Cotton genome evolution and features of its structural and functional organization

  • Ksenia Strygina Federal Research Center N.I. Vavilov All-Russian Institute of Plant Genetic Resources, Bol'shaya Morskaya ul., 42–44, Saint Petersburg, 190000, Russian Federation https://orcid.org/0000-0001-6938-1348
  • Elena Khlestkina Federal Research Center N.I. Vavilov All-Russian Institute of Plant Genetic Resources, Bol'shaya Morskaya ul., 42–44, Saint Petersburg, 190000, Russian Federation https://orcid.org/0000-0002-8470-8254
  • Larisa Podolnaya Federal Research Center N.I. Vavilov All-Russian Institute of Plant Genetic Resources, Bol'shaya Morskaya ul., 42–44, Saint Petersburg, 190000, Russian Federation https://orcid.org/0000-0002-4962-1989

Abstract

Allotetraploid cotton Gossypium hirsutum L. is not only an important crop, but also a model organism used to study such processes as polyploidization, plant genome evolution and the influence of polyploidy on gene expression. The present article provides a review of studies devoted to the taxonomy of the genus Gossypium, the evolution of the genomes of its representatives (including 45 diploid and 7 allotetraploid species), and the functional divergence of duplicated copies of the same genes in allotetraploid species. The discussion concerns the areas of individual species’ origin, as well as the reasons of the high variation in genome size (from ~880 Mb to ~2400 Mb), which was influenced by both full-genome duplications and the spread of mobile genetic elements. The data support the fact that the expression of genes in allotetraploid cotton changes as a result of polyploidization, and that one of the two subgenomes dominates in the formation of one or another trait. The considered data shed light on the features of the evolution of plant genes and genomes.

Keywords:

Allopolyploid genome, cotton, evolution, functional divergence, gene duplication, Gossypium, homoeologous genes, mobile genetic elements

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References

Adams, K. L., Cronn, R., Percifield, R., and Wendel, J. F. 2003. Genes duplicated by polyploidy show unequal contributions to the transcriptome and organ-specific reciprocal silencing. Proceedings of the National Academy of Sciences USA 100(8):4649–4654. https://doi.org/10.1073/pnas.0630618100

Adams, K. L., Percifield, R., and Wendel, J. F. 2004. Organ-specific silencing of duplicated genes in a newly synthesized cotton allotetraploid. Genetics 168(4):2217–2226. https://doi.org/10.1534/genetics.104.033522

Alix, K., Gérard, P. R., Schwarzacher, T., and Heslop-Harrison, J. S. (Pat). 2017. Polyploidy and interspecific hybridization: Partners for adaptation, speciation and evolution in plants. Annals of Botany 120(2):183–194. https://doi.org/10.1093/aob/mcx079

Bennetzen, J. L., Ma, J., and Devos, K. M. 2005. Mechanisms of recent genome size variation in flowering plants. Annals of Botany 95(1):127–132. https://doi.org/10.1093/aob/mci008

Birchler, J. A., Riddle, N. C., Auger, D. L., and Veitia, R. A. 2005. Dosage balance in gene regulation: Biological implications. Trends in Genetics 21(4):219–226. https://doi.org/10.1016/j.tig.2005.02.010

Bowers, J. E., Chapman, B. A., Rong, J., and Paterson, A. H. 2003. Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events. Nature 422(6930):433–438. https://doi.org/10.1038/nature01521

Brubaker, C. L., Paterson, A. H., and Wendel, J. F. 1999. Comparative genetic mapping of allotetraploid cotton and its diploid progenitors. Genome 42(2):184–203. https://doi.org/10.1139/g98-118

Buggs, R. J. A., Chamala, S., Wu, W., Gao, L., May, G. D., Schnable, P. S., Soltis, D. E., Soltis, P. S., and Barbazuk, W. B. 2010. Characterization of duplicate gene evolution in the recent natural allopolyploid Tragopogon miscellus by next-generation sequencing and Sequenom iPLEX MassARRAY genotyping. Molecular Ecology 19:132–146. https://doi.org/10.1111/j.1365-294X.2009.04469.x

Campbell, B. T., Saha, S., Percy, R., Frelichowski, J., Jenkins, J. N., Park, W., Mayee, C. D., Gotmare, V., Dessauw, D., Giband, M., Du, X., Jia, Y., Constable, G., Dillon, S., Abdurakhmonov, I. Y., Abdukarimov, A., Rizaeva, S. M., Adullaev, A., Barroso, P. A. V., Pádua, J. G., Hoffmann, L. V., and Podolnaya, L. 2010. Status of the global cotton germplasm resources. Crop Science 50(4):1161–1179. https://doi.org/10.2135/cropsci2009.09.0551

