Cotton (Gossypium spp.) included 5 tetraploid (2n=4x=52) and more than 45 diploid (2n=2x=26) species. Tetraploid species of cotton are formed through hybridization between an A- genome and a D- genome. Genome mapping analyses showed that there is high level of similarity between diploid A- and D- genomes with tetraploid At- and Dt- genomes. G. stocksii and G.longicalyx belong to D genome, which is an important wild bio-source for the cotton breeding and genetic research. Present study was conducted to study and compare the complete chloroplast sequence of two diploid species of cotton (G.stocksii and G.longicalyx) compared with two tetraploid species (G.hirsutum and G.barbadense), analyses of their genome structure, gene content and organization, repeated sequences and codon usage has been carried out. G.longicalyx chloroplast (cp) genome is 160,248 bp in length which longer than G.stocksii and shorter than two tetraploid species. G.stocksii chloroplast (cp) genome is 159,039 bp in length which shorter than G.longicalyx and shorter than two tetraploid species. In both species single copy regions of cp genome is separated by the two inverted repeats. The plastidic genomes of G.stocksii and G.longicalyx comprised of 79 protein coding genes, 4 ribosomal RNA genes and 30 transfer RNA genes, 113 single genes in total and 20 duplicated genes in inverted repeats. In both diploid species 5 ycf genes with unknown function have been identified. These genes considered essential for plants and are highly conserved in plant taxa.
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