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• W3002661013 abstract "Cotton is an important natural fiber crop cultivated worldwide that also provides an ideal model for investigating evolution and domestication of polyploidsCombinations of the latest technologies, such as optical mapping, high-throughput chromosome conformation capture (Hi-C), and Pacific Biosciences (PacBio) long-reads, have been used to generate multiple high-quality reference genomes of diploid and allotetraploid cotton.Comparative population genomics illuminated the genetic history of cotton domestication and identified the genomic variation determining fiber yield, quality, and stress resistance. Cotton (Gossypium spp.) is the most important natural fiber crop worldwide. The diversity of Gossypium species also provides an ideal model for investigating evolution and domestication of polyploids. However, the huge and complex cotton genome hinders genomic research. Technical advances in high-throughput sequencing and bioinformatics analysis have now largely overcome these obstacles, bringing about a new era of cotton genomics. Here, we review recent progress in Gossypium genomics based on whole genome sequencing, resequencing, and comparative genomics, which have provided insights about the genomic basis of fiber biogenesis and the landscape of cotton functional genomics. We address current challenges and present multidisciplinary genomics-enabled breeding strategies covering the breadth of high fiber yield, quality, and environmental resilience for future cotton breeding programs. Cotton (Gossypium spp.) is the most important natural fiber crop worldwide. The diversity of Gossypium species also provides an ideal model for investigating evolution and domestication of polyploids. However, the huge and complex cotton genome hinders genomic research. Technical advances in high-throughput sequencing and bioinformatics analysis have now largely overcome these obstacles, bringing about a new era of cotton genomics. Here, we review recent progress in Gossypium genomics based on whole genome sequencing, resequencing, and comparative genomics, which have provided insights about the genomic basis of fiber biogenesis and the landscape of cotton functional genomics. We address current challenges and present multidisciplinary genomics-enabled breeding strategies covering the breadth of high fiber yield, quality, and environmental resilience for future cotton breeding programs. As the world’s most important fiber crop and a major source of seed oil and protein, cotton is cultivated in more than 75 countries around the globe [1.Chen Z.J. et al.Toward sequencing cotton (Gossypium) genomes.Plant Physiol. 2007; 145: 1303-1310Crossref PubMed Scopus (296) Google Scholar]. Cotton fibers are seed trichomes, up to 65 mm long, composed of almost pure cellulose, and provide a unique single-celled model system for studying cell elongation and cell wall biogenesis [2.Lee J.J. et al.Gene expression changes and early events in cotton fibre development.Ann. Bot. 2007; 100: 1391-1401Crossref PubMed Scopus (251) Google Scholar]. The Gossypium genus is extraordinarily diverse, with eight diploid genome groups (A–G, and K) and one allopolyploid group (AD) [3.Li F. et al.Genome sequence of the cultivated cotton Gossypium arboreum.Nat. Genet. 2014; 46: 567-572Crossref PubMed Scopus (618) Google Scholar,4.Wendel J.F. New World tetraploid cottons contain Old World cytoplasm.Proc. Natl. Acad. Sci. U. S. A. 1989; 86: 4132-4136Crossref PubMed Google Scholar]. Hybridization and polyploidization of two parental diploids, an A genome-like species with a D genome-like species, has resulted in at least seven allotetraploid species. Two allotetraploid species, Gossypium hirsutum and Gossypium barbadense, evolved independently; these two account for over 90% of annual commercial fiber production. Gossypium is ideal for investigating the origin, evolution, and domestication of polyploids [5.Qin Y.M. Zhu Y.X. How cotton fibers elongate: a tale of linear cell-growth mode.Curr. Opin. Plant Biol. 2011; 14: 106-111Crossref PubMed Scopus (188) Google Scholar, 6.Hu G. Wendel J.F. Cis-trans controls and regulatory novelty accompanying allopolyploidization.New Phytol. 