Complete plastome sequencing resolves taxonomic relationships among species of Calligonum L. (Polygonaceae) in China

Feng Song,Ying Feng,Xue-Jun Ge,Kevin S Burgess,Ting Li

doi:10.1186/s12870-020-02466-5

Abstract

BackgroundCalligonum (Polygonaceae) is distributed from southern Europe through northern Africa to central Asia, and is typically found in arid, desert regions. Previous studies have revealed that standard DNA barcodes fail to discriminate Calligonum species. In this study, the complete plastid genomes (plastome) for 32 accessions of 21 Calligonum species is sequenced to not only generate the first complete plastome sequence for the genus Calligonum but to also 1) Assess the ability of the complete plastome sequence to discern species within the group, and 2) screen the plastome sequence for a cost-effective DNA barcode that can be used in future studies to resolve taxonomic relationships within the group.ResultsThe whole plastomes of Calligonum species possess a typical quadripartite structure. The size of the Calligonum plastome is approximately 161 kilobase pairs (kbp), and encodes 113 genes, including 79 protein-coding genes, 30 tRNA genes, and four rRNA genes. Based on ML phylogenetic tree analyses, the complete plastome has higher species identification (78%) than combinations of standard DNA barcodes (rbcL + matK + nrITS, 56%). Five newly screened gene regions (ndhF, trnS-G, trnC-petN, ndhF-rpl32, rpl32-trnL) had high species resolution, where ndhF and trnS-G were able to distinguish the highest proportion of Calligonum species (56%).ConclusionsThe entire plastid genome was the most effective barcode for the genus Calligonum, although other gene regions showed great potential as taxon-specific barcodes for species identification in Calligonum.

Highlights

Calligonum (Polygonaceae) is distributed from southern Europe through northern Africa to central Asia, and is typically found in arid, desert regions
Gene regions of the plastid genome, as well as the nuclear ribosomal internal transcribed spacer region, have been widely used as standard DNA barcodes for species identification in general [7,8,9], DNA barcoding analyses based on these standard regions, as well as other plastid DNA sequences fail to discriminate Calligonum species [10,11,12]
We addressed the following three objectives: 1) Generate the complete plastome sequence for the genus Calligonum; 2) Assess the ability of the complete plastome sequence to discern species within the group, and 3) Screen the plastome sequence for a cost-effective barcode that can be used in future studies to resolve taxonomic relationships within the group

Summary

Introduction

Calligonum (Polygonaceae) is distributed from southern Europe through northern Africa to central Asia, and is typically found in arid, desert regions. Recent molecular sequence analysis [13] has treated five species (C. mongolicum, C. pumilum, C. chinense, C. alashanicum, and C. zaidamense) as a complex group, C. mongolicum. Given such discrepancies, more discerning genetic markers for the genus Calligonum are required to solve taxonomic confusion within the group. The compete plastome, in addition to all the standard plastid barcodes, should provide a wealth of informative and variable sites for the genetic identification and phylogenetic analyses of plant species [18, 19]: see e.g., Ficus [20], Lilium [21], Panax [22], Stipa [23], Taxus [24], and Diospyros [25]

Methods

Results

Discussion

Conclusion