Ali J., Li J., Gao Q., Niu Y., Yue Z., Naredo M.E.B., Talag J., Wang X., Li J., Fang X., Yin Y., Glaszmann J.C., Zhang J., Li J., Hamilton R.S., Wing R.A., Ruan J., Zhang G., Wei C., Alexandrov N., McNally K.L., Li Z., Leung H. Genomic variation in 3,010 diverse accessions of Asian cultivated rice. Nature, 2018, 557(7703): 43-49 CrossRef
  7. Glazko V., Zybailov B., Glazko T. Asking the right question about the genetic basis of domestication: what is the source of genetic diversity of domesticated species? Adv. Genet. Eng., 2015, 4: 2 CrossRef
  8. Glazko V., Zybaylov B., Glazko T. Domestication and genome evolution. International Journal of Genetics and Genomics, 2014, 2(4): 47-56 CrossRef
  9. Crow M., Suresh H., Lee J., Gillis J. Coexpression reveals conserved gene programs that co-vary with cell type across kingdoms. Nucleic Acids Res., 2022, 50(8): 4302-4314 CrossRef
  10. Wang M., Li W., Fang C., Xu F., Liu Y., Wang Z., Yang R., Zhang M., Liu S., Lu S., Lin T., Tang J., Wang Y., Wang H., Lin H., Zhu B., Chen M., Kong F., Liu B., Zeng D., Jackson S.A., Chu C., Tian Z. Parallel selection on a dormancy gene during domestication of crops from multiple families. Nat. Genet., 2018, 50(10): 1435-1441 CrossRef
  11. Nevo E. Molecular evolutionary genetics of isozymes: pattern, theory, and application. Prog. Clin. Biol. Res., 1990, 344: 701-742.
  12. Nevo E. Ecological genomics of natural plant populations: the Israeli perspective. Methods Mol. Biol., 2009, 513: 321-344 CrossRef
  13. Cooper B., Clarke J.D., Budworth P., Kreps J., Hutchison D., Park S., Guimil S., Dunn M., Luginbühl P., Ellero C., Goff S.A., Glazebrook J. A network of rice genes associated with stress response and seed development. Proc. Natl. Acad. Sci. USA, 2003, 100(8): 4945-4950 CrossRef
  14. Glazko V.I., Andreichenko I.N., Kovalchuk S.N., Glazko T.T., Kosovsky G.Yu. Candidate genes for control of cattle milk production traits. Russ. Agricult. Sci., 2016, 42: 458-464 CrossRef
  15. Glazko G., Makarenkov V., Liu J., Mushegian A. Evolutionary history of bacteriophages with double-stranded DNA genomes. Biol. Direct., 2007, 2: 36 CrossRef
  16. Rancati G., Pavelka N., Fleharty B., Noll A., Trimble R., Walton K., Perera A., Staehling-Hampton K., Seidel C.W., Li R. Aneuploidy underlies rapid adaptive evolution of yeast cells deprived of a conserved cytokinesis motor. Cell, 2008, 135(5): 879-893 CrossRef
  17. Isalan M., Lemerle C., Michalodimitrakis K., Horn C., Beltrao P., Raineri E., Garriga-Canut M., Serrano L. Evolvability and hierarchy in rewired bacterial gene networks. Nature, 2008, 452(7189): 840-845 CrossRef
  18. Koonin EV. How many genes can make a cell: the minimal-gene-set concept. Annu. Rev. Genomics Hum. Genet., 2000, 1: 99-116 CrossRef
  19. Foster C.S.P., Van Dyke J.U., Thompson M.B., Smith N.M.A., Simpfendorfer C.A., Murphy C.R., Whittington C.M. Different genes are recruited during convergent evolution of pregnancy and the placenta. Mol. Biol. Evol., 2022, 39(4): msac077 CrossRef
  20. Cai G., Zhao W., Zhou Z., Gu X. MATTE: a pipeline of transcriptome module alignment for anti-noise phenotype-gene-related analysis. Brief Bioinform., 2023, 24(4): bbad207 CrossRef
  21. Heng J., Heng H.H. Karyotype coding: the creation and maintenance of system information for complexity and biodiversity. Biosystems, 2021, 208: 104476 CrossRef
  22. Heng H.H. Genes and genomes represent different biological entities. In: Genome Chaos. Rethinking genetics, evolution, and molecular medicine, Chapter 2. H.H. Heng (ed.). Academic Press, 2019: 53-94 CrossRef
  23. Comaills V., Castellano-Pozo M. Chromosomal instability in genome evolution: from cancer to macroevolution. Biology (Basel), 2023, 12(5): 671 CrossRef
  24. Heng E., Thanedar S., Heng H.H. Challenges and opportunities for clinical cytogenetics in the 21st century. Genes (Basel), 2023, 14(2): 493 CrossRef
  25. Schubert I. Macromutations yielding karyotype alterations (and the process(es) behind them) are the favored route of carcinogenesis and speciation. Cancers (Basel), 2024, 16(3): 554 CrossRef