2019; 221: 1691-1700Crossref PubMed Scopus (29) Google Scholar, 7.Wendel J.F. et al.The long and short of doubling down: polyploidy, epigenetics, and the temporal dynamics of genome fractionation.Curr. Opin. Genet. Dev. 2018; 49: 1-7Crossref PubMed Scopus (101) Google Scholar]. Whole genome sequencing (WGS) is now the basic foundation for evolutionary, functional, quantitative trait loci (QTL) (see Glossary) mapping and population genomic studies [8.Fang L. et al.Genomic insights into divergence and dual domestication of cultivated allotetraploid cottons.Genome Biol. 2017; 18: 33Crossref PubMed Scopus (71) Google Scholar, 9.Shen C. et al.Population genomics reveals a fine-scale recombination landscape for genetic improvement of cotton.Plant J. 2019; 99: 494-505Crossref PubMed Scopus (19) Google Scholar, 10.Tang S.Y. et al.Construction of genetic map and QTL analysis of fiber quality traits for upland cotton (Gossypium hirsutum L.).Euphytica. 2015; 201: 195-213Crossref Scopus (70) Google Scholar, 11.Wang B.H. et al.QTL mapping for plant architecture traits in upland cotton using RILs and SSR markers.Yi Chuan Xue Bao. 2006; 33: 161-170PubMed Google Scholar]. Due to their huge and complex genomes, high-quality genome assembly of Gossypium species is a challenging task. Draft genomes of cultivated tetraploids and their diploid progenitors have been published; however, the intergenic DNA such as telomeres, centromeres, and repeat-rich regions are poorly represented, resulting in uncertainty about functionally important genomic features. To explore the global genetic and molecular basis of the origin, speciation, and diversification of Gossypium species and to advance genomics-enabled breeding requires a detailed and robust understanding of genomic organization. Recent advances in sequencing technology, decreasing cost of high-throughput sequencing, and increasing efforts toward functional genomics have promoted rapid and impressive cotton genomics research. Some recent studies covering high-quality de novo assembly of Gossypium genomes and resequencing of hundreds of diverse cotton accessions, including modern cultivars, landraces, and wild relatives, have led to a better understanding of key facets of Gossypium genomics (Figure 1). Comparative genomics studies have highlighted genomic changes involved in cotton domestication and functional genomics identified candidate genes controlling the biology of important agronomic traits. Here, we review the recent progress and advances of cotton genomics, provide new insights into cotton fiber development, and outline future perspectives for genomics-enabled cotton breeding. The Gossypium genus comprises approximately 45 diploid and seven tetraploid species [12.Wang K. et al.The draft genome of a diploid cotton Gossypium raimondii.Nat. Genet. 2012; 44: 1098-1103Crossref PubMed Scopus (691) Google Scholar]. The diploid species experienced extensive chromosomal evolution in terms of rearrangements and structural differences during the process of diversification. All of the diploid species have a total of 13 chromosomes, but the genome sizes of some species are up to threefold larger than those of other species [1.Chen Z.J. et al.Toward sequencing cotton (Gossypium) genomes.Plant Physiol. 2007; 145: 1303-1310Crossref PubMed Scopus (296) Google Scholar]. The D genome is the smallest and has the simplest genomic features. Importantly, the D genome (G. raimondii) together with the A genome (Gossypium arboreum or Gossypium herbaceum) is the likely ancestor of G. hirsutum and G. barbadense, two important cotton fiber-producing species [4.Wendel J.F. New World tetraploid cottons contain Old World cytoplasm.Proc. Natl. Acad. Sci. U. S. A. 1989; 86: 4132-4136Crossref PubMed Google Scholar]. G. raimondii was therefore selected as the first species for WGS by two different research groups [12.Wang K. et al.The draft genome of a diploid cotton Gossypium raimondii.Nat. Genet. 2012; 44: 1098-1103Crossref PubMed Scopus (691) Google Scholar,13.Paterson A.H. et al.Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres.Nature. 2012; 492: 423-427Crossref PubMed Scopus (834) Google Scholar]. The genome assembly length of G. raimondii was reported in 2012 to be approximately 740 Mb, with a contig N50 of 44.9 and 135.5 kb, coupled with ~60% annotation as repeated sequences; thousands of gaps existed in these assemblies [12.Wang K. et al.The draft genome of a diploid cotton Gossypium raimondii.Nat. Genet. 