Vimala Y, Lavania S, Lavania UC. Chromosome change and karyotype differentiation–implications in speciation and plant systematics. Nucleus. 2021;64:33–54.
Fuchs J, Brandes A, Schubert I. Telomere sequence localization and karyotype evolution in higher plants. Plant Syst Evol. 1995;196:227–41.
Peruzzi L, Eroğlu HE. Karyotype asymmetry: again, how to measure and what to measure? Comp Cytogenet. 2013;7:1–9.
Article PubMed PubMed Central Google Scholar
Weiss-Scheeweiss H, Stuessy T. Chromosome numbers, karyotypes, and evolution in Melampodium (Asteraceae). Int J Plant Sci. 2009;170:1168–82.
Lazar NH, Nevonen KA, O’Connell B, McCann C. Epigenetic maintenance of topological domains in the highly rearranged gibbon genome. Genome Res. 2018;28:983–97.
Article CAS PubMed PubMed Central Google Scholar
Renschler G, Richard G, Valsecchi CIK, Toscano S, Arrigoni L, Ramírez F, Akhtar A. Hi-C guided assemblies reveal conserved regulatory topologies on X and autosomes despite extensive genome shuffling. Genes Dev. 2019;33:1591–612.
Article CAS PubMed PubMed Central Google Scholar
Liao Y, Wang J, Zhu Z, Liu Y, Chen J, Zhou Y, Liu F, Lei J, Gaut BS, Cao B, et al. The 3D architecture of the pepper genome and its relationship to function and evolution. Nat Commun. 2022;13:3479.
Article CAS PubMed PubMed Central Google Scholar
Yin Y, Fan H, Zhou B, Hu Y, Fan G, Wang J, Zhou F, Nie W, Zhang C, Liu L. Molecular mechanisms and topological consequences of drastic chromosomal rearrangements of muntjac deer. Nat Commun. 2021;12:1–15.
Pope BD, Ryba T, Dileep V, Yue F, Wu W, Denas O, Vera DL, Wang Y, Hansen RS, Canfield TK. Topologically associating domains are stable units of replication-timing regulation. Nature. 2014;515:402–5.
Article CAS PubMed PubMed Central Google Scholar
Lieberman-Aiden E, Berkum N, Williams L, Imakaev M, Ragoczy T, Telling A, Amit I, Lajoie B, Sabo P, Dorschner M, et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science. 2009;326:289–93.
Article CAS PubMed PubMed Central Google Scholar
Wang C, Liu C, Roqueiro D, Grimm D, Schwab R, Becker C, Lanz C, Weigel D. Genome-wide analysis of local chromatin packing In Arabidopsis thaliana Genome Res. 2015;25:246–56.
Article PubMed PubMed Central Google Scholar
Tian L, Ku L, Yuan Z, Wang C, Su H, Wang S, Song X, Dou D, Ren Z, Lai J, et al. Large-scale reconstruction of chromatin structures of maize temperate and tropical inbred lines. J Exp Bot. 2021;72:3582–96.
Article CAS PubMed Google Scholar
Szabo Q, Jost D, Chang JM, Cattoni DI, Cavalli G. TADs are 3D structural units of higher-order chromosome organization in Drosophila Science Advances. 2018;4:eaar8082.
Article PubMed PubMed Central Google Scholar
Lupiáñez Darío G, Kraft K, Heinrich V, Krawitz P, Brancati F, Klopocki E, Horn D, Kayserili H, Opitz John M, Laxova R, et al. Disruptions of topological chromatin domains cause pathogenic rewiring of gene-enhancer interactions. Cell. 2015;161:1012–25.
Article PubMed PubMed Central Google Scholar
Ke Y, Xu Y, Chen X, Feng S, Liu Z, Sun Y, Yao X, Li F, Zhu W, Gao L. 3D chromatin structures of mature gametes and structural reprogramming during mammalian embryogenesis. Cell. 2017;170:367–81.
Article CAS PubMed Google Scholar
Feng S, Cokus S, Schubert V, Zhai J, Pellegrini M, Jacobsen S. Genome-wide Hi-C analyses in wild-type and mutants reveal high-resolution chromatin interactions in Arabidopsis Mol Cell. 2014;55:694–707.
Article CAS PubMed PubMed Central Google Scholar
Dong P, Tu X, Chu P-Y, Lü P, Zhu N, Grierson D, Du B, Li P, Zhong S. 3D chromatin architecture of large plant genomes determined by local A/B compartments. Mol Plant. 2017;10:1497–509.
Article CAS PubMed Google Scholar
Liu C. In situ Hi-C library preparation for plants to study their Three-Dimensional Chromatin Interactions on a genome-wide scale. Methods Mol Biol. 2017;1629:15566.
Sotelo-Silveira M, Chávez Montes RA, Sotelo-Silveira JR, Marsch-Martínez N, de Folter S. Entering the next dimension: plant genomes in 3D. Trends Plant Sci. 2018;23:598–612.