  26. Markert C.L. Neoplasia: a disease of cell differentiation. Cancer Res., 1968, 28(9): 1908-1914..
  27. Carethers J.M., Jung B.H. Genetics and genetic biomarkers in sporadic colorectal cancer. Gastroenterology, 2015, 149(5): 1177-1190.e3 CrossRef
  28. Heng J., Heng H.H. Genome chaos, information creation, and cancer emergence: searching for new frameworks on the 50th Anniversary of the "War on Cancer". Genes (Basel), 2021, 13(1): 101 CrossRef
  29. Glazko T.T. The independent variability of different karyotypic characteristics during the spontaneous neoplastic evolution of mouse embryo fibroblasts. Tsitologiia, 1993, 35(1): 36-45.
  30. Glazko G.V., Koonin E.V., Rogozin I.B. Mutation hotspots in the p53 gene in tumors of different origin: correlation with evolutionary conservation and signs of positive selection. Biochim Biophys Acta, 2004, 1679(2): 95-106. CrossRef
  31. Koonin E.V., Rogozin I.B., Glazko G.V. p53 Gain-of-function: tumor biology and bioinformatics come together. Cell Cycle, 2005, 4(5): 686-688 CrossRef
  32. Chetverikov S.S. On some moments of the evolutionary process from the point of view of modern genetics. Journal of Experimental Biology, 1926, Ser. A, 2(1): 3-54.
  33. Wang Z., Zarlenga D., Martin J., Abubucker S., Mitreva M. Exploring metazoan evolution through dynamic and holistic changes in protein families and domains. BMC Evol. Biol., 2012, 12: 138 CrossRef
  34. Yang W., Yu J., Yao Y., Chen S., Zhao B., Liu S., Zhou L., Fang L., Liu J. Comparative immune-relevant transcriptome reveals the evolutionary basis of complex traits. iScience, 2022, 25(12): 105572 CrossRef
  35. Liu S., Yu Y., Zhang S., Cole J.B., Tenesa A., Wang T., McDaneld T.G., Ma L., Liu G.E., Fang L. Epigenomics and genotype-phenotype association analyses reveal conserved genetic architecture of complex traits in cattle and human. BMC Biol., 2020, 18(1): 80 CrossRef
  36. Wang L., Zhou S., Lyu T., Shi L., Dong Y., He S., Zhang H. Comparative genome analysis reveals the genomic basis of semi-aquatic adaptation in American mink (Neovison vison). Animals (Basel), 2022, 12(18): 2385 CrossRef
  37. Damas J., Corbo M., Kim J., Turner-Maier J., Farré M., Larkin D.M., Ryder O.A., Steiner C., Houck M.L., Hall S., Shiue L., Thomas S., Swale T., Daly M., Korlach J., Uliano-Silva M., Mazzoni C.J., Birren B.W., Genereux D.P., Johnson J., Lindblad-Toh K., Karlsson E.K., Nweeia M.T., Johnson R.N., Zoonomia Consortium, Lewin H.A. Evolution of the ancestral mammalian karyotype and syntenic regions. Proc. Natl. Acad. Sci. USA, 2022, 119(40): e2209139119 CrossRef
  38. Christmas M.J., Kaplow I.M., Genereux D.P., Dong M.X., Hughes G.M., Li X., Sullivan P.F., Hindle A.G., Andrews G., Armstrong J.C., Bianchi M., Breit A.M., Diekhans M., Fanter C., Foley N.M., Goodman D.B., Goodman L., Keough K.C., Kirilenko B., Kowalczyk A., Lawless C., Lind A.L., Meadows J.R.S., Moreira L.R., Redlich R.W., Ryan L., Swofford R., Valenzuela A., Wagner F., Wallerman O., Brown A.R., Damas J., Fan K., Gatesy J., Grimshaw J., Johnson J., Kozyrev S.V., Lawler A.J., Marinescu V.D., Morrill K.M., Osmanski A., Paulat N.S., Phan B.N., Reilly