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The first complete chloroplast genome sequences of Ulmus species by de novo sequencing: Genome comparative and taxonomic position analysis

Elm (Ulmus) has a long history of use as a high-quality heavy hardwood famous for its resistance to drought, cold, and salt. It grows in temperate, warm temperate, and subtropical regions. This is the first report of Ulmaceae chloroplast genomes by de novo sequencing. The Ulmus chloroplast genomes e...

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Autores principales: Zuo, Li-Hui, Shang, Ai-Qin, Zhang, Shuang, Yu, Xiao-Yue, Ren, Ya-Chao, Yang, Min-Sheng, Wang, Jin-Mao
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5291543/
https://www.ncbi.nlm.nih.gov/pubmed/28158318
http://dx.doi.org/10.1371/journal.pone.0171264
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author Zuo, Li-Hui
Shang, Ai-Qin
Zhang, Shuang
Yu, Xiao-Yue
Ren, Ya-Chao
Yang, Min-Sheng
Wang, Jin-Mao
author_facet Zuo, Li-Hui
Shang, Ai-Qin
Zhang, Shuang
Yu, Xiao-Yue
Ren, Ya-Chao
Yang, Min-Sheng
Wang, Jin-Mao
author_sort Zuo, Li-Hui
collection PubMed
description Elm (Ulmus) has a long history of use as a high-quality heavy hardwood famous for its resistance to drought, cold, and salt. It grows in temperate, warm temperate, and subtropical regions. This is the first report of Ulmaceae chloroplast genomes by de novo sequencing. The Ulmus chloroplast genomes exhibited a typical quadripartite structure with two single-copy regions (long single copy [LSC] and short single copy [SSC] sections) separated by a pair of inverted repeats (IRs). The lengths of the chloroplast genomes from five Ulmus ranged from 158,953 to 159,453 bp, with the largest observed in Ulmus davidiana and the smallest in Ulmus laciniata. The genomes contained 137–145 protein-coding genes, of which Ulmus davidiana var. japonica and U. davidiana had the most and U. pumila had the fewest. The five Ulmus species exhibited different evolutionary routes, as some genes had been lost. In total, 18 genes contained introns, 13 of which (trnL-TAA(+), trnL-TAA(−), rpoC1(-), rpl2(-), ndhA(-), ycf1, rps12(-), rps12(+), trnA-TGC(+), trnA-TGC(-), trnV-TAC(-), trnI-GAT(+), and trnI-GAT) were shared among all five species. The intron of ycf1 was the longest (5,675bp) while that of trnF-AAA was the smallest (53bp). All Ulmus species except U. davidiana exhibited the same degree of amplification in the IR region. To determine the phylogenetic positions of the Ulmus species, we performed phylogenetic analyses using common protein-coding genes in chloroplast sequences of 42 other species published in NCBI. The cluster results showed the closest plants to Ulmaceae were Moraceae and Cannabaceae, followed by Rosaceae. Ulmaceae and Moraceae both belonged to Urticales, and the chloroplast genome clustering results were consistent with their traditional taxonomy. The results strongly supported the position of Ulmaceae as a member of the order Urticales. In addition, we found a potential error in the traditional taxonomies of U. davidiana and U. davidiana var. japonica, which should be confirmed with a further analysis of their nuclear genomes. This study is the first report on Ulmus chloroplast genomes, which has significance for understanding photosynthesis, evolution, and chloroplast transgenic engineering.
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spelling pubmed-52915432017-02-17 The first complete chloroplast genome sequences of Ulmus species by de novo sequencing: Genome comparative and taxonomic position analysis Zuo, Li-Hui Shang, Ai-Qin Zhang, Shuang Yu, Xiao-Yue Ren, Ya-Chao Yang, Min-Sheng Wang, Jin-Mao PLoS One Research Article Elm (Ulmus) has a long history of use as a high-quality heavy hardwood famous for its resistance to drought, cold, and salt. It grows in temperate, warm temperate, and subtropical regions. This is the first report of Ulmaceae chloroplast genomes by de novo sequencing. The Ulmus chloroplast genomes exhibited a typical quadripartite structure with two single-copy regions (long single copy [LSC] and short single copy [SSC] sections) separated by a pair of inverted repeats (IRs). The lengths of the chloroplast genomes from five Ulmus ranged from 158,953 to 159,453 bp, with the largest observed in Ulmus davidiana and the smallest in Ulmus laciniata. The genomes contained 137–145 protein-coding genes, of which Ulmus davidiana var. japonica and U. davidiana had the most and U. pumila had the fewest. The five Ulmus species exhibited different evolutionary routes, as some genes had been lost. In total, 18 genes contained introns, 13 of which (trnL-TAA(+), trnL-TAA(−), rpoC1(-), rpl2(-), ndhA(-), ycf1, rps12(-), rps12(+), trnA-TGC(+), trnA-TGC(-), trnV-TAC(-), trnI-GAT(+), and trnI-GAT) were shared among all five species. The intron of ycf1 was the longest (5,675bp) while that of trnF-AAA was the smallest (53bp). All Ulmus species except U. davidiana exhibited the same degree of amplification in the IR region. To determine the phylogenetic positions of the Ulmus species, we performed phylogenetic analyses using common protein-coding genes in chloroplast sequences of 42 other species published in NCBI. The cluster results showed the closest plants to Ulmaceae were Moraceae and Cannabaceae, followed by Rosaceae. Ulmaceae and Moraceae both belonged to Urticales, and the chloroplast genome clustering results were consistent with their traditional taxonomy. The results strongly supported the position of Ulmaceae as a member of the order Urticales. In addition, we found a potential error in the traditional taxonomies of U. davidiana and U. davidiana var. japonica, which should be confirmed with a further analysis of their nuclear genomes. This study is the first report on Ulmus chloroplast genomes, which has significance for understanding photosynthesis, evolution, and chloroplast transgenic engineering. Public Library of Science 2017-02-03 /pmc/articles/PMC5291543/ /pubmed/28158318 http://dx.doi.org/10.1371/journal.pone.0171264 Text en © 2017 Zuo et al http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Zuo, Li-Hui
Shang, Ai-Qin
Zhang, Shuang
Yu, Xiao-Yue
Ren, Ya-Chao
Yang, Min-Sheng
Wang, Jin-Mao
The first complete chloroplast genome sequences of Ulmus species by de novo sequencing: Genome comparative and taxonomic position analysis
title The first complete chloroplast genome sequences of Ulmus species by de novo sequencing: Genome comparative and taxonomic position analysis
title_full The first complete chloroplast genome sequences of Ulmus species by de novo sequencing: Genome comparative and taxonomic position analysis
title_fullStr The first complete chloroplast genome sequences of Ulmus species by de novo sequencing: Genome comparative and taxonomic position analysis
title_full_unstemmed The first complete chloroplast genome sequences of Ulmus species by de novo sequencing: Genome comparative and taxonomic position analysis
title_short The first complete chloroplast genome sequences of Ulmus species by de novo sequencing: Genome comparative and taxonomic position analysis
title_sort first complete chloroplast genome sequences of ulmus species by de novo sequencing: genome comparative and taxonomic position analysis
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5291543/
https://www.ncbi.nlm.nih.gov/pubmed/28158318
http://dx.doi.org/10.1371/journal.pone.0171264
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