Chang, P. L., Dilkes, B. P., McMahon, M., Comai, L., and Nuzhdin, S. V. 2010. Homoeolog-specific retention and use in allotetraploid Arabidopsis suecica depends on parent of origin and network partners. Genome Biology 11(12):R125. https://doi.org/10.1186/gb-2010-11-12-r125

Chaudhary, B., Flagel, L., Stupar, R. M., Udall, J. A., Verma, N., Springer, N. M., and Wendel, J. F. 2009. Reciprocal silencing, transcriptional bias and functional divergence of homeologs in polyploid cotton (Gossypium). Genetics 182(2):503–517. https://doi.org/10.1534/genetics.109.102608

Chen, Z. J. 2007. Genetic and epigenetic mechanisms for gene expression and phenotypic variation in plant polyploids. Annual Review of Plant Biology 58(1):377–406. https://doi.org/10.1146/annurev.arplant.58.032806.103835

Cronn, R. C., Zhao, X., Paterson, A. H., and Wendel, J. F. 1996. Polymorphism and concerted evolution in a tandemly repeated gene family: 5S ribosomal DNA in diploid and allopolyploid cottons. Journal of Molecular Evolution 42(6):685–705. https://doi.org/10.1007/BF02338802

Cronn, R. and Wendel, J. F. 2003. Cryptic trysts, genomic mergers, and plant speciation. New Phytologist 161:133–142. https://doi.org/10.1046/j.1469-8137.2003.00947.x

Cui, X., Liu, F., Liu, Y., Zhou, Z., Wang, C., Zhao, Y., Wang, C., Zhao, Y., Meng, F., Wang, X., Cai, X., Wang, Y., Peng, R., and Wang, K. 2016. Screening and chromosome localization of two cotton BAC clones. Comparative Cytogenetics 10(1):1–15. https://doi.org/10.3897/CompCytogen.v10i1.5304

Davie, H. J. 1933. Cytological studies in the Malvaceae and certain related families. Journal of Genetics 28(1):33–67. https://doi.org/10.1007/BF02981768

Denham, H. J. 1924. The cytology of the cotton plant. I. Microspore formation in sea island cotton. Annals of Botany 38(151):407–432. https://doi.org/10.1093/oxfordjournals.aob.a089908

Dillehay, T. D., Rossen, J., Andres, T. C., and Williams, D. E. 2007. Preceramic adoption of peanut, squash, and cotton in Northern Peru. Science 316(5833):1890–1893. https://doi.org/10.1126/science.1141395

Dong, S. and Adams, K. L. 2011. Differential contributions to the transcriptome of duplicated genes in response to abiotic stresses in natural and synthetic polyploids. New Phytologist 190(4):1045–1057. https://doi.org/10.1111/j.1469-8137.2011.03650.x

Endrizzi, J. E., Turcotte, E. L., and Kohel, R. J. 1985. Genetics, cytology, and evolution of Gossypium. Advances in Genetics 23: 271–375. https://doi.org/10.1016/S0065-2660(08)60515-5

Fang, D. D. 2018. Cotton fiber: physics, chemistry and biology. Springer. https://doi.org/10.1007/978-3-030-00871-0

Flagel E. L. and Wendel F. J. 2010. Evolutionary rate variation, genomic dominance and duplicate gene expression evolution during allotetraploid cotton speciation. New Phytologist 186(1):184–193. https://doi.org/10.1111/j.1469-8137.2009.03107.x

Flagel, L., Udall, J., Nettleton, D., and Wendel, J. 2008. Duplicate gene expression in allopolyploid Gossypium reveals two temporally distinct phases of expression evolution. BMC Biology 6(1):16. https://doi.org/10.1186/1741-7007-6-16

Fryxell, P. A. 1968. A classification of Gossypium L. (Malvaceae). Taxon 18(5):585–591. https://doi.org/10.2307/1218405

Fryxell, P. A. 1971. Phenetic analysis and the phylogeny of the diploid species of Gossypium L. (Malvaceae). Evolution 25:554–562. https://doi.org/10.2307/2407355

Fryxell, P. A. 1978. The natural history of the cotton tribe (Malvaceae, tribe Gossypieae). Texas A and M University Press.

Fryxell, P. A. 1992. A revised taxonomic interpretation of Gossypium L. (Malvaceae). Rheedea 2:108–165.