S.K., Schäffer D.E., Steiner C., Supple M.A., Wilder A.P., Wirthlin M.E., Xue J.R., Zoonomia Consortium, Birren B.W., Gazal S., Hubley R.M., Koefli K.P., Marques-Bonet T., Meyer W.K., Nweeia M., Sabeti P.C., Shapiro B., Smit A.F.A., Springer M.S., Teeling E.C., Weng Z., Hiller M., Levesque D.L., Lewin H.A., Murphy W.J., Navarro A., Paten B., Pollard K.S., Ray D.A., Ruf I., Ryder O.A., Pfenning A.R., Lindblad-Toh K., Karlsson E.K. Evolutionary constraint and innovation across hundreds of placental mammals. Science, 2023, 380(6643): eabn3943 CrossRef
  39. Glazko V.I., Kosovsky G.Yu., Blokhina T.V., Zhirkova A.A., Glazko T.T. Socialization and genetic variability as a driver of domestication (by the example of dog breeds). Sel’skokhozyaistvennaya biologiya [Agricultural Biology], 2021, 56(2): 292-303 CrossRef
  40. Ermakova E.A., Glazko V.I. Krolikovodstvo i zverovodstvo, 2022, 3: 36-43 CrossRef (in Russ.).
  41. Kuderna L.F.K., Ulirsch J.C., Rashid S., Ameen M., Sundaram L., Hickey G., Cox A.J., Gao H., Kumar A., Aguet F., Christmas M.J., Clawson H., Haeussler M., Janiak M.C., Kuhlwilm M., Orkin J.D., Bataillon T., Manu S., Valenzuela A., Bergman J., Rouselle M., Silva F.E. Agueda L., Blanc J., Gut M., de Vries D., Goodhead I., Harris R.A., Raveendran M., Jensen A., Chuma I.S., Horvath J.E., Hvilsom C., Juan D., Frandsen P., Schraiber J.G., de Melo F.R., Bertuol F., Byrne H., Sampaio I., Farias I., Valsecchi J., Messias M., da Silva M.N.F., Trivedi M., Rossi R., Hrbek T., Andriaholinirina N., Rabarivola C.J., Zaramody A., Jolly C.J., Phillips-Conroy J., Wilkerson G., Abee C., Simmons J.H., Fernandez-Duque E., Kanthaswamy S., Shiferaw F., Wu D., Zhou L., Shao Y., Zhang G., Keyyu J.D., Knauf S., Le M.D., Lizano E., Merker S., Navarro A., Nadler T., Khor C.C., Lee J., Tan P., Lim W.K., Kitchener A.C., Zinner D., Gut I., Melin A.D., Guschanski K., Schierup M.H., Beck R.M.D., Karakikes I., Wang K.C., Umapathy G., Roos C., Boubli J.P., Siepel A., Kundaje A., Paten B., Lindblad-Toh K., Rogers J., Marques Bonet T., Farh K.K. Identification of constrained sequence elements across 239 primate genomes. Nature, 2024, 625(7996): 735-742 CrossRef
  42. Benjelloun B., Leempoel K., Boyer F., Stucki S., Streeter I., Orozco-terWengel P., Alberto F.J., Servin B., Biscarini F., Alberti A., Engelen S., Stella A., Colli L., Coissac E., Bruford M.W., Ajmone-Marsan P., Negrini R., Clarke L., Flicek P., Chikhi A., Joost S., Taberlet P., Pompanon F. Multiple genomic solutions for local adaptation in two closely related species (sheep and goats) facing the same climatic constraints. Molecular Ecology, 2023, 00: e17257 CrossRef
  43. Frantz L.A.F., Bradley D.G., Larson G., Orlando L. Animal domestication in the era of ancient genomics. Nat. Rev. Genet., 2020, 21(8): 449-460 CrossRef
  44. Hu Y., Yuan S., Du X., Liu J., Zhou W., Wei F. Comparative analysis reveals epigenomic evolution related to species traits and genomic imprinting in mammals. Innovation (Camb), 2023, 4(3): 100434 CrossRef
  45. Zheng X.M., Chen J., Pang H.B., Liu S., Gao Q., Wang J.R., Qiao W.H., Wang H., Liu J., Olsen K.M., Yang Q.W. Genome-wide analyses reveal the role of noncoding variation in complex traits during rice domestication. Sci. Adv., 2019, 5(12): eaax3619 CrossRef