2012; 44: 1098-1103Crossref PubMed Scopus (691) Google Scholar,13.Paterson A.H. et al.Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres.Nature. 2012; 492: 423-427Crossref PubMed Scopus (834) Google Scholar]. The draft genome of diploid G. arboreum was released in 2014. Next generation sequencing technologies (NGS, Illumina) was used to generate the contigs and the assembly was fragmented with 40 381 contigs (contig N50 equal to 72 kb). The annotated gene numbers from G. arboreum are similar to those of G. raimondii, despite the assembly size of G. arboreum being more than twice that of G. raimondii [3.Li F. et al.Genome sequence of the cultivated cotton Gossypium arboreum.Nat. Genet. 2014; 46: 567-572Crossref PubMed Scopus (618) Google Scholar]. With the successful sequencing and assembly of two extant diploid progenitors, it was imperative to sequence the genomes of cultivated allotetraploid cotton. In 2015, the drafts of G. hirsutum TM-1 were released in two independent studies. Like G. raimondii and G. arboreum, NGS technologies were used to generate the contigs. The draft genome assemblies were highly fragmented (Figure 1). Comparative genome analyses showed that the Dt and At subgenomes had highly collinear relationships with the genomes of G. raimondii and G. arboreum, respectively [14.Li F. et al.Genome sequence of cultivated upland cotton (Gossypium hirsutum TM-1) provides insights into genome evolution.Nat. Biotechnol. 2015; 33: 524-530Crossref PubMed Scopus (704) Google Scholar,15.Zhang T. et al.Sequencing of allotetraploid cotton (Gossypium hirsutum L. acc. TM-1) provides a resource for fiber improvement.Nat. Biotechnol. 2015; 33: 531-537Crossref PubMed Scopus (1030) Google Scholar]. The allotetraploid cotton G. barbadense produces high-quality, extra-long fibers and shares a common progenitor with G. hirsutum; however, these species have substantial differences in agronomic traits. Two groups published draft genomes for G. barbadense, which together paved the way to understanding the genomic differences between the two tetraploid cotton species [16.Liu X. et al.Gossypium barbadense genome sequence provides insight into the evolution of extra-long staple fiber and specialized metabolites.Sci. Rep. 2015; 5: 14139Crossref PubMed Scopus (181) Google Scholar,17.Yuan D. et al.The genome sequence of sea-island cotton (Gossypium barbadense) provides insights into the allopolyploidization and development of superior spinnable fibres.Sci. Rep. 2015; 5: 17662Crossref PubMed Scopus (191) Google Scholar]. The lack of reliable genomic information has been a major limitation for cotton improvement through breeding. Our team updated the G. arboreum genome using PacBio long reads, thereby improving the sequence continuity by ~15 fold (Contig N50: 1100 versus 72 kb) and increasing assembly size from 1561 to 1710 Mb. The newly assembled sequences were mainly repeated sequence (85%) and the long terminal repeat (LTR) sequences were well-assembled. Moreover, misassembly was effectively avoided in the updated reference genome, illustrating that the A2 genome had a strong collinearity with the D genome and A subgenome of G. hirsutum. In addition, updated reference sequences demonstrated some interesting findings. For instance, as the less divergent LTRs (young LTRs) were well-assembled, we found that most LTRs in the A2 genome were young and active; a similar situation was also found in the At subgenome of G. hirsutum, indicating that most of the transposable elements, which had expanded in the progenitor genomes, were subsequently retained after allopolyploid formation [18.Du X. et al.Resequencing of 243 diploid cotton accessions based on an updated A genome identifies the genetic basis of key agronomic traits.Nat. Genet. 2018; 50: 796-802Crossref PubMed Scopus (258) Google Scholar]. Two recent studies updated the genomes of important cultivated allotetraploid cottons G. hirsutum and G. barbadense using advanced strategies. Both had high-quality assemblies along with improved assembly of centromere regions [19.Wang M. et al.Reference genome sequences of two cultivated allotetraploid cottons, Gossypium hirsutum and Gossypium barbadense.Nat. Genet. 