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

Melih Temel; Yasin Kaymaz; Duygu Ateş; Abdullah Kahraman; Muhammed Bahattin Tanyolaç

doi:10.2174/1389202923666220211113708

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

Curr Genomics. 2022 Apr 7;23(1):50-65. doi: 10.2174/1389202923666220211113708.

Authors

Melih Temel¹, Yasin Kaymaz¹, Duygu Ateş¹, Abdullah Kahraman^{1

2}, Muhammed Bahattin Tanyolaç¹

Affiliations

¹ Department of Bioengineering, Faculty of Engineering, Ege University, 35100 Bornova-Izmir, Turkey.
² Department of Field Crops, Faculty of Agriculture, Harran University, 64000 S. Urfa, Turkey.

Abstract

Background: Chickpea is one of Turkey's most significant legumes, and because of its high nutritional value, it is frequently preferred in human nourishment.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. Except for Cicer arietinum, there has been no study on the chloroplast genome sequence of Cicer species.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.

Keywords: Cicer bijugum; Wild type chickpea; bioinformatics; chloroplast genome; comparative genome analysis; genome organization.