  46. Chen S., Liu S., Shi S., Jiang Y., Cao M., Tang Y., Li W., Liu J., Fang L., Yu Y., Zhang S. Comparative epigenomics reveals the impact of ruminant-specific regulatory elements on complex traits. BMC Biol., 2022, 20(1): 273 CrossRef
  47. Kern C., Wang Y., Xu X., Pan Z., Halstead M., Chanthavixay G., Saelao P., Waters S., Xiang R., Chamberlain A., Korf I., Delany M.E., Cheng H.H., Medrano J.F., Van Eenennaam A.L., Tuggle C.K., Ernst C., Flicek P., Quon G., Ross P., Zhou H. Functional annotations of three domestic animal genomes provide vital resources for comparative and agricultural research. Nat. Commun., 2021, 12(1): 1821 CrossRef
  48. Yadav A., Mathan J., Dubey A.K., Singh A. The emerging role of non-coding RNAs (ncRNAs) in plant growth, development, and stress response signaling. Noncoding RNA, 2024, 10(1): 13 CrossRef
  49. Bui Q.T., Grandbastien M.A. LTR retrotransposons as controlling elements of genome response to stress? In: Plant transposable elements: impact on genome structure and function. M.A. Grandbastien, J. Casacuberta (eds.). Springer Verlag, Berlin, 2012: 273-296 CrossRef
  50. Bourque G., Leong B., Vega V.B., Chen X., Lee Y.L., Srinivasan K.G., Chew J.L., Ruan Y., Wei C.L., Ng H.H., Liu E.T. Evolution of the mammalian transcription factor binding repertoire via transposable elements. Genome Res., 2008, 18(11): 1752-1762 CrossRef
  51. Mukherjee K., Moroz L.L. Transposon-derived transcription factors across metazoans. Front. Cell Dev. Biol., 2023, 11: 1113046 CrossRef
  52. Osmanski A.B., Paulat N.S., Korstian J., Grimshaw J.R., Halsey M., Sullivan K.A.M., Moreno-Santillán D.D., Crookshanks C., Roberts J., Garcia C., Johnson M.G., Densmore L.D., Stevens R.D., Zoonomia Consortium†, Rosen J., Storer .J.M., Hubley R., Smit A.F.A., Dávalos L.M., Karlsson E.K., Lindblad-Toh K., Ray D.A. Insights into mammalian TE diversity through the curation of 248 genome assemblies. Science, 2023, 380(6643): eabn1430 CrossRef
  53. Fueyo R., Judd J., Feschotte C., Wysocka J. Roles of transposable elements in the regulation of mammalian transcription. Nat. Rev. Mol. Cell Biol., 2022, 23(7): 481-497CrossRef
  54. Gebrie A. Transposable elements as essential elements in the control of gene expression.  Mobile DNA, 2023, 14(1): 9 CrossRef
  55. Roces V., Guerrero S., Álvarez A., Pascual J., Meijón M. PlantFUNCO: Integrative functional genomics database reveals clues into duplicates divergence evolution. Mol. Biol. Evol., 2024, 41(3): msae042 CrossRef
  56. Yang L.L., Zhang X.Y., Wang L.Y., Li Y.G., Li X.T., Yang Y., Su Q., Chen N., Zhang Y.L., Li N., Deng C.L., Li S.F., Gao W.J. Lineage-specific amplification and epigenetic regulation of LTR-retrotransposons contribute to the structure, evolution, and function of Fabaceae species. BMC Genomics, 2023, 24(1): 423 CrossRef
  57. Moawad A.S., Wang F., Zheng Y., Chen C., Saleh A.A., Hou J., Song C. Evolution of endogenous retroviruses in the subfamily of Caprinae. Viruses, 2024, 16: 398 CrossRef
