Nucleotide Evolution And Genetic Relationships In The Genus Gossypium Based On Chloroplast Genomes

Cotton is one of the most important economic and fiber crops in the world,it has experienced a long-term of evolution and domestication process from wild cotton to cultivated cotton.However,the plastid genome variation and genetic relationship in the process of cotton evolution and domestication are still controversial.In this study,72 maternally inherited plastid genome sequences of cotton samples were collected,and their molecular evolution was studied.These Gossypium materials included 29newly sequenced individuals of allotetraploid upland cotton cultivars,7 semi-wild races of upland cotton,and 36 Gossypium species sequences downloaded from the NCBI database.Based on the obtained chloroplast genome sequence,the phylogenetic relationship of Gossypium species was reconstructed,and the divergence time of Gossypium species and the evolutionary rate of plastid genome nucleotides were calculated.At the same time,based on the single nucleotide polymorphism（SNP）loci,the genetic diversity,gene flow and genetic structure of semi-wild races and cultivated accessions of upland cotton were tested.The principal results are as follows:1.The chloroplast genome sequence of 72 cotton samples was compared and analyzed,and it was found that the chloroplast genome of Gossypium was a closed ring-shaped tetrad structure composed of four parts:large single copy region（LSC）,short single copy region（SSC）and two inverted repeat regions（IRs）were between159,039-163,142 bp in length.Selection pressure analysis showed that 16 genes in the wild cotton material were positively selected,namely atp B,atp E,rps2,rps3,rps12,pet B,pet D,pet N,ndh G,rpo C2,rpl16,ccs A,cem A,rbc L,ycf1 and ycf2;only one gene locus（rpl2）in the semi-wild and cultivated cotton group was subject to positive selection,which may be a domesticated selection gene.The results of phylogenetic analysis based on the plastid genome showed that the whole Gossypium was mainly composed of six major evolutionary branches,namely A+AD genome,F-genome,E-genome,D-genome,B-genome and C+G+K genome branches,which were in accordance with the results of previous reports.In the phylogenetic tree,seven samples of upland cotton semi-wild races and 29 upland cotton cultivars were clustered into a large genetic branch.The latifolium in the semi-wild cotton races has the closest genetic relationship with upland cotton,proving the conclusion of cultivated upland cotton may have originated from the semi-wild race latifolium.In addition,the A-genome and AD-genome species were gathered into an independent genetic branch,further confirming the conclusion that the A-genome may be the maternal donor species of the allotetraploid AD-genome.2.Using the chloroplast genome protein coding sequence,combined with the results of the species differentiation time test of the three fossil calibration points,it was found that the whole Gossypium originated about 9.45 million years ago（Mya）during the Miocene;the B genome（Africa）and the Australian branch（C+G+K genome）diverged about 7.83 Mya.The divergence time between semi-wild races and cultivated accessions occurred about 2.74 Mya in the Pleistocene,and the ancestor species of the D-genome originated at about 5.17 Mya in the Pliocene era.The AD-genome clade of allotetraploid cultivated upland cotton originated and differentiated about 2.50 Mya during the Pleistocene.3.The detection of plastid genome conversion and transversion rate found that the transition/transversion rate in semi-wild and cultivated cotton groups was higher than that in the wild cotton group.Also,in the wild cotton group,a faster nucleotide evolution of plastid genome was detected,with an evolutionary rate of 1.2×10^–9 per site per year,while in the semi-wild and cultivated cotton group,the evolutionary rate of nucleotide substitution was lower,0.18×10^–9 per site per year.In addition,a total of 479 indel mutations were identified in wild cotton species,and the evolutionary rate of indel mutations was 0.4×10^–9 per site per year;while in the semi-wild and cultivated cotton groups,24 indels were detected,the evolutionary rate was 0.05×10^–11 per site per year,it showed that the wild cotton species has maintained a faster evolutionary rate during the long-term natural evolution process,while the semi-wild and cultivated cotton have experienced a strong process of artificial selection and domestication selection in the process of domestication.4.Based on the population genetic analysis of the semi-wild and cultivated accessions of upland cotton based on the plastid genome,a total of 7 chloroplast haplotypes were identified in the semi-wild races,and a total of 22 chloroplast haplotypes were identified in the cultivated cotton accessions.In addition,the haplotype diversity（H_d）and nucleotide diversity（π）of semi-wild races were higher than that of cultivated cotton accessions.The results of genetic structure analysis showed that semi-wild races and cultivated cotton accessions can be clustered into two genetic groups corresponding to their respective samples.Among them,the latifolium and marie-galante race in the semi-wild cotton group and the cultivated cotton group have obvious genetic infiltration,which further proved that the cultivated cotton accessions may originate from the semi-wild race latifolium;the cultivated cotton accessions were in the long-term domestication process,it has experienced obvious bottleneck effects resulting in a decrease in genetic diversity.Gene flow analysis found that in the process of cotton cultivation and domestication,the contemporary gene flow from semi-wild races to cultivated accessions was significantly higher than the historical gene flow,which may be related to the origin of domestication,resulting in a two-way asymmetric gene flow.