The Complete Chloroplast Genome Sequence of Cicer bijugum, Genome Organization, and Comparison with Related Species

Abstract

Background: Chickpea is one of the legumes that is very important for Turkey and is frequently preferred especially in human nourishment thanks to its rich nutritional content. Chloroplasts, which have their own genetic material, are organelles responsible for photosynthesis in plant cells and their genome contains non-trivial information about the molecular features and evolutionary process of plants. Objective: Current study aimed at revealing complete chloroplast genome sequence of one of the wild type Cicer species Cicer bijugum and comparing its genome with cultivated Cicer species Cicer arietinum by using bioinformatics analysis tools. There are no study about revealing chloroplast genome sequence of Cicer species except the cultivated one Cicer arietinum. Therefore, we targeted to reveal the complete chloroplast genome sequence of wild type Cicer species Cicer bijugum and compare the chloroplast genome of Cicer bijugum with the cultivated one Cicer arietinum. Methods: In this study, we sequenced the whole chloroplast genome of Cicer bijugum, one of the wild types of chickpea species, with the help Next Generation Sequencing platform and compared it with the chloroplast genome of the cultivated chickpea species, Cicer arietinum by using online bioinformatics analysis tools. Results: We determined the size of the chloroplast genome of C. bijugum as 124,804 bp and found that C. bijugum did not contain an inverted repeat region in its chloroplast genome. Comparative analysis of the C. bijugum chloroplast genome uncovered thirteen hotspot regions (psbA, matK, rpoB, rpoC1, rpoC2, psbI, psbK, accD, rps19, ycf2, ycf1, rps15 and ndhF) and seven of them (matK, accD, rps19, ycf1, ycf2, rps15 and ndhF) could potentially be used as strong molecular markers for species identification. It has been determined that C. bijugum was phylogenetically closer to cultivated chickpea as compared to the other species. Conclusion: It is aimed that the data obtained from this study, which is the first study in which whole chloroplast genomes of wild chickpea species were sequenced, will guide researchers in future molecular, evolutionary and genetic engineering studies with chickpea species.

Complete chloroplast genome of Lens lamottei reveals intraspecies variation among with Lens culinaris

“…The common consensus is that plastid SSRs are mostly composed of A/T repeats, with G/C repeats considered as rare 37 . Similar results were found in the wild chickpea species belonging to Fabaceae family and in the L. ervoides cp genome 20 , 50 , 51 . SSRs have been identified in various organelle genomes and have great application potential for studies on the molecular evolution of plant population genetics and crop breeding 52 .…”

“…On the other hand, the remaining amino acids are encoded by two to six codons. Similar codon usage results are observed in wild lentil and chickpea species 20 , 50 , 51 . Codon usage could be helpful for phylogenetic association research as codon use can influence the manner of gene mutation 31 .…”

“…Thus, these three Lens species are expected to be closer to each other than to other species. Therefore, it should present close branching with L. lamottei , and cicer species belonging to the IRLC family 24 , 50 , 51 . Therefore, as a result of the phylogenetic tree, these two species are expected to be closer to each other than the other species.…”