Complete Chloroplast Genomes and Comparative Analysis of Sequences Evolution among Seven Aristolochia (Aristolochiaceae) Medicinal Species.

Xiaoqin Li,Xinxin Zhu,Shuai Liao,Yunjuan Zuo,Jinshuang Ma

doi:10.3390/ijms20051045

Abstract

Aristolochiaceae, comprising about 600 species, is a unique plant family containing aristolochic acids (AAs). In this study, we sequenced seven species of Aristolochia, and retrieved eleven chloroplast (cp) genomes published for comparative genomics analysis and phylogenetic constructions. The results show that the cp genomes had a typical quadripartite structure with conserved genome arrangement and moderate divergence. The cp genomes range from 159,308 bp to 160,520 bp in length and have a similar GC content of 38.5%–38.9%. A total number of 113 genes were identified, including 79 protein-coding genes, 30 tRNAs and four rRNAs. Although genomic structure and size were highly conserved, the IR-SC boundary regions were variable between these seven cp genomes. The trnH-GUG genes, are one of major differences between the plastomes of the two subgenera Siphisia and Aristolochia. We analyzed the features of nucleotide substitutions, distribution of repeat sequences and simple sequences repeats (SSRs), positive selections in the cp genomes, and identified 16 hotspot regions for genomes divergence that could be utilized as potential markers for phylogeny reconstruction. Phylogenetic relationships of the family Aristolochiaceae inferred from the 18 cp genome sequences were consistent and robust, using maximum parsimony (MP), maximum likelihood (ML), and Bayesian analysis (BI) methods.

Highlights

Aristolochia sensu lato, comprising about 500 species, is the largest genus of Aristolochiaceae, with a broad distribution range from tropical to subtropical, extending to temperate regions [1,2]
The complete cp genomes of involved species comprise an large single copy (LSC) region (88,652–89,859 bp) and an small single copy (SSC) region (19,322–19,799 bp), separated by a pair of inverted repeat (IR) ranging from 25,242 bp to 25,700 bp in length (Figure 1, Table 1)
A total of 113 unique genes were identified in the seven cp genomes, including 79 protein coding genes, 30 tRNAs and four rRNAs, 19 or 18 genes of which duplicated in the IR region (Tables 1 and 2)

Summary

Introduction

Aristolochia sensu lato, comprising about 500 species, is the largest genus of Aristolochiaceae, with a broad distribution range from tropical to subtropical, extending to temperate regions [1,2]. The monophyly of Aristolochiaceae was well supported in most analysis, and was divided into two subfamilies, Asaroideae and Aristolochioideae [10,11]. The genus Aristolochia of subfamily Aristolochioideae was classified into two major lineages, as indicated by previous studies based on morphological characters and molecular phylogenetic methods [10,14,15,16]. The selected loci failed to provide sufficient phylogenetic information to elucidate the evolutionary relationships among Aristolochia species. A universal barcode either using whole chloroplast (cp) genomes or hyper-variable regions are urgently needed, which may significantly improve the low resolution in plant relationships and contribute to the conservation, domestication, and utilization of Aristolochia plants

Methods

Results

Conclusion