title: The Complete Chloroplast Genome Sequences of Five Epimedium Species: Lights into Phylogenetic and Taxonomic Analyses.
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.
authors.affiliation: Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences Wuhan, China.
authors.forename: Yanjun
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of SciencesWuhan, China; College of Life Science, University of Chinese Academy of SciencesBeijing, China.
authors.forename: Liuwen
authors.initials: L
authors.lastname: Du
authors.affiliation: Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of SciencesWuhan, China; College of Life Science, University of Chinese Academy of SciencesBeijing, China.
authors.forename: Ao
authors.initials: A
authors.lastname: Liu
authors.affiliation: Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences Wuhan, China.
authors.forename: Jianjun
authors.initials: J
authors.lastname: Chen
authors.affiliation: Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences Wuhan, China.
authors.forename: Li
authors.initials: L
authors.lastname: Wu
authors.affiliation: Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences Wuhan, China.
authors.forename: Weiming
authors.initials: W
authors.lastname: Hu
authors.affiliation: College of Life Sciences, Xinyang Normal University Xinyang, China.
authors.forename: Wei
authors.initials: W
authors.lastname: Zhang
authors.affiliation: Department of Plant Science, College of Agriculture and Life Sciences, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, Seoul National UniversitySeoul, South Korea; Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of SciencesGuangzhou, China.
authors.forename: Kyunghee
authors.initials: K
authors.lastname: Kim
authors.affiliation: Department of Plant Science, College of Agriculture and Life Sciences, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, Seoul National University Seoul, South Korea.
authors.forename: Sang-Choon
authors.initials: SC
authors.lastname: Lee
authors.affiliation: Department of Plant Science, College of Agriculture and Life Sciences, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, Seoul National University Seoul, South Korea.
authors.forename: Tae-Jin
authors.initials: TJ
authors.lastname: Yang
authors.affiliation: Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences Guangzhou, China.
authors.forename: Ying
authors.initials: Y
authors.lastname: Wang
keywords: Epimedium; chloroplast genome; genome structure; phylogenetic relationships; taxonomic identification