The Complete Chloroplast Genome Sequences of Five Epimedium Species: Lights into Phylogenetic and Taxonomic Analyses.

Yanjun Zhang,Ying Wang,Jianjun Chen,Tae-Jin Yang,Sang-Choon Lee,Kyunghee Kim,Wei Zhang,Weiming Hu,Liuwen Du,Li Wu,Ao Liu

doi:10.3389/fpls.2016.00306

Abstract

Epimedium L. is a phylogenetically and economically important genus in the family Berberidaceae. We here sequenced the complete chloroplast (cp) genomes of four Epimedium species using Illumina sequencing technology via a combination of de novo and reference-guided assembly, which was also the first comprehensive cp genome analysis on Epimedium combining the cp genome sequence of E. koreanum previously reported. The five Epimedium cp genomes exhibited typical quadripartite and circular structure that was rather conserved in genomic structure and the synteny of gene order. However, these cp genomes presented obvious variations at the boundaries of the four regions because of the expansion and contraction of the inverted repeat (IR) region and the single-copy (SC) boundary regions. The trnQ-UUG duplication occurred in the five Epimedium cp genomes, which was not found in the other basal eudicotyledons. The rapidly evolving cp genome regions were detected among the five cp genomes, as well as the difference of simple sequence repeats (SSR) and repeat sequence were identified. Phylogenetic relationships among the five Epimedium species based on their cp genomes showed accordance with the updated system of the genus on the whole, but reminded that the evolutionary relationships and the divisions of the genus need further investigation applying more evidences. The availability of these cp genomes provided valuable genetic information for accurately identifying species, taxonomy and phylogenetic resolution and evolution of Epimedium, and assist in exploration and utilization of Epimedium plants.

Highlights

Epimedium comprising about 58 species, is a phylogenetically and economically important genus in the family Berberidaceae (Stearn, 2002; Ying et al, 2011)
Using the Illumina HiSeq 2000 system, five Epimedium species were sequenced to produce 4,573,881–4,675,703 paired-end raw reads (101 bp in average reads length). After screening these paired-end reads through alignment with reference cp genomes of Nandina domestica, 84,589 to 236,730 cp genome reads were extracted with 50 × to 145 × coverage (Table 1)
Four junction regions and 10 cp genes were validated by PCRbased sequencing in each of the five Epimedium cp genomes

Summary

Introduction

Epimedium comprising about 58 species, is a phylogenetically and economically important genus in the family Berberidaceae (Stearn, 2002; Ying et al, 2011). The samples of four Chinese species were used for complete cp genome sequencing, while that of E. koreanum from Korea was only used for PCR-based validating its cp genome sequence (KM207675) previously reported (Lee et al, 2015). Based on the reference cp genome, the four junctions between LSC/IRs and SSC/IRs of the five sampled Epimedium species were validated with PCR-based conventional Sanger sequencing, respectively.

Results

Conclusion