Fryxell, P. A., Craven, L. A., and Stewart, J. M. 1992. A revision of Gossypium sect. Grandicalyx (Malvaceae), including the description of six new species. Systematic Botany 17(1):91–114. https://doi.org/10.2307/2419068

Gallagher, J. P., Grover, C. E., Rex, K., Moran, M., and Wendel, J. F. 2017. A new species of cotton from Wake Atoll, Gossypium stephensii (Malvaceae). Systematic Botany 42(1):115–123. https://doi.org/10.1600/036364417x694593

Geever, R. F. I., Katterman, F. R. H., and Endrizzi, J. E. 1989. DNA hybridization analyses of a Gossypium allotetraploid and two closely related diploid species. Theoretical and Applied Genetics 77:553–559. https://doi.org/10.1007/BF00274278

Golubets, V. 1991. Wild cottons of Africa and of the Arabian Peninsula. Plant industry, breeding and genetics of industrial plants. Bulletin of applied botany, genetics and plant breeding 144:26–30. (In Russian)

Gong, L., Salmon, A., Yoo, M. J., Grupp, K. K., Wang, Z., Paterson, A. H., and Wendel, J. F. 2012. The cytonuclear dimension of allopolyploid evolution: an example from cotton using rubisco. Molecular Biology and Evolution 29(10):3023–3036. https://doi.org/10.1093/molbev/mss110

Grover, C. E., Zhu, X., Grupp, K. K., Jareczek, J. J., Gallagher, J. P., Szadkowski, E., Seijo, J. G., and Wendel, J. F. 2014. Molecular confirmation of species status for the allopolyploid cotton species, Gossypium ekmanianum Wittmack. Genetic Resources and Crop Evolution 62(1):103–114. https://doi.org/10.1007/s10722-014-0138-x

Grover, C. E., Kim, H. R., Wing, R. A., Paterson, A. H., and Wendel, J. F. 2004. Incongruent patterns of local and global genome size evolution in cotton. Genome Research 14(8):1474–1482. https://doi.org/10.1101/gr.2673204

Grover, C. E, Arick II, M. A., Thrash, A., Conover, J. L., Sanders, W. S., Peterson, D. G., Frelichowski, J. E., Scheffler, J. A., Scheffler, B. E., and Wendel, J. F. 2018. Insights into the evolution of the New World diploid cottons (Gossypium, subgenus Houzingenia) based on genome sequencing. Genome Biology and Evolution 11(1):53–71. https://doi.org/10.1093/gbe/evy256

Guan, X., Pang, M., Nah, G., Shi, X., Ye, W., Stelly, D. M., and Chen, Z. J. 2014. MiR828 and miR858 regulate homoeologous MYB2 gene functions in Arabidopsis trichome and cotton fibre development. Nature Communications 5:3050. https://doi.org/10.1038/ncomms4050

Guan, X., Song, Q., and Chen, Z. J. 2014. Polyploidy and small RNA regulation of cotton fiber development. Trends in Plant Science 19(8):516–528. https://doi.org/10.1016/j.tplants.2014.04.007

Hawkins, J. S., Kim, H. R., Nason, J. D., Wing, R. A., and Wendel, J. F. 2006. Differential lineage-specific amplification of transposable elements is responsible for genome size variation in Gossypium. Genome Research 16(10):1252–1261. https://doi.org/10.1101/gr.5282906

Hendrix, B. and Stewart, J. M. 2005. Estimation of the nuclear DNA content of Gossypium species. Annals of Botany 95(5):789–797. https://doi.org/10.1093/aob/mci078

Hovav, R., Udall, J. A., Chaudhary, B., Rapp, R., Flagel, L., and Wendel, J. F. 2008. Partitioned expression of duplicated genes during development and evolution of a single cell in a polyploid plant. Proceedings of the National Academy of Sciences USA 105(16):6191–6195. https://doi.org/10.1073/pnas.0711569105

Ishida, T., Kurata, T., Okada, K., and Wada, T. 2008. A genetic regulatory network in the development of trichomes and root hairs. Annual Review of Plant Biology 59(1):365–386. https://doi.org/10.1146/annurev.arplant.59.032607.092949

Jiang, C.-X., Wright, R. J., El-Zik, K. M., and Paterson, A. H. 1998. Polyploid formation created unique avenues for response to selection in Gossypium (cotton). Proceedings of the National Academy of Sciences USA 95:4419–4424. https://doi.org/10.1073/pnas.95.8.4419

Jiao, Y. and Paterson, A. H. 2014. Polyploidy-associated genome modifications during land plant evolution. Philosophical Transactions of the Royal Society B: Biological Sciences 369(1648):20130355. https://doi.org/10.1098/rstb.2013.0355

