Analysis Of Genetic Diversity And Genome In Gossypium Genus

The Genus Gossypium is a plant species that is globally distributed and economically significant,with more than 50 different species.While four species are cultivated and provide natural fibers for the textile industry,most wild species of this genus thrive in tropical or subtropical regions.Despite the importance of this plant,few studies have focused on its genetic diversity,adaptive differentiation,and domestication history.To address this gap in knowledge,we conducted a study to investigate the genomic basis of adaptive radiation and domestication in both diploid and tetraploid species of cotton.Our goal was to produce new insights into the global radiation of this genus and provide resources for the genetic breeding of cotton.The genome of G.klotzschianum(Gklo)was analyzed along with 24 other published genomes of species from the Genus Gossypium in order to gain insights into its speciation.The comparison of the genomes with a reconstructed species tree of the genus revealed numerous regions in the genome that exhibited conflicting phylogenetic relationships among cotton E and D genome species.Additionally,incongruence was observed between the nuclear and chloroplast tree in D genome species of cotton,indicating genetic introgression(GI)and incomplete lineage sorting(ILS)as possible causes.A high-resolution ILS map of recently differentiated lineages-G.davidsonii(Gdav),Gklo,and G.raimondii(Grai)-was then constructed.The results showed that ILS regions were non-randomly distributed across the genome,and strong natural selection was targeting these regions.To assess the impact of ILS on the speciation of Genus Gossypium,then we identified divergence-related differences between the sister species Gklo and Gdav and found that approximately 15.74% of the divergence structure variation(DSV)and12.04% of the speciation-associated genes(SAG)overlapped with ILS signal.Two important environmental adaptation genes,Prx66 and Glyt3,were among the genes that showed overlap with the ILS signal,indicating the involvement of ILS in adaptive radiation in cotton.Three new assemblies of tetraploid cotton species,G.ekmanianum(AD6,Ge),G.stephensii(AD7,Gs),and G.hirsutum race punctatum(AD1,Ghp),were used to investigate the evolutionary divergence of tetraploid cotton species through systematic comparative genomics analysis.The study revealed numerous genomic structural variations that occurred during the differentiation of tetraploid cotton.The researchers also described phenotypic differentiation,genetic isolation,and convergent domestication as factors contributing to species diversity and domestication of cultivated cotton species.Presence/absence variation(PAV)is an important type of genomic structural variation that can result in phenotypic diversity.For example,during the genome differentiation of tetraploid cotton species,a gene encoding a phosphopeptide-binding protein related to fiber length exhibited a changed expression level due to PAV.The study also found that Ghp,a semi-wild cotton genome,showed high tolerance to biotic and abiotic stress.The researchers identified two genes,enoyl-Co A delta isomerase 3 and RAP2-7,which belong to an expanded gene family in the Ghp genome,that may enhance Ghp tolerance to abiotic stress by regulating plant hormone-related biological pathways.The analysis of population genomics has revealed that wild tetraploid cotton species possess greater genetic diversity than cultivated cotton varieties,which could significantly enhance the gene pool for cultivated cotton breeding.The study has also found that upland cotton was domesticated around 9,000 years ago,followed by improvement at 5,400 years ago,while island cotton was domesticated around 4,000 years ago and improved around 300 years ago.Within the 7 populations of tetraploid cotton,approximately 20,000 genomic islands of divergence were discovered,including65 shared islands between Gh W(G.hirsutum race)vs.Gh C(Cultivar of G.hirsutum)and Gb W(Wild type of G.barbadense)vs.Gb C(Cultivar of G.barbadense).These shared islands contain genes such as Gh MML4＿D12,Gh HOX3＿D12,and Gh MML3＿D12,which control fiber initiation,fiber length,and short fiber initiation,respectively.The findings suggest that human convergence selection contributed to the differentiation of Gb-like clade or Gh-like clade populations.The study also identified gene flow,one from G.tomentosum to G.darwinii,and another one from cultivars of upland cotton to cultivars of island cotton.The introgressed region from the cultivar of upland cotton to cultivar of island cotton was under positive selection during cotton improvement process,indicating that gene flow promoted the improvement of island cotton.A segment on chromosome D11 of island cotton was found to have come from cultivars of upland cotton,which contains a QTL locus Cs9＿PF＿21＿(3.82+)related to fiber yield.During the genetic improvement process of island cotton,a selective sweep signal was discovered,which is located on chromosome A10 shared with upland cotton,containing two genes,MADXbox and SOC1,related to the photoperiod of flowering plants.These two genes may have contributed to the global expansion of upland cotton and island cotton.However,further experimental evidence is required to support this conclusion.