The complete chloroplast genome of Cicer reticulatum and comparative analysis against relative Cicer species

• Published in: Scientific reports Vol. 13; no. 1; p. 17871
• Main Authors: Mehmetoğlu, Ezgi, Kaymaz, Yasin, Ateş, Duygu, Kahraman, Abdullah, Tanyolaç, Muhammed Bahattin
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 19-10-2023; Nature Publishing Group; Nature Portfolio
• Subjects: 631/1647/2217; 631/208/212/748; Bioinformatics; Chloroplast DNA; Chloroplasts; Cicer; Cicer reticulatum; Comparative analysis; DNA sequencing; Frequency analysis; Genomes; Genomic analysis; Genomics; Homology; Humanities and Social Sciences; Inverted repeat; multidisciplinary; Nucleotide sequence; Phylogenetics; Phylogeny; Plant species; rRNA; Science; Science (multidisciplinary); Species; tRNA
• ISSN: 2045-2322; 2045-2322
• DOI: 10.1038/s41598-023-44599-1

The chloroplast (cp) genome is an adequate genomic resource to investigate evolutionary relationships among plant species and it carries marker genes available for species identification. The
Cicer reticulatum
is one of perennial species as the progenitor of cultivated chickpeas. Although a large part of the land plants has a quadruple chloroplast genome organization, the cp genome of
C. reticulatum
consists of one LSC (Large Single Copy Region), one SSC (Small Single Copy Region), and one IR (Inverted Repeat) region, which indicates that it has an untypical and unique structure. This type of chloroplast genome belongs to the IR-lacking clade. Chloroplast DNA (cpDNA) was extracted from fresh leaves using a high salt-based protocol and sequencing was performed using DNA Nanoball Sequencing technology. The comparative analysis employed between the species to examine genomic differences and gene homology. The study also included codon usage frequency analysis, hotspot divergence analysis, and phylogenetic analysis using various bioinformatics tools. The cp genome of
C. reticulatum
was found 125,794 bp in length, with an overall GC content of 33.9%. With a total of 79 protein-coding genes, 34 tRNA genes, and 4 rRNA genes. Comparative genomic analysis revealed 99.93% similarity between
C. reticulatum
and
C. arietinum
. Phylogenetic analysis further indicated that the closest evolutionary relative to
C. arietinum
was
C. reticulatum
, whereas the previously sequenced wild
Cicer
species displayed slight distinctions across their entire coding regions. Several genomic regions, such as
clpP
and
ycf1
, were found to exhibit high nucleotide diversity, suggesting their potential utility as markers for investigating the evolutionary relationships within the
Cicer
genus. The first complete cp genome sequence of
C. reticulatum
will provide novel insights for future genetic research on
Cicer
crops.