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

Identifieur interne : 000035 ( Main/Exploration ); précédent : 000034; suivant : 000036

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

Auteurs : Yanjun Zhang [République populaire de Chine] ; Liuwen Du [République populaire de Chine] ; Ao Liu [République populaire de Chine] ; Jianjun Chen [République populaire de Chine] ; Li Wu [République populaire de Chine] ; Weiming Hu [République populaire de Chine] ; Wei Zhang [République populaire de Chine] ; Kyunghee Kim [Corée du Sud, République populaire de Chine] ; Sang-Choon Lee [Corée du Sud] ; Tae-Jin Yang [Corée du Sud] ; Ying Wang [République populaire de Chine]

Source :

RBID : PMC:4791396

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.


Url:
DOI: 10.3389/fpls.2016.00306
PubMed: 27014326
PubMed Central: 4791396


Affiliations:


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Le document en format XML

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<p>
<italic>Epimedium</italic>
L. is a phylogenetically and economically important genus in the family Berberidaceae. We here sequenced the complete chloroplast (cp) genomes of four
<italic>Epimedium</italic>
species using Illumina sequencing technology via a combination of
<italic>de novo</italic>
and reference-guided assembly, which was also the first comprehensive cp genome analysis on
<italic>Epimedium</italic>
combining the cp genome sequence of
<italic>E. koreanum</italic>
previously reported. The five
<italic>Epimedium</italic>
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
<italic>trnQ</italic>
-
<italic>UUG</italic>
duplication occurred in the five
<italic>Epimedium</italic>
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
<italic>Epimedium</italic>
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
<italic>Epimedium</italic>
, and assist in exploration and utilization of
<italic>Epimedium</italic>
plants.</p>
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