Chloroplast genome characterization and divergence time estimation of Persicaria capitata

Abstract

Objective: With Persicaria capitata as test materials, we compared and analyzed the chloroplast (cp) genome characteristics as well as their phylogenetic relationships and evolutionary history with related species of Persicaria nepalensis, Persicaria japonica, Persicaria chinensis, Persicaria filiformis, Persicaria perfoliata, Persicaria pubescens, Persicaria hnydropiper.
Methods: The Illumina HiSeq high-throughput sequencing platform was used for the first time for P. capitata cp genome sequencing. NOVOPlasty and CpGAVAS2 were used for assembly and annotation, and Codon W, DnaSP, and MISA were used to conduct a series of comparative genomic analyses between the plant and seven species of the same genus. A phylogenetic tree was constructed using the maximum likelihood (ML) and neighbor-joining (NJ) methods, and divergence time was estimated using BEAST.
Results: The total length of P. capitata cp genome was 158,821 bp, with a guanine and cytosine (GC) content of 38.0%, exhibiting a typical circular tetrad structure. The genome contains 127 annotated genes, including 82 protein-coding and 45 tRNA-encoding genes. The cp genome harbors simple sequence repeat (SSR) loci primarily composed of A/T. The conserved species structure of this genus is reinforced by the expansion and contraction of the inverted repeat (IR) region. The non-coding regions of the cp genomes exhibited significant differences among the genera. Six different mutation hotspots (psbK-psbI, atpI-rps2, petN-psbD, atpB-rbcL, cemA-petA, ndhI-ndhA-ycf1) were screened from the non-coding regions of genes with high nucleotide variability (pI). These hotspots were expected to define the phylogenetic species of Persicaria. Furthermore, phylogenetic analysis of Polygonaceae plants showed that P. capitata was more closely related to P. chinensis than P. nepalensis. Analysis of divergence time indicated that Polygonaceae originated in the Late Cretaceous (~180 Ma) and began to differentiate during the Middle Miocene. Persicaria differentiated ~66.44 million years ago, during the Miocene.
Conclusions: Our findings will serve as a scientific basis for further research on species identification and evolution, population genetics, and phylogenetic analysis of P. capitata. Further, we provide valuable information for understanding the origin and evolution of Persicaria in Polygonaceae and estimating the differentiation time of Persicaria and its population.

Keywords

Chloroplast genomes / Comparative analysis / Divergence time / Persicaria capitata / Phylogenetic relationship

Conflict of interest statement

The authors declare no conflict of interest.

Funding

This study was supported by the National Natural Science Foundation of China (82060913).

Author contributions

Zeng XF: Conceptualization (lead), data curation (lead), methodology (equal), resources (lead), software (lead), visualization (lead), and writing the original draft (lead). Liu C: Funding acquisition (lead) and writing, review, and editing (lead). Yang XY: Conceptualization (equal); data curation (equal); writing-original draft (equal); writing-review and editing (equal). Luo JL: Methodology (equal) and resources (equal).Wang XY: Data curation (equal);Zhou Y: Formal analysis (equal); visualization (equal); funding acquisition (equal). Zhang LY: Resources (equal), software (lead);Gao ZJ: Software (lead); Xiang Pu: Funding acquisition (equal); writing-review and editing (equal). All authors contributed to the manuscript revision and approved the final manuscript.

Ethical approval of studies and informed consent

Not applicable.

Acknowledgments

None.

Data availability

The assembled cp genome sequences of P. capitata and P. nepalensis were uploaded to GenBank under the accession numbers OR148685 and OR148686, respectively.

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