2019; 51: 224-229Crossref PubMed Scopus (281) Google Scholar,20.Hu Y. et al.Gossypium barbadense and Gossypium hirsutum genomes provide insights into the origin and evolution of allotetraploid cotton.Nat. Genet. 2019; 51: 739-748Crossref PubMed Scopus (292) Google Scholar]. Wang et al. combined an optical map with high-throughput chromosome conformation capture (Hi-C) and PacBio long-reads to generate the reference genomes of two cultivated tetraploid species. The sequence contiguity improved from less than 80 kb to approximately 2000 kb. Furthermore, a study by Wang et al. [19.Wang M. et al.Reference genome sequences of two cultivated allotetraploid cottons, Gossypium hirsutum and Gossypium barbadense.Nat. Genet. 2019; 51: 224-229Crossref PubMed Scopus (281) Google Scholar] confirmed and extended the previously observed phenomenon that G. hirsutum and G. barbadense are interfertile, but their interspecific hybrids exhibit genetic breakdown during segregation (Box 1). Their study found large interspecies paracentric/pericentric inversions across 14 chromosomes that probably occurred after polyploidization. Large-scale rearrangements would have restricted chromosome recombination in the interspecies hybrids and biased the phenotype. Interspecies genetic breakdown with the introgression from G. barbadense to G. hirsutum was observed across 26 chromosomes. Hu et al. [20.Hu Y. et al.Gossypium barbadense and Gossypium hirsutum genomes provide insights into the origin and evolution of allotetraploid cotton.Nat. Genet. 2019; 51: 739-748Crossref PubMed Scopus (292) Google Scholar] combined NGS, a 10 × genomics library, optical maps, and Hi-C to update G. hirsutum and G. barbadense genome assemblies. This study did not significantly improve sequence contiguity, but the assembly size increased compared with previously reported assemblies. For example, the contig size of the G. hirsutum assembly was increased from 2160 to 2211 Mb, which is only slightly shorter than that of Wang et al. (2282 Mb). Hu et al. illustrated that the Copia elements (LTR type) in coding DNA sequence are the major reason for presence/absence variants (PAV) between the two allotetraploid cotton species. Moreover, the expression level of genes with LTR insertions was lower than that of genes with PAVs. Among other inconsistencies between these two studies, large-scale paracentric/pericentric inversions identified by Wang et al. were not reproduced in the Hu et al. study, a discrepancy which will require further investigation.Box 1Dynamics of Cotton Fiber ElongationCotton fibers elongate through a unique tip-biased diffuse growth mode [84.Yu Y. et al.Live-cell imaging of the cytoskeleton in elongating cotton fibres.Nat. Plants. 2019; 5: 498-504Crossref PubMed Scopus (22) Google Scholar]. Asymmetric domestication, phytohormonal changes, reactive oxygen species (ROS) homeostasis, and differential expression patterns of key regulatory genes together regulate fiber elongation in present-day cultivated cotton. Appropriate amounts of ethylene promote fiber elongation; however, high ethylene levels in G. raimondii ovules during the elongation stage are known to restrict fiber growth [3.Li F. et al.Genome sequence of the cultivated cotton Gossypium arboreum.Nat. Genet. 2014; 46: 567-572Crossref PubMed Scopus (618) Google Scholar,85.Shi Y.H. et al.Transcriptome profiling, molecular biological, and physiological studies reveal a major role for ethylene in cotton fiber cell elongation.Plant Cell. 2006; 18: 651-664Crossref PubMed Scopus (431) Google Scholar]. Large amounts of ethylene will induce overproduction of ROS [86.Qin Y.M. et al.The ascorbate peroxidase regulated by H2O2 and ethylene is involved in cotton fiber cell elongation by modulating ROS homeostasis.Plant Signal. Behav. 2008; 3: 194-196Crossref PubMed Scopus (42) Google Scholar] and high ROS concentrations can initiate an early transition to secondary cell wall synthesis and thereby terminate fiber elongation (Figure IA) [37.Wang M. et al.Asymmetric subgenome selection and cis-regulatory divergence during cotton domestication.Nat. Genet. 