Structural Variation And Evolution Of Chloroplast Genomes In Gossypium

As the most important fiber crop,cotton plants are widely distributed around the world,including eight diploid genomes in group A-G and K and one AD genome in allotetraploid group.However,the chloroplast genome evolution and sequence variation of cotton plants have been controversial for a long time.In this study,Illumina sequencing technology was used to assemble and annotate the chloroplast genome sequences of six semi-wild AD1genomes.At the same time,molecular phylogenetic studies were carried out and the structural characteristics of tRNA gene on its chloroplast genome were discussed by combining the A genome and D genomic cotton data in NCBI database.The main research results are as follows:1.The complete chloroplast genome sequence of six semi-wild species were determined and annotated.Bioinformatics analysis showed that the chloroplast genomes of Gossypium were relatively conservative with typical tetrad structure?LSC,SSC,IRb and IRa?,with the length range of 159,947 bp-160,476 bp.A total of 2,590 repeats and 1,808 simple repeats?SSRs?were identified.The variation level of cotton in D genome?2.44%?was significantly higher than that of cotton in A genome?0.06%?and AD genome?0.66%?.And the variation level of non-coding region was higher than that of coding region,and the variation level of LSC and SSC was higher than that of IR regions.A total of seven divergence hotspot regions?trn R-ACG-trn N-GUU,trn M-CAU-atp E,psb Z-trn G-UCC,psb E-pet L,ycf1,atp E,and atp B?were identified,which can provide potential molecular markers for DNA barcoding.By analyzing the contraction and expansion of IR boundary,it was determined that rps19 and trn H-GUG genes were the"footprints"of chloroplast genome evolution of Gossypium.G.heraceum subsp.africanum?A1-a and G.arboretum?A2;G.lobatum?D7 and G.schwendimanii?D11;G.morrilli?AD1-MLE and G.mariegalante?AD1-MLJ were three groups with the same IR boundaries,which were also closely related.A total of 6 genes?atp B,atp E,ycf1,cem A,rbc L and rpo C1?were detected to be positive selected,which may be the result of the adaptive evolution of Gossypium species.Based on chloroplast genome,protein-coding genes and divergence hotspot regions separately build phylogenetic relationship of A genome,D genome and AD genome.The result is roughly same,showed AD genome and A genome formed a clade.Based on the relaxed molecular clock theory,the divergence time of Gossypium species was estimated to be 49.85?38.55-66.72?million years,and most species of Gossypium were radiating in a relatively narrow time range shortly after the origin of cotton.2.Reannotation of tRNA genes on cotton chloroplast genomes were carried out,and A total of 807 tRNA genes were identified.Almost tRNA in the secondary structures are conservative"clover"structure,and all the tRNA T?C ring conservative highly and have A consistent sequence X_0-1-U-U-C-X-A-X₂.In addition,some special tRNA structures were found:the first time the intron in the anti-codon ring of tRNA^Val and tRNA^Ilehave been found;Some of the tRNA genes have a circular structure in the V ring and there is more than a dozen of these circular structures.Starting from the conservatism of tRNA,the structural variation of tRNA genes were analyzed,and the evolutionary characteristics of tRNA sequence were discussed,which can further reveal the evolutionary history and evolutionary mechanism of tRNA genes.