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Comparative Analysis of Chloroplast Genomes for Five Dicliptera Species (Acanthaceae): Molecular Structure, Phylogenetic Relationships, and Adaptive Evolution

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Comparative Analysis of Chloroplast Genomes for Five Dicliptera Species (Acanthaceae): Molecular Structure, Phylogenetic Relationships, and Adaptive Evolution

Sunan Huang et al. PeerJ.

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.

Keywords: Adaptive evolution; Chloroplast genome; Dicliptera; Molecular markers; Phylogeny; Species identification.

Conflict of interest statement

The authors declare there are no competing interests.

Figures

Figure 1
Figure 1. Gene maps of chloroplast genomes.
(A) Dicliptera acuminata; (B) D. peruviana; (C) D. montana; (D) D. ruiziana; (E) D. mucronata. Genes shown outside of the circle are transcribed clockwise, whereas genes inside of the circle are transcribed counterclockwise. The colored bars indicate known protein-coding genes, tRNA and rRNA. The dark gray area in the inner circle indicates GC content, while the light gray area indicates AT content. LSC, large single copy; SSC, small single copy; IR, inverted repeats.
Figure 2
Figure 2. Comparison of the border regions of the LSC, SSC and IR among six Acanthaceae chloroplast genomes.
The IRb/SSC junction extended into the ycf1 genes creating various lengths of ycf1 pseudogenes (Ψycf1) among the six cp genomes. The number above, below or adjacent to genes shows the distance between the ends of genes and the boundary sites. The figure features are not to scale.
Figure 3
Figure 3. Comparison of the five Dicliptera chloroplast genomes using mVISTA.
CNS indicates conserved noncoding sequences. The Y-scale represents the percent identity between 50% and 100%.
Figure 4
Figure 4. Comparative analysis of the nucleotide diversity (Pi) value among five Dicliptera chloroplast genomes.
(A) Coding regions. (B) Non-coding regions.
Figure 5
Figure 5. Amino acid frequencies in five Dicliptera species protein-coding sequences.
As shown in the column diagram, Leucine was the most frequent amino acid (10.8%), Cysteine was the least (1.2%).
Figure 6
Figure 6. The type and presence of simple sequence repeats (SSRs) and long repeated sequences in the chloroplast genomes of five Dicliptera species.
(A) Percentage of SSR types; (B) number of SSRs and their types; (C) percentage of five repeat types; (D) number of five repeats types.
Figure 7
Figure 7. The maximum Likelihood (ML) tree of Acanthaceae.
Numbers associated with branches are ML bootstrap values, MP bootstrap values and Bayesian posterior probabilities, respecively. Hyphens indicate the bootstrap support or posterior probability lower than 50% or 0.5. Mentha spicata (NC_037247) and Sesamum indicum (NC_016433) were used as outgroups.
Figure 8
Figure 8. Synonymous (KS) substitution rates and ω values (ω= KA/KS) among all Acanthaceae species.
As shown in the column diagram, the order of genes is alphabetical. The ω value of the ycf15 gene (1.4453) is clearly higher than other genes.

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Grant support

This work was financially supported by the International Partnership Program of Chinese Academy of Sciences (Grant No. 151644KYSB20160005, GJHZ1620), the National Natural Science Foundation of China (Grant no. 31470302, 31670191), and “One-Three-Five” Strategic Planning of SCBG, CAS to Yunfei Deng and Xuejun Ge. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
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