2017; 49: 579-587Crossref PubMed Scopus (227) Google Scholar]. G. hirsutum and G. barbadense originated from a common allotetraploid ancestor and independently domesticated into commonly cultivated cotton as fiber crops [87.Jiang Y. et al.Overexpression of GhSusA1 increases plant biomass and improves cotton fiber yield and quality.Plant Biotechnol. J. 2012; 10: 301-312Crossref PubMed Scopus (103) Google Scholar,88.Arpat A.B. et al.Functional genomics of cell elongation in developing cotton fibers.Plant Mol. Biol. 2004; 54: 911-929Crossref PubMed Scopus (221) Google Scholar]; however, they were improved toward different goals. A direct genomic comparison of G. hirsutum and G. barbadense identified many paracentric/pericentric inversions and presence/absence variations (PAVs) containing 220 fiber-related genes that were highly expressed during cotton fiber elongation. These specific structural variants were found to be associated with functional differences and may contribute to the formation of superior fiber quality in G. barbadense [19.Wang M. et al.Reference genome sequences of two cultivated allotetraploid cottons, Gossypium hirsutum and Gossypium barbadense.Nat. Genet. 2019; 51: 224-229Crossref PubMed Scopus (281) Google Scholar]. Furthermore, the evolution rate in G. barbadense was faster than that in G. hirsutum, and introgression events from local wild G. hirsutum races into G. barbadense, which contain genes related to fiber and seed development, may have helped confer the long fiber trait [8.Fang L. et al.Genomic insights into divergence and dual domestication of cultivated allotetraploid cottons.Genome Biol. 2017; 18: 33Crossref PubMed Scopus (71) Google Scholar].A prolonged fiber elongation phase likely leads to longer fibers in G. barbadense. Furthermore, cell turgor pressure drives fiber cell elongation. The sucrose transporter (GbTST1), vacuole-localized vacuolar invertase (VIN), Na+/H+ antiporter (GbNHX1), and aluminum-activated malate transporter (GbALMT16) genes had a longer period of expression in the tonoplast of G. barbadense fibers than the corresponding genes in G. hirsutum. These transporters pump more sucrose, potassium ions (K+), and malate (M–) into the vacuole and enhance the osmotic potential required for fiber elongation. Furthermore, the plasmodesmata remain open for a longer time in of G. barbadense than in G. hirsutum, which enables import of sucrose from seed coat cells into developing fiber cells, which ultimately enables increased osmotic potential through hydrolysis into fructose and glucose [89.Kim H.J. Triplett B.A. Cotton fiber growth in planta and in vitro. Models for plant cell elongation and cell wall biogenesis.Plant Physiol. 2001; 127: 1361-1366Crossref PubMed Scopus (475) Google Scholar, 90.Ruan Y.L. et al.Genotypic and developmental evidence for the role of plasmodesmatal regulation in cotton fiber elongation mediated by callose turnover.Plant Physiol. 2004; 136: 4104-4113Crossref PubMed Scopus (122) Google Scholar, 91.Ruan Y.L. et al.The control of single-celled cotton fiber elongation by developmentally reversible gating of plasmodesmata and coordinated expression of sucrose and K+ transporters and expansin.Plant Cell. 2001; 13: 47-60PubMed Google Scholar]. More accumulation of soluble sugar, K+, and M– cause higher cell turgor pressure, which drives the fiber elongation in G. barbadense [20.Hu Y. et al.Gossypium barbadense and Gossypium hirsutum genomes provide insights into the origin and evolution of allotetraploid cotton.Nat. Genet. 2019; 51: 739-748Crossref PubMed Scopus (292) Google Scholar] (Figure IB). Cotton fibers elongate through a unique tip-biased diffuse growth mode [84.Yu Y. et al.Live-cell imaging of the cytoskeleton in elongating cotton fibres.Nat. Plants. 2019; 5: 498-504Crossref PubMed Scopus (22) Google Scholar]. Asymmetric domestication, phytohormonal changes, reactive oxygen species (ROS) homeostasis, and differential expression patterns of key regulatory genes together regulate fiber elongation in present-day cultivated cotton. Appropriate amounts of ethylene promote fiber elongation; however, high ethylene levels in G. raimondii ovules during the elongation stage are known to restrict fiber growth [3.Li F. et al.Genome sequence of the cultivated cotton Gossypium arboreum.Nat. Genet. 2014; 46: 567-572Crossref PubMed Scopus (618) Google Scholar,85.Shi Y.H. et al.Transcriptome profiling, molecular biological, and physiological studies reveal a major role for ethylene in cotton fiber cell elongation.Plant Cell. 2006; 18: 651-664Crossref PubMed Scopus (431) Google Scholar]. Large amounts of ethylene will induce overproduction of ROS [86.Qin Y.M. et al.The ascorbate peroxidase regulated by H2O2 and ethylene is involved in cotton fiber cell elongation by modulating ROS homeostasis.Plant Signal. Behav. 