Kim, H. J. 2015. Fiber Biology. In: Cotton, 2nd ed., Agron. Monogr. 57. ASA, CSSA, and SSSA, Madison, pp. 97–128. https://doi.org/10.2134/agronmonogr57.2013.0022

Lawrence, W. J. C. 1931. The secondary association of chromosomes. Cytologia 2(4):352–384. https://doi.org/10.1508/cytologia.2.352

Lemeshev, N. 1991. The problems of origin of allotetraploid cotton species. Plant industry, breeding and genetics of industrial plants. Bulletin of applied botany, genetics and plant breeding 144:3–9. (In Russian)

Li, F., Fan, G., Lu, C., Xiao, G., Zou, C., Kohel, R. J., Ma, Z., Shang, H., Ma, X., Wu, J., Liang, X., Huang, G., Percy, R. G., Liu, K., Yang, W., Chen, W., Du, X., Shi, C., Yuan, Y., Ye, W., Liu, X., Zhang, X., Liu, W., Wei, H., Wei, S., Huang, G., Zhang, X., Zhu, S., Zhang, H., Sun, F., Wang, X., Liang, J., Wang, J., He, Q., Huang, L., Wang, J., Cui, J., Song, G., Wang, K., Xu, X., Yu, J. Z., Zhu, Y., and Yu, S. 2015. Genome sequence of cultivated Upland cotton (Gossypium hirsutum TM-1) provides insights into genome evolution. Nature Biotechnology 33(5):524–530. https://doi.org/10.1038/nbt.3208

Li, F., Fan, G., Wang, K., Sun, F., Yuan, Y., Song, G., Li, Q., Ma, Z., Lu, C., Zou, C., Chen, W., Liang, X., Shang, H., Liu, W., Shi, C., Xiao, G., Gou, C., Ye, W., Xu, X., Zhang, X., Wei, H., Li, Z., Zhang, G., Wang, J., Liu, K., Kohel, R. J., Percy, R. G., Yu, J. Z., Zhu Y. X., Wang J., and Yu, S. 2014. Genome sequence of the cultivated cotton Gossypium arboreum. Nature Genetics 46(6):567–572. https://doi.org/10.1038/ng.2987

Liu, X., Zhao, B., Zheng, H. J., Hu, Y., Lu, G., Yang, C. Q., Chen, J. D., Chen, J. J., Chen D. Y., Zhang, L., Zhou, Y., Wang, L. J., Guo, W. Z., Bai, Y. L., Ruan, J. X., Shangguan, X. X., Mao, Y. B., Shan, C. M., Jiang, J. P., Zhu, Y. Q., Jin, L., Kang, H., Chen, S. T., He, X. L., Wang, R., Wang, Y. Z., Chen, J., Wang, L. J., Yu, S. T., Wang, B. Y., Wei, J., Song, S. C., Lu, X. Y., Gao, Z. C., Gu, W. Y., Deng, X., Ma, D., Wang, S., Liang, W. H., Fang, L., Cai, C. P., Zhu, X. F., Zhou, B. L., Chen, Z. J., Xu, S. H., Zhang, Y. G., Wang, S. Y., Zhang, T. Z., Zhao, G. P., and Chen, X. Y. 2015. Gossypium barbadense genome sequence provides insight into the evolution of extra-long staple fiber and specialized metabolites. Scientific Reports 5:1–14. https://doi.org/10.1038/srep14139

Liu, Z. and Adams, K. L. 2007. Expression partitioning between genes duplicated by polyploidy under abiotic stress and during organ development. Current Biology 17(19):1669–1674. https://doi.org/10.1016/j.cub.2007.08.030

Lu, H., Cui, X., Liu, Z., Liu, Y., Wang, X., Zhou, Z., Cai, X., Zhang, Z., Guo, X., Hua, J., Ma, Z., Wang, X., Zhang, J., Zhang, H., Liu, F., and Wang, K. 2018. Discovery and annotation of a novel transposable element family in Gossypium. BMC Plant Biology 18(1):307. https://doi.org/10.1186/s12870-018-1519-7

Osborn, T. C., Pires, J. C., Birchler, J. A., Auger, D. L., Chen, Z. J., Lee, H.-S., Comai, L., Madlung, A., Doerge, R. W., Colot, V., and Martienssen, R. A. 2003. Understanding mechanisms of novel gene expression in polyploids. Trends in Genetics 19(3):141–147. https://doi.org/10.1016/S0168-9525(03)00015-5

Ozkan, H., Tuna, M., Kilian, B., Mori, N., and Ohta, S. 2010. Genome size variation in diploid and tetraploid wild wheats. AoB Plants plq015. https://doi.org/10.1093/aobpla/plq015