  58. Glazko G.V., Koonin E.V., Rogozin I.B., Shabalina S.A. A significant fraction of conserved noncoding DNA in human and mouse consists of predicted matrix attachment regions. Trends Genet., 2003, 19(3): 119-124 CrossRef
  59. Jordan I.K., Rogozin I.B., Glazko G.V., Koonin E.V. Origin of a substantial fraction of human regulatory sequences from transposable elements. Trends Genet., 2003, 19(2): 68-72 CrossRef
  60. Pathak R.U., Phanindhar K., Mishra R.K. Transposable elements as scaffold/matrix attachment regions: shaping organization and functions in genomes. Frontiers in Molecular Biosciences, 2024, 10: 1326933 CrossRef
  61. Lawson H.A., Liang Y., Wang T. Transposable elements in mammalian chromatin organization. Nat. Rev. Genet., 2023, 24(10): 712-723 CrossRef
  62. Belyayev A. Bursts of transposable elements as an evolutionary driving force. J. Evol. Biol., 2014, 27(12): 2573-2584 CrossRef
  63. Li Y., Li C., Xia J., Jin Y. Domestication of transposable elements into microRNA genes in plants. PLoS ONE, 2011, 6(5): e19212 CrossRef
  64. Glazko V.I., Kosovskii G.Yu., Glazko T.T. The sources of genome variability as domestication drivers (review). Sel'skokhozyaistvennaya biologiya[Agricultural Biology], 2022, 57(5): 832-851 CrossRef
  65. Yang L., Feng H. Cross-kingdom regulation by plant-derived miRNAs in mammalian systems. Animal Models and Experimental Medicine, 2023, 6(6): 518-525 CrossRef
  66. Li D., Yang J., Yang Y., Liu J., Li H., Li R., Cao C., Shi L., Wu W., He K. A timely review of cross-kingdom regulation of plant-derived microRNAs. Front. Genet., 2021, 12: 613197 CrossRef
  67. Colonna Romano N., Fanti L. Transposable elements: major players in shaping genomic and evolutionary patterns. Cells, 2022, 11: 1048 CrossRef
  68. Lerat E. Recent bioinformatic progress to identify epigenetic changes associated to transposable elements. Front. Genet., 2022, 13: 891194 CrossRef
  69. Buckley R.M., Kortschak R.D., Raison J.M., Adelson D.L. Similar evolutionary trajectories for retrotransposon accumulation in mammals, Genome Biology and Evolution, 2017, 9(9): 2336-2353 CrossRef
  70. Gao C., Xiao M., Ren X., Hayward A., Yin J., Wu L., Fu D., Li J. Characterization and functional annotation of nested transposable elements in eukaryotic genomes. Genomics, 2012, 100(4): 222-230 CrossRef
  71. Lexa M., Jedlicka P., Vanat I., Cervenansky M., Kejnovsky E. TE-greedy-nester: structure-based detection of LTR retrotransposons and their nesting. Bioinformatics, 2020, 36(20): 4991-4999 CrossRef
  72. Zhang X., Zhao M., McCarty D.R., Lisch D. Transposable elements employ distinct integration strategies with respect to transcriptional landscapes in eukaryotic genomes. Nucleic Acids Res., 2020, 48(12): 6685-6698 CrossRef
  73. Wang J., Han G.Z. Genome mining shows that retroviruses are pervasively invading vertebrate genomes. Nat. Commun., 2023, 14(1): 4968 CrossRef
  74. Voss J.D., Goodson M.S., Leon J.C. Phenotype diffusion and one health: a proposed framework for investigating the plurality of obesity epidemics across many species. Zoonoses and Public Health, 2018, 65(3): 279-290 CrossRef