2008; 3: 194-196Crossref PubMed Scopus (42) Google Scholar] and high ROS concentrations can initiate an early transition to secondary cell wall synthesis and thereby terminate fiber elongation (Figure IA) [37.Wang M. et al.Asymmetric subgenome selection and cis-regulatory divergence during cotton domestication.Nat. Genet. 2017; 49: 579-587Crossref PubMed Scopus (227) Google Scholar]. G. hirsutum and G. barbadense originated from a common allotetraploid ancestor and independently domesticated into commonly cultivated cotton as fiber crops [87.Jiang Y. et al.Overexpression of GhSusA1 increases plant biomass and improves cotton fiber yield and quality.Plant Biotechnol. J. 2012; 10: 301-312Crossref PubMed Scopus (103) Google Scholar,88.Arpat A.B. et al.Functional genomics of cell elongation in developing cotton fibers.Plant Mol. Biol. 2004; 54: 911-929Crossref PubMed Scopus (221) Google Scholar]; however, they were improved toward different goals. A direct genomic comparison of G. hirsutum and G. barbadense identified many paracentric/pericentric inversions and presence/absence variations (PAVs) containing 220 fiber-related genes that were highly expressed during cotton fiber elongation. These specific structural variants were found to be associated with functional differences and may contribute to the formation of superior fiber quality in G. barbadense [19.Wang M. et al.Reference genome sequences of two cultivated allotetraploid cottons, Gossypium hirsutum and Gossypium barbadense.Nat. Genet. 2019; 51: 224-229Crossref PubMed Scopus (281) Google Scholar]. Furthermore, the evolution rate in G. barbadense was faster than that in G. hirsutum, and introgression events from local wild G. hirsutum races into G. barbadense, which contain genes related to fiber and seed development, may have helped confer the long fiber trait [8.Fang L. et al.Genomic insights into divergence and dual domestication of cultivated allotetraploid cottons.Genome Biol. 2017; 18: 33Crossref PubMed Scopus (71) Google Scholar]. A prolonged fiber elongation phase likely leads to longer fibers in G. barbadense. Furthermore, cell turgor pressure drives fiber cell elongation. The sucrose transporter (GbTST1), vacuole-localized vacuolar invertase (VIN), Na+/H+ antiporter (GbNHX1), and aluminum-activated malate transporter (GbALMT16) genes had a longer period of expression in the tonoplast of G. barbadense fibers than the corresponding genes in G. hirsutum. These transporters pump more sucrose, potassium ions (K+), and malate (M–) into the vacuole and enhance the osmotic potential required for fiber elongation. Furthermore, the plasmodesmata remain open for a longer time in of G. barbadense than in G. hirsutum, which enables import of sucrose from seed coat cells into developing fiber cells, which ultimately enables increased osmotic potential through hydrolysis into fructose and glucose [89.Kim H.J. Triplett B.A. Cotton fiber growth in planta and in vitro. Models for plant cell elongation and cell wall biogenesis.Plant Physiol. 2001; 127: 1361-1366Crossref PubMed Scopus (475) Google Scholar, 90.Ruan Y.L. et al.Genotypic and developmental evidence for the role of plasmodesmatal regulation in cotton fiber elongation mediated by callose turnover.Plant Physiol. 2004; 136: 4104-4113Crossref PubMed Scopus (122) Google Scholar, 91.Ruan Y.L. et al.The control of single-celled cotton fiber elongation by developmentally reversible gating of plasmodesmata and coordinated expression of sucrose and K+ transporters and expansin.Plant Cell. 2001; 13: 47-60PubMed Google Scholar]. More accumulation of soluble sugar, K+, and M– cause higher cell turgor pressure, which drives the fiber elongation in G. barbadense [20.Hu Y. et al.Gossypium barbadense and Gossypium hirsutum genomes provide insights into the origin and evolution of allotetraploid cotton.Nat. Genet. 2019; 51: 739-748Crossref PubMed Scopus (292) Google Scholar] (Figure IB). Very recently, Udall et al. reported the de novo assembly of the genome of G. raimondii and its close relative Gossypium turneri using PacBio long reads, Hi-C, and Bionano optical mapping technologies, which helped to correct some minor assembly errors in previous version of the G. raimondii genome assembly [21.Udall J.A. et al.De novo genome sequence assemblies of Gossypium raimondii and Gossypium turneri.G3 (Bethesda). 