Page, J. T., Huynh, M. D., Liechty, Z. S., Grupp, K., Stelly, D., Hulse, A. M., Ashrafi, H., Deynze, A. V., Wendel, J. F., and Udall, J. A. 2013. Insights into the evolution of cotton diploids and polyploids from whole-genome re-sequencing. G3: GENES, GENOMES, GENETICS 3(10):1809–1818. https://doi.org/10.1534/g3.113.007229

Panchy, N., Lehti-Shiu, M. D., and Shiu, S.-H. 2016. Evolution of gene duplication in plants. Plant Physiology 171(4):2294–2316. https://doi.org/10.1104/pp.16.00523

Pang, M., Woodward, A. W., Agarwal, V., Guan, X., Ha, M., Ramachandran, V., Chen, X., Triplett, B. A., Stelly, D. M., and Chen, Z. J. 2009. Genome-wide analysis reveals rapid and dynamic changes in miRNA and siRNA sequence and expression during ovule and fiber development in allotetraploid cotton (Gossypium hirsutum L.). Genome Biology 10(11):R122. https://doi.org/10.1186/gb-2009-10-11-r122

Paterson, A. H. 2009. Genetics and genomics of cotton. Springer. https://doi.org/10.1007/978-0-387-70810-2

Paterson, A. H., Wendel, J. F., Gundlach, H., Guo, H., Jenkins, J., Jin, D., Llewellyn, D., Showmaker, K. C., Shu, S., Udall, J., Yoo, M. J., Byers, R., Chen, W., Doron-Faigenboim, A., Duke, M. V., Gong, L., Grimwood, J., Grover, C., Grupp, K., Hu, G., Lee, T. H., Li, J., Lin, L., Liu, T., Marler, B. S., Page, J. T., Roberts, A. W., Romanel, E., Sanders, W. S., Szadkowski, E., Tan, X., Tang, H., Xu, C., Wang, J., Wang, Z., Zhang, D., Zhang, L., Ashrafi, H., Bedon, F., Bowers, J. E., Brubaker, C. L., Chee, P. W., Das, S., Gingle, A. R., Haigler, C. H., Harker, D., Hoffmann, L. V., Hovav, R., Jones, D. C., Lemke, C., Mansoor, S., Rahman, M. U., Rainville, L. N., Rambani, A., Reddy, U. K., Rong, J. K., Saranga, Y., Scheffler, B. E., Scheffler, J. A., Stelly, D. M., Triplett, B. A., Deynze, A. V., Vaslin, M. F. S., Waghmare, V. N., Walford, S. A., Wright, R. J., Zaki, E. A., Zhang, T., Dennis, E. S., Mayer, K. F. X., Peterson, D. G., Rokhsar, D. S., Wang, X., and Schmutz, J. 2012. Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres. Nature 492(7429):423–427. https://doi.org/10.1038/nature11798

Pesch, M. and Hülskamp, M. 2009. One, two, three...models for trichome patterning in Arabidopsis? Current Opinion in Plant Biology 12(5):587–592. https://doi.org/10.1016/j.pbi.2009.07.015

Phuphathanaphong, L. 2006. Thepparatia (Malvaceae), a new genus from Thailand. Thai Forest Bulletin (Botany) 34:195–200.

Podolnaya, L. P. 1991. Seedlings morphology of wild species of the genus Gossypium. Plant industry, breeding and genetics of industrial plants. Bulletin of applied botany, genetics and plant breeding 144:18–25. (In Russian)

Qin, Y.-M., Hu, C.-Y., Pang, Y., Kastaniotis, A. J., Hiltunen, J. K., and Zhu, Y.-X. 2007. Saturated very-long-chain fatty acids promote cotton fiber and Arabidopsis cell elongation by activating ethylene biosynthesis. The Plant Cell Online 19(11):3692–3704. https://doi.org/10.1105/tpc.107.054437

Rapp, R. A., Udall, J. A., and Wendel, J. F. 2009. Genomic expression dominance in allopolyploids. BMC Biology 7(1):18. https://doi.org/10.1186/1741-7007-7-18

Renny-Byfield, S., Gallagher, J. P., Grover, C. E., Szadkowski, E., Page, J. T., Udall, J. A., Wang, X., Paterson, A. H., and Wendel, J. F. 2014. Ancient gene duplicates in Gossypium (cotton) exhibit near-complete expression divergence. Genome Biology and Evolution 6(3):559–571. https://doi.org/10.1093/gbe/evu037

