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

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.

Fig. (1)

Physical chloroplast genome map of Cicer bijugum. The genes in the inner part of the circle represent the genes encoded in the clockwise direction, and the genes in the outer surface of the circle represent the genes encoded in the counterclockwise direction. The dark gray peaks on the inner circle indicate the GC ratio of the genome, and the light gray peaks indicate the AT ratio of the genomes. (A higher resolution / colour version of this figure is available in the electronic copy of the article).

Fig. (2)

Sequence similarity graph of chloroplast genomes of Cicer bijugum and Cicer arietinum. (A higher resolution / colour version of this figure is available in the electronic copy of the article).

Fig. (3)

Analysis graph of the homologous regions in the chloroplast genomes of C. bijugum and C. arietinum species using the MAUVE program. Each colored block in the figure is called Locally Collinear Blocks (LCB) and represents regions showing homology in the genome. The small boxes below the centerlines in the graph represent the genes encoded in the chloroplast genomes. In the horizontal line where the genes are shown, the genes above the line are coded clockwise, while the genes below the line are encoded in the counterclockwise direction. (A higher resolution / colour version of this figure is available in the electronic copy of the article).

Fig. (4)

Amino acid compositions of C. bijugum.

Fig. (5)

Codon usage graph of C. bijugum. (A higher resolution / colour version of this figure is available in the electronic copy of the article).

Fig. (6A)

A) Simple sequence repeat types of C. bijugum.

Fig. (6B)

B) Simple sequence repeat motifs of C. bijugum.

Fig. (6C)

C) Forward, reverse, palindromic, complementary and tandem repeats of C. bijugum (A higher resolution / colour version of this figure is available in the electronic copy of the article).

Fig. (7)

Nucleotide diversity analysis graph.

Fig. (8)

Phylogenetic relationship tree of legumes and outgroup species.