Comparative analysis of chloroplast genomes for five Dicliptera species (Acanthaceae): molecular structure, phylogenetic relationships, and adaptive evolution

• Published in: PeerJ (San Francisco, CA) Vol. 8; p. e8450
• Main Authors: Huang, Sunan, Ge, Xuejun, Cano, Asunción, Salazar, Betty Gaby Millán, Deng, Yunfei
• Format: Journal Article
• Language: English
• Published: United States PeerJ. Ltd 06.02.2020; PeerJ, Inc; PeerJ Inc
• Subjects: Acanthaceae; Adaptive evolution; Chloroplast genome; Chloroplasts; Comparative analysis; Cytosine; Dicliptera; Evolution; Evolution & development; Evolutionary biology; Evolutionary Studies; Genes; Genomes; Genomics; Guanine; Herbal medicine; Inverted repeat; Molecular Biology; Molecular markers; Morphology; Phylogenetics; Phylogeny; Plant Science; Positive selection; Ribosomal RNA; rRNA; Simple sequence repeats; Species; Species identification; Taxonomy; Transfer RNA; tRNA; Montana; China; Central America; Peru; Adaptive evolution; Molecular markers; Dicliptera; Phylogeny; Chloroplast genome; Species identification
• ISSN: 2167-8359; 2167-8359
• DOI: 10.7717/peerj.8450

The genus (Justicieae, Acanthaceae) consists of approximately 150 species distributed throughout the tropical and subtropical regions of the world. Newly obtained chloroplast genomes (cp genomes) are reported for five species of ( , , , and ) in this study. These cp genomes have circular structures of 150,689-150,811 bp and exhibit quadripartite organizations made up of a large single copy region (LSC, 82,796-82,919 bp), a small single copy region (SSC, 17,084-17,092 bp), and a pair of inverted repeat regions (IRs, 25,401-25,408 bp). Guanine-Cytosine (GC) content makes up 37.9%-38.0% of the total content. The complete cp genomes contain 114 unique genes, including 80 protein-coding genes, 30 transfer RNA (tRNA) genes, and four ribosomal RNA (rRNA) genes. Comparative analyses of nucleotide variability (Pi) reveal the five most variable regions ( GUA UUC GCC GCC and UUA), which may be used as molecular markers in future taxonomic identification and phylogenetic analyses of . A total of 55-58 simple sequence repeats (SSRs) and 229 long repeats were identified in the cp genomes of the five species. Phylogenetic analysis identified a close relationship between and , followed by , , and . Evolutionary analysis of orthologous protein-coding genes within the family Acanthaceae revealed only one gene, to be under positive selection, which may contribute to future studies of its adaptive evolution. The completed genomes are useful for future research on species identification, phylogenetic relationships, and the adaptive evolution of the species.