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

Sunan Huang,Asunción Cano,Yunfei Deng,Xuejun Ge,Betty Gaby Millán Salazar

doi:10.7717/peerj.8450

Abstract

The genus Dicliptera (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 Dilciptera (D. acuminata, D. peruviana, D. montana, D. ruiziana and D. mucronata) 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 (trnY-GUA-trnE-UUC, trnG-GCC, psbZ-trnG-GCC, petN-psbM, and rps4-trnL-UUA), which may be used as molecular markers in future taxonomic identification and phylogenetic analyses of Dicliptera. A total of 55-58 simple sequence repeats (SSRs) and 229 long repeats were identified in the cp genomes of the five Dicliptera species. Phylogenetic analysis identified a close relationship between D. ruiziana and D. montana, followed by D. acuminata, D. peruviana, and D. mucronata. Evolutionary analysis of orthologous protein-coding genes within the family Acanthaceae revealed only one gene, ycf15, 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 Dicliptera species.

Highlights

The genus Dicliptera Juss. belongs to tribe Justicieae of the family Acanthaceae; it consists of approximately 150 species, which are typically found in the tropical and subtropical regions of the world (Scotland & Vollesen, 2000; Mabberley, 2017; Hu et al, 2011)
The space in Dicliptera from psbA to the IRb/large single copy region (LSC) boundary (364 bp) is enlarged compared to that of A. paniculata (333 bp). These findings reveal that the inverted regions (IRs) regions in the cp genome of Dicliptera have expanded compared to those of A. paniculata
The results of our study showed that the cp genomes of five Peruvian Dicliptera species were similar in structure, content, and order (Table 2, Fig. 1)

Summary

Introduction

The genus Dicliptera Juss. belongs to tribe Justicieae of the family Acanthaceae; it consists of approximately 150 species, which are typically found in the tropical and subtropical regions of the world (Scotland & Vollesen, 2000; Mabberley, 2017; Hu et al, 2011). Belongs to tribe Justicieae of the family Acanthaceae; it consists of approximately 150 species, which are typically found in the tropical and subtropical regions of the world (Scotland & Vollesen, 2000; Mabberley, 2017; Hu et al, 2011). It is readily recognized by umbellately arranged, rarely solitary, cymose inflorescence units (cymules) subtended by conspicuously paired bracts, anthers with two partially or completely superposed thecae and, in the Palaeotropics, resupinate corollas that lack a rugula (Darbyshire, 2008). Eleven species of Dicliptera are found in Peru, most of which are located in the Andes (Brako & Zarucchi, 1993; León, 2006). The interspecific relationships within Dicliptera have not been determined because of the limited number of samples available

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