  75. Smith H.J. An ethical investigation into the microbiome: the intersection of agriculture, genetics, and the obesity epidemic. Gut Microbes, 2020, 12(1): 1760712 CrossRef
  76. Saito S., Hosomichi K., Yamanaka M.P., Mizutani T., Takeshima S.N., Aida Y. Visualization of clonal expansion after massive depletion of cells carrying the bovine leukemia virus (BLV) integration sites during the course of disease progression in a BLV naturally-infected cow: a case report. Retrovirology, 2022, 19(1): 24 CrossRef
  77. Gillet N.A., Gutiérrez G., Rodriguez S.M., de Brogniez A., Renotte N., Alvarez I., Trono K., Willems L. Massive depletion of bovine leukemia virus proviral clones located in genomic transcriptionally active sites during primary infection. PLoS Pathogens, 2013, 9(10): e1003687 CrossRef
  78. Davenport K.M., Massa A.T., Bhattarai S., McKay S.D., Mousel M.R., Herndon M.K., White S.N., Cockett N.E., Smith T.P.L., Murdoch B.M. Characterizing genetic regulatory elements in ovine tissues. Front. Genet., 2021, 12: 628849 CrossRef
  79. Chadaeva I., Ponomarenko P., Kozhemyakina R., Suslov V., Bogomolov A., Klimova N., Shikhevich S., Savinkova L., Oshchepkov D., Kolchanov N.A., Markel A., Ponomarenko M. Domestication explains two-thirds of differential-gene-expression variance between domestic and wild animals; the remaining one-third reflects intraspecific and interspecific variation. Animals, 2021, 11: 2667 CrossRef
  80. Son K.H., Aldonza M.B.D., Nam A.R., Lee K.H., Lee J.W., Shin K.J. Kang K., Cho J.Y. Integrative mapping of the dog epigenome: reference annotation for comparative intertissue and cross-species studies. Sci. Adv., 2023, 9(27): eade3399 CrossRef
  81. Xiang R., Berg I.V.D., MacLeod I.M., Hayes B.J., Prowse-Wilkins C.P., Wang M., Bolormaa S., Liu Z., Rochfort S.J., Reich C.M., Mason B.A., Vander Jagt C.J., Daetwyler H.D., Lund M.S., Chamberlain A.J., Goddard M.E. Quantifying the contribution of sequence variants with regulatory and evolutionary significance to 34 bovine complex traits. Proc. Natl. Acad. Sci. USA, 2019, 116(39): 19398-19408 CrossRef
  82. Kojima S., Koyama S., Ka M., Saito Y., Parrish E.H., Endo M., Takata S., Mizukoshi M., Hikino K., Takeda A., Gelinas A.F., Heaton S.M., Koide R., Kamada A.J., Noguchi M., Hamada M. Biobank Japan Project Consortium. Kamatani Y., Murakawa Y., Ishigaki K., Nakamura Y., Ito K., Terao C., Momozawa Y., Parrish N.F. Mobile element variation contributes to population-specific genome diversification, gene regulation and disease risk. Nat. Genet., 2023, 55(6): 939-951 CrossRef
  83. Zhao P., Peng C., Fang L., Wang Z., Liu G.E. Taming transposable elements in livestock and poultry: a review of their roles and applications. Genetics, Selection, Evolution, 2023, 55(1): 50 CrossRef
  84. McDowell J.M., Meyers B.C. A transposable element is domesticated for service in the plant immune system. Proc. Natl. Acad. Sci. USA, 2013, 10(37): 14821-14822 CrossRef
  85. Mengistu A.A., Tenkegna T.A. The role of miRNA in plant-virus interaction: a review. Molecular Biology Reports, 2021, 48(3): 2853-2861 CrossRef