Article CAS PubMed Google Scholar
Grob S, Grossniklaus U. Invasive DNA elements modify the nuclear architecture of their insertion site by KNOT-linked silencing in Arabidopsis thaliana Genome Biol. 2019;20:120.
Article PubMed PubMed Central Google Scholar
Fullwood MJ, Liu MH, Pan YF, Liu J, Xu H, Mohamed YB, Orlov YL, Velkov S, Ho A, Mei PH, et al. An oestrogen-receptor-alpha-bound human chromatin interactome. Nature. 2009;462:58–64.
Article CAS PubMed PubMed Central Google Scholar
Dixon J, Selvaraj S, Yue F, Kim A, Li Y, Shen Y, Hu M, Liu J, Ren B. Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature. 2012;485:376–80.
Article CAS PubMed PubMed Central Google Scholar
Zheng H, Xie W. The role of 3D genome organization in development and cell differentiation. Nat Rev Mol Cell Biol. 2019;20:535–50.
Article CAS PubMed Google Scholar
Hug CB, Grimaldi AG, Kruse K, Vaquerizas JM. Chromatin architecture emerges during zygotic genome activation independent of transcription. Cell. 2017;169:216–28.
Article CAS PubMed Google Scholar
Torosin NS, Anand A, Golla TR, Cao W, Ellison CE. 3D genome evolution and reorganization in the Drosophila melanogaster species group. PLoS Genet. 2020;16.
Article CAS PubMed PubMed Central Google Scholar
Fishman V, Battulin N, Nuriddinov M, Maslova A, Zlotina A, Strunov A, Chervyakova D, Korablev A, Serov O, Krasikova A. 3D organization of chicken genome demonstrates evolutionary conservation of topologically associated domains and highlights unique architecture of erythrocytes' chromatin. Nucleic Acids Res. 2019;47:648–65.
Article CAS PubMed Google Scholar
Krefting J, Andrade-Navarro MA, Ibn-Salem J. Evolutionary stability of topologically associating domains is associated with conserved gene regulation. BMC Biol. 2018;16:87.
Article PubMed PubMed Central Google Scholar
Lukyanchikova V, Nuriddinov M, Belokopytova P, Taskina A, Liang J, Reijnders M, Ruzzante L, Feron R, Waterhouse RM, Wu Y, et al. Anopheles mosquitoes reveal new principles of 3D genome organization in insects. Nat Commun. 2022;13:1960.
Article CAS PubMed PubMed Central Google Scholar
Corbo M, Damas J, Bursell MG, Lewin HA. Conservation of chromatin conformation in carnivores. Proc Natl Acad Sci U S A. 2022;119.
Article CAS PubMed PubMed Central Google Scholar
Wendel JF, Brubaker C, Seelanan T. The Origin and Evolution of Gossypium In: Physiology of Cotton. 2009. p. 1–18.
Grover CE, Arick MA 2nd, Conover JL, Thrash A, Hu G, Sanders WS, Hsu CY, Naqvi RZ, Farooq M, Li X, et al. Comparative genomics of an unusual biogeographic disjunction in the cotton tribe (Gossypieae) yields insights into genome downsizing. Genome Biol Evol. 2017;9:3328–44.
Article CAS PubMed PubMed Central Google Scholar
Udall JA, Long E, Ramaraj T, Conover JL, Yuan D, Grover CE, Gong L, Arick MA II, Masonbrink RE, Peterson DG, Wendel JF. The genome sequence of Gossypioides kirkii Illustrates a descending dysploidy in plants. Front Plant Sci. 2019;10:1541.
Article PubMed PubMed Central Google Scholar
Wendel JF, Grover CE. Taxonomy and evolution of the cotton genus, Gossypium In: Cotton. 2015. p. 25–44.
Hu G, Grover CE, Jareczek J, Yuan D, Dong Y, Miller E, Conover JL, Wendel JF. Correction to: evolution and diversity of the cotton genome. In Cotton Precision Breeding. Rahman Mu, Zafar Y, Zhang T, editors. Cham: Springer International Publishing; 2021. p. C1. https://doi.org/10.1007/978-3-030-64504-5_18.
Gerstel DU. Chromosomal translocations in interspecific hybrids of the genus Gossypium Evolution. 1953;7:233–4.
Huang G, Wu Z, Percy RG, Bai M, Zhu Y. Genome sequence of Gossypium herbaceum and genome updates of Gossypium arboreum and Gossypium hirsutum provide insights into cotton A-genome evolution. Nat Genet. 2020;52:516–24.
Article CAS PubMed PubMed Central Google Scholar
Udall JA, Long E, Hanson C, Yuan D, Ramaraj T, Conover JL, Gong L, Arick MA, Grover CE, Peterson DG, Wendel JF. De novo genome sequence assemblies of Gossypium raimondii and Gossypium turneri G3 (Bethesda). 2019;9:3079–85.
留言 (0)