New Insights For The Donor Of Cytoplasm About Cotton And The Mitochondrial Genomes Evalution In Eurosids

Cotton is an interesting species for the study of genome evolution not only for its economic importantance but also for recent polyploidization in genome across the genus.The mitochondrial genomes from five cotton species with different ploidy sequenced by Illumina Hi Seq 2000 system and Pacific Biosciences RS II sequencing platform with one single molecule real time cell technology,respectively.Eventually,we acquired complete mitochondrial genome sequences of Gossypium barbadense and Gossypium herbaceum with the size of 622,852 bp and 623,359 bp.The longest scaffold in G.barbadense assembled sequence is 119,408 bp and 182,442 bp in G.herbaceum.Ten scaffolds larger than 8.9 kb and eight scaffolds greater than 28 kb were obtained with 55.1% GC content in common.Data generated by Illumina from Gossypium arboreum and Gossypium raimondii were assembled to scaffolds with the length of 615,380 bp and 658,958 bp,the length of N50 is 4,214 bp and 6,003 bp,the Gossypium hirsutum mitochondrial genome was assembled into a circular molecule with the length of 622,760 bp.The distributions of mutations were also detected in the mitochondrial genome and its coding sequences.The G.herbaceum share the most number of SNP,which occupied approximately 50% the total identified SNP.More over,we acquired the positions of SNP on exons.SSR among the cotton mitochondrial genome are unique with each other which located in the same exon of rps3 gene.Gossypium is belonging to the clade of eurosids,which stand out as the least-resolved major clade of angiosperms.So we collected chloroplast and mitochondrial genome sequences from Gossypium together with other species in eurosid to perform a comparative study of the mitochondrial genomic characteristics.We found abundant chloroplast like genome sequence and the preferences of these horizontal gene transfers were identified in the mitochondrial genome.We propose that cp-likes are the major resource for the mitochondrial genome size expanding.The conservative property of RNA editing among different gene species: After analysis of RNA editing sites in the mitochondrial genome among different species,Cytochrome c biogenesis genes(ccm B,ccm Fn and ccm C)and Complex I genes(nad2,nad4 and nad5)are found to be highly edited.The preferences of codon as the start codon of nad1 gene before RNA editing site is always ACG codon while the outgroup is ATG.The branches with close evolutionary relationship own the same genes clusters and the conservate gene clusters can be found among different clades in eurosids.As the mitochondria originate from the same ancestor,phylogenetic trees based on the sequences of 24 mitochondrial genes were constructed to demonstrate that the clade of all of the Gossypium that contain A genome is sister to G.raimondii with the D genome.The clade of the allotetraploid cotton is sister to the clade of diploid A genome species and the donor of the cytoplasm of tetraploid cotton is sister to the progenitor diploid species of the clade of G.arboreum and/or G.herbaceum.Phylogenetic tree was constructed with gene sequences of mitochondrial genome from different clades to strongly support for APG III classification in a new sight.