  86. Jiang L., Wang P., Jia H., Wu T., Yuan S., Jiang B., Sun S., Zhang Y., Wang L., Han T. Haplotype analysis of GmSGF14 gene family reveals its roles in photoperiodic flowering and regional adaptation of soybean. Int. J. Mol. Sci., 2023, 24: 9436 CrossRef
  87. Kirov I. Toward transgene-free transposon-mediated biological mutagenesis for plant breeding. Int. J. Mol. Sci., 2023, 24(23): 17054 CrossRef
  88. Galbraith J.D., Hayward A. The influence of transposable elements on animal colouration. Trends Genet., 2023, 39(8): 624-638 CrossRef
  89. Gong Y., Li Y., Liu X., Ma Y., Jiang L. A review of the pangenome: how it affects our understanding of genomic variation, selection and breeding in domestic animals? J. Anim. Sci. Biotechnol., 2023, 14(1): 73 CrossRef
  90. Smith T.P.L., Bickhart D.M., Boichard D., Chamberlain A.J., Djikeng A., Jiang Y., Low W.Y., Pausch H., Demyda-Peyrás S., Prendergast J., Schnabel R.D., Rosen B.D., Bovine Pangenome Consortium. The Bovine Pangenome Consortium: democratizing production and accessibility of genome assemblies for global cattle breeds and other bovine species. Genome Biol., 2023, 24(1): 139 CrossRef
  91. Zhou Y., Yang L., Han X., Han J., Hu Y., Li F., Xia H., Peng L., Boschiero C., Rosen B.D., Bickhart D.M., Zhang S., Guo A., Van Tassell C.P., Smith T.P.L., Yang L., Liu G.E. Assembly of a pangenome for global cattle reveals missing sequences and novel structural variations, providing new insights into their diversity and evolutionary history. Genome Res., 2022, 32(8): 1585-1601 CrossRef
  92. Xia X., Qu K., Wang Y., Sinding M.S., Wang F., Hanif Q., Ahmed Z., Lenstra J.A., Han J., Lei C., Chen N. Global dispersal and adaptive evolution of domestic cattle: a genomic perspective. Stress Biol., 2023, 3(1): 8 CrossRef
  93. Li R., Gong M., Zhang X., Wang F., Liu Z., Zhang L., Yang Q., Xu Y., Xu M., Zhang H., Zhang Y, Dai X, Gao Y, Zhang Z, Fang W, Yang Y, Fu W, Cao C, Yang P, Ghanatsaman ZA, Negari N.J., Nanaei H.A., Yue X., Song Y., Lan X., Deng W., Wang X., Pan C., Xiang R., Ibeagha-Awemu E.M., Heslop-Harrison P.J.S., Rosen B.D., Lenstra J.A., Gan S., Jiang Y. A sheep pangenome reveals the spectrum of structural variations and their effects on tail phenotypes. Genome Res., 2023, 33(3): 463-477 CrossRef
  94. Li Z., Liu X., Wang C., Li Z., Jiang B., Zhang R., Tong L., Qu Y., He S., Chen H., Mao Y., Li Q., Pook T., Wu Y., Zan Y., Zhang H., Li L., Wen K., Chen Y. The pig pangenome provides insights into the roles of coding structural variations in genetic diversity and adaptation. Genome Res., 2023, 33(10): 1833-1847 CrossRef
  95. Nguyen T.V., Vander Jagt C.J., Wang J., Daetwyler H.D., Xiang R., Goddard M.E., Nguyen L.T., Ross E.M., Hayes B.J., Chamberlain A.J., MacLeod I.M. In it for the long run: perspectives on exploiting long-read sequencing in livestock for population scale studies of structural variants. Genetics, Selection, Evolution, 2023, 55(1): 9 CrossRef
  96. Lanciano S., Philippe C., Sarkar A., Pratella D., Domrane C., Doucet A.J., van Essen D., Saccani S., Ferry L., Defossez P.A., Cristofari G. Locus-level L1 DNA methylation profiling reveals the epigenetic and transcriptional interplay between L1s and their integration sites. Cell Genomics, 2024, 4(2): 100498 CrossRef