Renny-Byfield, S., Gong, L., Gallagher, J. P., and Wendel, J. F. 2015. Persistence of subgenomes in paleopolyploid cotton after 60 my of evolution. Molecular Biology and Evolution 32(4):1063–1071. https://doi.org/10.1093/molbev/msv001

Riddle, N. C. and Birchler, J. A. 2003. Effects of reunited diverged regulatory hierarchies in allopolyploids and species hybrids. Trends in Genetics 19(11):593–597. https://doi.org/10.1016/j.tig.2003.09.009

Rodermel, S., Haley, J., Jiang, C. Z., Tsai, C. H., and Bogorad, L. 1996. A mechanism for intergenomic integration: abundance of ribulose bisphosphate carboxylase small-subunit protein influences the translation of the large-subunit mRNA. Proceedings of the National Academy of Sciences USA 93(9):3881–3885. https://doi.org/10.1073/pnas.93.9.3881

Rong, J., Feltus, F. A., Liu, L., Lin, L., and Paterson, A. H. 2010. Gene copy number evolution during tetraploid cotton radiation. Heredity 105(5):463–472. https://doi.org/10.1038/hdy.2009.192

SanMiguel, P. and Bennetzen, J. L. 1998. Evidence that a recent increase in maize genome size was caused by the massive amplification of intergene retrotransposons. Annals of Botany 82:37–44. https://doi.org/10.1006/anbo.1998.0746

Sattler, M. C., Carvalho, C. R., and Clarindo, W. R. 2016. The polyploidy and its key role in plant breeding. Planta 243(2):281–296. https://doi.org/10.1007/s00425-015-2450-x

Schnable, J. C., Springer, N. M., and Freeling, M. 2011. Differentiation of the maize subgenomes by genome dominance and both ancient and ongoing gene loss. Proceedings of the National Academy of Sciences USA 108(10):4069–4074. https://doi.org/10.1073/pnas.1101368108

Seelanan, T., Brubaker, C. L., Stewart, J. M., Craven, L. A., Wendel, J. F., and Liston, A. 1999. Molecular systematics of Australian Gossypium section Grandicalyx (Malvaceae). Systematic Botany 24(2):183–208. https://doi.org/10.2307/2419548

Seelanan, T., Schnabel, A., and Wendel, J. F. 1997. Congruence and consensus in the cotton tribe (Malvaceae). Systematic Botany 22(2):259–290. https://doi.org/10.2307/2419457

Senchina, D. S., Alvarez, I., Cronn, R. C., Liu, B., Rong, J., Noyes, R. D., Paterson, A. H., Wing, R. A., Wilkins, T. A., and Wendel, J. F. 2003. Rate variation among nuclear genes and the age of polyploidy in Gossypium. Molecular Biology and Evolution 20(4):633–643. https://doi.org/10.1093/molbev/msg065

Shi, Y.-H., Zhu, S.-W., Mao, X.-Z., Feng, J.-X., Qin, Y.-M., Zhang, L., Cheng, J., Wei, L. P., Wang, Z.-Y., and Zhu, Y.-X. 2006. Transcriptome profiling, molecular biological, and physiological studies reveal a major role for ethylene in cotton fiber cell elongation. The Plant Cell 18(3):651–664. https://doi.org/10.1105/tpc.105.040303

Skovsted, A. 1933. Cytological studies in cotton. I. The mitosis and the meiosis in diploid and triploid Asiatic cotton. Annals of Botany 47(186):227–251. https://doi.org/10.1093/oxfordjournals.aob.a090380

Skovsted, A. 1934. Cytological studies in cotton. II. Two interspecific hybrids between Asiatic and new world cottons. Journal of Genetics 28(3):407–424. https://doi.org/10.1007/BF02981763

Small, R. L. and Wendel, J. F. 1999. The mitochondrial genome of allotetraploid cotton (Gossypium L.). The Journal of Heredity 90(1):251–253. https://doi.org/10.1093/jhered/90.1.251

Taliercio, E. W. and Boykin, D. 2007. Analysis of gene expression in cotton fiber initials. BMC Plant Biology 7(1):22. https://doi.org/10.1186/1471-2229-7-22

Tang, H., Woodhouse, M. R., Cheng, F., Schnable, J. C., Pedersen, B. S., Conant, G., Wang, X., Freeling, M., and Pires, J. C. 2012. Altered patterns of fractionation and exon deletions in Brassica rapa support a two-step model of paleohexaploidy. Genetics 190(4):1563–1574. https://doi.org/10.1534/genetics.111.137349

Tiwari, R. S., Zhang, J., and Stewart, J. Mac. 2014. Molecular diversity based on AFLP markers and possible natural hybridization among the Australian arid zone Gossypium species. Australian Journal of Crop Science 8(5):674–679.

