Chloroplast genomes of Caragana tibetica and Caragana turkestanica: structures and comparative analysis

• Published in: BMC plant biology 2024-04, Vol.24 (1), p.254-254, Article 254
• Main Authors: Liu, LiE, Li, HongYan, Li, JiaXin, Li, XinJuan, Hu, Na, Sun, Jing, Zhou, Wu
• Format: Article
• Language: English
• Subjects: Analysis; Bats; Beans; Caragana; Caragana - genetics; Caragana arborescens; Chloroplast DNA; chloroplast genome; Chloroplasts; Comparative analysis; Diseases and pests; Divergence; DNA-directed RNA polymerase; ecological value; Genes; Genetic aspects; Genetic engineering; genetic variation; Genome, Chloroplast - genetics; Genomes; Genomics; genus; Growth; Health aspects; Inverted repeat; Legumes; Medicinal plants; Medicine, Botanic; Medicine, Herbal; Mimosaceae; Morphology; Nucleotide sequence; nucleotide sequences; Nucleotides; Phylogenetics; Phylogenomics; Phylogeny; Physical characteristics; Plant species; Proteins; Rheumatoid arthritis; RNA polymerase; rRNA; sequence homology; Sequencing; Sibling species; species; Species divergence; Species identification; Taxonomy; Transfer RNA
• ISSN: 1471-2229; 1471-2229
• DOI: 10.1186/s12870-024-04979-9

The genus Caragana encompasses multiple plant species that possess medicinal and ecological value. However, some species of Caragana are quite similar in morphology, so identifying species in this genus based on their morphological characteristics is considerably complex. In our research, illumina paired-end sequencing was employed to investigate the genetic organization and structure of Caragana tibetica and Caragana turkestanica, including the previously published chloroplast genome sequence of 7 Caragana plants. The lengths of C. tibetica and C. turkestanica chloroplast genomes were 128,433 bp and 129,453 bp, respectively. The absence of inverted repeat sequences in these two species categorizes them under the inverted repeat loss clade (IRLC). They encode 110 and 111 genes (4 /4 rRNA genes, 30 /31tRNA genes, and 76 /76 protein-coding genes), respectively. Comparison of the chloroplast genomes of C. tibetica and C. turkestanica with 7 other Caragana species revealed a high overall sequence similarity. However, some divergence was observed between certain intergenic regions (matK-rbcL, psbD-psbM, atpA-psbI, and etc.). Nucleotide diversity (π) analysis revealed the detection of five highly likely variable regions, namely rps2-atpI, accD-psaI-ycf4, cemA-petA, psbN-psbH and rpoA-rps11. Phylogenetic analysis revealed that C. tibetica's sister species is Caragana jubata, whereas C. turkestanica's closest relative is Caragana arborescens. The present study provides worthwhile information about the chloroplast genomes of C. tibetica and C. turkestanica, which aids in the identification and classification of Caragana species.