  97. Workman S., Richardson S.R. Every repeat is unique: exploring the genomic impact of human L1 retrotransposons at locus-specific resolution. Cell Genomics, 2024, 4(2): 100504 CrossRef
  98. Guo Y., Xue Z., Gong M., Jin S., Wu X., Liu W. CRISPR-TE: a web-based tool to generate single guide RNAs targeting transposable elements. Mobile DNA, 2024, 15(1): 3 CrossRef
  99. Woźniak T., Sura W., Kazimierska M., Kasprzyk M.E., Podralska M., Dzikiewicz-Krawczyk A. TransCRISPR-sgRNA design tool for CRISPR/Cas9 experiments targeting specific sequence motifs. Nucleic Acids Res., 2023, 51(W1): W577-W586 CrossRef
  100. Fröhlich A., Hughes L.S., Middlehurst B., Pfaff A.L., Bubb V.J., Koks S., Quinn J.P. CRISPR deletion of a SINE-VNTR-Alu (SVA_67) retrotransposon demonstrates its ability to differentially modulate gene expression at the MAPT locus. Front Neurol., 2023, 14: 1273036 CrossRef
  101. Ozata D.M., Gainetdinov I., Zoch A., O’Carroll D., Zamore P.D. PIWI-interacting RNAs: small RNAs with big functions. Nat. Rev. Genet., 2019, 20(2): 89-108 CrossRef
  102. Meseuren D., Alsibai K.D. Part 1: The PIWI-piRNA pathway is an immune-like surveillance process that controls genome integrity by silencing transposable elements. In: Chromatin and epigenetics. C. Logie, T.A. Knoch (eds.). IntechOpen, Rijeka, 2018 CrossRef
  103. Farmiloe G., van Bree E.J., Robben S.F., Janssen L.J.M., Mol L., Jacobs F.M.J. Structural evolution of gene promoters driven by primate-specific KRAB zinc finger proteins. Genome Biol. Evol., 2023, 15(11): evad184 CrossRef
  104. Zhang Y., He F., Zhang Y., Dai Q., Li Q., Nan J., Miao R., Cheng B. Exploration of the regulatory relationship between KRAB-Zfp clusters and their target transposable elements via a gene editing strategy at the cluster specific linker-associated sequences by CRISPR-Cas9. Mobile DNA, 2022, 13(1): 25 CrossRef
  105. Ilık İ.A., Glažar P., Tse K., Brändl B., Meierhofer D., Müller F.J., Smith Z.D., Aktaş T. Autonomous transposons tune their sequences to ensure somatic suppression. Nature, 2024, 626(8001): 1116-1124 CrossRef
  106. Glazko V.I., Kosovsky G.Yu., Glazko T.T., Fedorova L.M. DNA markers and microsatellite code (review). Sel'skokhozyaistvennaya biologiya [Agricultural Biology], 2023, 58(2): 223-248 CrossRef
  107. Glazko V.I., Kosovsky G.Yu., Glazko T.T. The sources of genome variability as domestication drivers (review). Sel'skokhozyaistvennaya biologiya [Agricultural Biology], 2022, 57(5): 832-851 CrossRef
  108. Dornburg A., Mallik R., Wang Z., Bernal M.A., Thompson B., Bruford E.A., Nebert DW, Vasiliou V., Yohe L.R., Yoder J.A., Townsend J.P. Placing human gene families into their evolutionary context. Hum. Genomics, 2022, 16(1): 56 CrossRef
  109. Golicz A.A., Batley J., Edwards D. Towards plant pangenomics. Plant Biotechnol. J., 2016, 14(4): 1099-1105 CrossRef
  110. Dong X., Luo H., Yao J., Guo Q., Yu S., Ruan Y., Li F., Jin W., Meng D. The conservation of allelic DNA methylation and its relationship with imprinting in maize. J. Exp. Bot., 2024, 75(5): 1376-1389 CrossRef

 

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