Ulloa, M. 2014. The diploid D genome cottons (Gossypium spp.) of the New World. IntechOpen. https://doi.org/10.5772/58387

Vollesen, K. 1987. The native species of Gossypium (Malvaceae) in Africa, Arabia and Pakistan. Kew Bulletin 42(2):337–349. https://doi.org/10.2307/4109688

Walford, S. A., Wu, Y., Llewellyn, D. J., and Dennis, E. S. 2011. GhMYB25-like: A key factor in early cotton fibre development. Plant Journal 65(5):785–797. https://doi.org/10.1111/j.1365-313X.2010.04464.x

Wang, J., Tian, L., Lee, H. S., Wei, N. E., Jiang, H., Watson, B., Madlung, A., Osborn, T. C., Doerge, R. W., Comai, L., and Chen, Z. J. 2006. Genomewide nonadditive gene regulation in Arabidopsis allotetraploids. Genetics 172(1):507–517. https://doi.org/10.1534/genetics.105.047894

Wang, K., Huang, G., and Zhu, Y. 2016. Transposable elements play an important role during cotton genome evolution and fiber cell development. Science China Life Sciences 59(2):112–121. https://doi.org/10.1007/s11427-015-4928-y

Wang, K., Wang, Z., Li, F., Ye, W., Wang, J., Song, G., Yue, Z., Cong, L., Shang, H., Zhu, S., Zou, C., Li, Q., Yuan, Y., Lu, C., Wei, H., Gou, C., Zheng, Z., Yin, Y., Zhang, X., Liu, K., Wang, B., Song, C., Shi, N., Kohel, R. J., Percy, R. G., Yu, J. Z., Zhu, Y. X., Cang, J., and Yu, S. 2012. The draft genome of a diploid cotton Gossypium raimondii. Nature Genetics 44(10):1098–1103. https://doi.org/10.1038/ng.2371

Wang, Q. Q., Liu, F., Chen, X. S., Ma, X. J., Zeng, H. Q., and Yang, Z. M. 2010. Transcriptome profiling of early developing cotton fiber by deep-sequencing reveals significantly differential expression of genes in a fuzzless/lintless mutant. Genomics 96(6):369–376. https://doi.org/10.1016/j.ygeno.2010.08.009

Wang, S., Wang, J.-W., Yu, N., Li, C.-H., Luo, B., Gou, J.-Y., Wang, L.-J., and Chen, X.-Y. 2004. Control of plant trichome development by a cotton fiber MYB gene. The Plant Cell 16(9):2323–2334. https://doi.org/10.1105/tpc.104.024844

Webber, J. M. 1938. Cytology of twin cotton plants. Journal of Agricultural Research 57(2):155–160.

Wendel, J. F. 1989. New World tetraploid cottons contain Old World cytoplasm. Proceedings of the National Academy of Sciences USA 86:4132–4136. https://doi.org/10.1073/pnas.86.11.4132

Wendel, J. F. and Percival, A. E. 1990. Molecular divergence in the Galapagos Islands — Baja California species pair, Gossypium klotzschianum and G . davidsonii (Malvaceae). Plant Systematics and Evolution 171:99–115. https://doi.org/10.1007/BF00940598

Wendel, J. F. and Albert, V. A. 1992. Phylogenetics of the cotton genus (Gossypium): character-state weighted parsimony analysis of chloroplast-DNA restriction site data and its systematic and biogeographic implications. Systematic Botany 17(1):115–143. https://doi.org/10.2307/2419069

Wendel, J. F. and Grover, C. E. 2015. Taxonomy and evolution of the cotton genus, Gossypium. In: Cotton, 2nd ed., Agron. Monogr. 57. ASA, CSSA, and SSSA, Madison, pp. 25–44. https://doi.org/10.2134/agronmonogr57.2013.0020

Wendel, J. F., Olson, P. D., and Stewart, J. M. 1989. Genetic diversity, introgression, and independent domestication of Old World cultivated cottons. American Journal of Botany 76(12):1795. https://doi.org/10.2307/2444478

Wendel, J. F., Stewart, J. M., and Rettig, J. H. 1991. Molecular evidence for homoploid reticulate evolution among Australian species of Gossypium. Evolution 45(3):694. https://doi.org/10.2307/2409921

Wendel, J. F, Brubaker, C., Alvarez, I., Cronn, R., and Stewart, J. M. 2009. Genetics and genomics of cotton. Springer. https://doi.org/10.1007/978-0-387-70810-2

