The complete chloroplast genome sequence of Cicer echinospermum, genome organization and comparison with related species

The Cicer genus, which has high agronomical importance, belongs to the Leguminosae family, and it comprises of 9 annual and 35 perennial species. Chloroplast (cp) DNA provides a detailed information for evolutionary and agronomic improvement studies. Due to high evolutionary conservation in its gene content and genomic organization, cpDNA is extremely useful for identification of taxonomic and phylogenetic relationships. In this study, we have constructed the complete chloroplast genome sequence of Cicer echinospermum, compared it with the cultivated type (Cicer arietinum), and re-examined the Cicers’ phylogenetic structure based on their cpDNAs among other legume species. We determined the chloroplast genome of Cicer echinospermum to be 126,713 bp in length with 83,129 bp of LSC, 13,288 bp of SSC and 30,296 bp of an IR region. This genome encodes 116 genes, 79 of which are protein coding, 33 tRNAs, and 4 rRNAs. Furthermore, our bioinformatic analysis revealed that this chloroplast genome has experienced an IR-loss in the evolutionary process like other IRLC family members and had undergone ∼21 kb inversion with respect to the Cicer arietinum. The result of the comparative analysis indicate that some regions showed certain nucleotide diversity, as in ycf1 and ycf2, which might be useful as potential markers for identification of Cicer genus. In the phylogenetic tree, C. arietinum and C. echinospermum clustered together among other legumes and confirmed the topology of Cicer species. These new genomic data are not only beneficial to elucidate phylogenetic relationships, but also provide information to develop and improve economically important crops through genetic engineering.