2019; 9: 3079-3085Crossref PubMed Scopus (32) Google Scholar]. Using the same strategy, another group published a draft genome of a disease-resistant species Gossypium australe with a contig N50 of 1.83 Mb [22.Cai Y. et al.Genome sequencing of the Australian wild diploid species Gossypium australe highlights disease resistance and delayed gland morphogenesis.Plant Biotechnol. J. 2019; (Published online September 3, 2019. https://doi.org/10.1111/pbi.13249)Crossref Scopus (26) Google Scholar]. In addition, high-resolution transcriptional landscape of G. arboreum is also available [23.Wang K. et al.Multi-strategic RNA-seq analysis reveals a high-resolution transcriptional landscape in cotton.Nat. Commun. 2019; 10: 4714Crossref PubMed Scopus (41) Google Scholar]. All these studies expand the resources of the cotton genome. Multiple genome assemblies of cotton (tetraploids and their diploid ancestors) are now available, but the effects of domestication and genetic improvement on chromosomes within single species are largely unknown. To address this question, our team assembled new reference genomes of two different genotypes of G. hirsutum [24.Yang Z. et al.Extensive intraspecific gene order and gene structural variations in upland cotton cultivars.Nat. Commun. 2019; 10: 2989Crossref PubMed Scopus (84) Google Scholar]. In these genomes, sequence contiguity improved significantly compared with previous studies (Figure 1). Genomic comparison was used to identify inversions and translocations within the two accessions. Three large-scale inversions on the A08 chromosome clearly divided a core collection of upland cotton into two groups, restricting the meiotic recombination of the heterozygote and subsequent reduction of haplotypes, as well as genetic diversity, and ultimately leading to population divergence in upland cotton. The rearrangements that occurred between the A2 genome (G. arboreum) and the upland cotton At subgenome were shown to be larger than rearrangements between the D genome (G. raimondii) and the upland cotton Dt subgenome, indicating that the bigger A genomes were more active than the smaller D genome. Furthermore, a rearrangement region of more than 620 Mb was identified between G. hirsutum acc.TM-1 At/Dt and the two diploid progenitors. Similarly, the rearrangement region of ~51 Mb between the two upland cotton accessions and ~170 Mb rearrangement region between G. hirsutum and G. barbadense illustrated that the degree of divergence between the genomic sequences of diploid and tetraploid species is greater than between tetraploid species; this also indicated that the degree of divergence between tetraploid species is greater than the degree of intraspecies divergence. These reference genomes deepen our understanding about the nature of cotton genomes, especially in terms structural variation. Despite this significant achievement, researchers could benefit from ongoing efforts to generate high-quality, nearly gap-free reference genome assemblies for representative cottons. Two A genomes evolved spinnable fibers after their divergence from the common ancestor with an F genome [13.Paterson A.H. et al.Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres.Nature. 2012; 492: 423-427Crossref PubMed Scopus (834) Google Scholar]. The merger of ancestral A genome and D genome with no spinnable fibers formed the common ancestor of cultivated allotetraploids, in which the fiber was further improved. Polyploidy followed a natural evolutionary pattern and effects of human selection were superimposed on the evolution of spinnable fiber [13.Paterson" @default.
• W3002661013 created "2020-01-30" @default.
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• W3002661013 date "2020-05-01" @default.
• W3002661013 modified "2023-10-14" @default.
• W3002661013 title "Gossypium Genomics: Trends, Scope, and Utilization for Cotton Improvement" @default.
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• W3002661013 doi "https://doi.org/10.1016/j.tplants.2019.12.011" @default.
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