Wendel, J. F. and Cronn, R. C. 2003. Polyploidy and the evolutionary history of cotton. Adavnce in Agronomy 78:139–186. https://doi.org/10.1016/S0065-2113(02)78004-8

Woodhouse, M. R., Schnable, J. C., Pedersen, B. S., Lyons, E., Lisch, D., Subramaniam, S., and Freeling, M. 2010. Following tetraploidy in maize, a short deletion mechanism removed genes preferentially from one of the two homeologs. PLoS Biology 8(6):e1000409. https://doi.org/10.1371/journal.pbio.1000409

Wu, Y., Llewellyn, D. J., White, R., Ruggiero, K., Al-Ghazi, Y., and Dennis, E. S. 2007. Laser capture microdissection and cDNA microarrays used to generate gene expression profiles of the rapidly expanding fibre initial cells on the surface of cotton ovules. Planta 226(6):1475–1490. https://doi.org/10.1007/s00425-007-0580-5

Wu, Y., Machado, A. C., White, R. G., Llewellyn, D. J., and Dennis, E. S. 2006. Expression profiling identifies genes expressed early during lint fibre initiation in cotton. Plant and Cell Physiology 47(1):107–127. https://doi.org/10.1093/pcp/pci228

Wu, Z., Yang, Y., Huang, G., Lin, J., Xia, Y., and Zhu, Y. 2017. Cotton functional genomics reveals global insight into genome evolution and fiber development. Journal of Genetics and Genomics 44(11):511–518. https://doi.org/10.1016/j.jgg.2017.09.009

Xu, Z., Yu, J., Kohel, R. J., Percy, R. G., Beavis, W. D., Main, D., and Yu, J. Z. 2015. Distribution and evolution of cotton fiber development genes in the fibreless Gossypium raimondii genome. Genomics 106(1):61–69. https://doi.org/10.1016/j.ygeno.2015.03.002

Yoo, M. J., Szadkowski, E., and Wendel, J. F. 2013. Homoeolog expression bias and expression level dominance in allopolyploid cotton. Heredity 110(2):171–180. https://doi.org/10.1038/hdy.2012.94

Yu, J., Jung, S., Cheng, C. H., Ficklin, S. P., Lee, T., Zheng, P., Jones, D., Percy, R. G., and Main, D. 2014. CottonGen: A genomics, genetics and breeding database for cotton research. Nucleic Acids Research 42(D1):D1229–D1236. https://doi.org/10.1093/nar/gkt1064

Zhang, F., Zuo, K., Zhang, J., Liu, X., Zhang, L., Sun, X., and Tang, K. 2010. An L1 box binding protein, GbML1, interacts with GbMYB25 to control cotton fibre development. Journal of Experimental Botany 61(13):3599–3613. https://doi.org/10.1093/jxb/erq173

Zhang, T., Hu, Y., Jiang, W., Fang, L., Guan, X., Chen, J., Zhang, J., Saski, C. A., Scheffler, B. E., Stelly, D. M., Hulse-Kemp, A. M., Wan, Q., Liu, B., Liu, C., Wang, S., Pan, M., Wang, Y., Wang, D., Ye, W., Chang, L., Zhang, W., Song, Q., Kirkbride, R. C., Chen, X., Dennis, E., Llewellyn, D. J., Peterson, D. G., Thaxton, P., Jones, D. C., Wang, Q., Xu, X., Zhang, H., Wu, H., Zhou, L., Mei, G., Chen, S., Tian, Y., Xiang, D., Li, X., Ding, J., Zuo, Q., Tao, L., Liu, Y., Li, J., Lin, Y., Hui, Y., Cao, Z., Cai, C., Zhu X., Jiang, Z., Zhou, B., Guo, W., Li, R., and Chen, Z. J. 2015. Sequencing of allotetraploid cotton (Gossypium hirsutum L. acc. TM-1) provides a resource for fiber improvement. Nature Biotechnology 33(5):531–537. https://doi.org/10.1038/nbt.3207

Zhao, X. P., Si, Y., Hanson, R. E., Crane, C. F., Price, H. J., Stelly, D. M., Wendel, J. F., and Paterson, A. H. 1998. Dispersed repetitive DNA has spread to new genomes since polyploid formation in cotton. Genome Research 8(5):479–492. https://doi.org/10.1101/gr.8.5.479

Published
2020-03-27
How to Cite
Strygina, K., Khlestkina, E., & Podolnaya, L. (2020). Cotton genome evolution and features of its structural and functional organization. Biological Communications, 65(1), 15–27. https://doi.org/10.21638/spbu03.2020.102
Section
Review communications

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