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Five Complete Chloroplast Genome Sequences from Diospyros: Genome Organization and Comparative Analysis

Diospyros is the largest genus in Ebenaceae, comprising more than 500 species with remarkable economic value, especially Diospyros kaki Thunb., which has traditionally been an important food resource in China, Korea, and Japan. Complete chloroplast (cp) genomes from D. kaki, D. lotus L., D. oleifera...

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Autores principales: Fu, Jianmin, Liu, Huimin, Hu, Jingjing, Liang, Yuqin, Liang, Jinjun, Wuyun, Tana, Tan, Xiaofeng
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4956199/
https://www.ncbi.nlm.nih.gov/pubmed/27442423
http://dx.doi.org/10.1371/journal.pone.0159566
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author Fu, Jianmin
Liu, Huimin
Hu, Jingjing
Liang, Yuqin
Liang, Jinjun
Wuyun, Tana
Tan, Xiaofeng
author_facet Fu, Jianmin
Liu, Huimin
Hu, Jingjing
Liang, Yuqin
Liang, Jinjun
Wuyun, Tana
Tan, Xiaofeng
author_sort Fu, Jianmin
collection PubMed
description Diospyros is the largest genus in Ebenaceae, comprising more than 500 species with remarkable economic value, especially Diospyros kaki Thunb., which has traditionally been an important food resource in China, Korea, and Japan. Complete chloroplast (cp) genomes from D. kaki, D. lotus L., D. oleifera Cheng., D. glaucifolia Metc., and Diospyros ‘Jinzaoshi’ were sequenced using Illumina sequencing technology. This is the first cp genome reported in Ebenaceae. The cp genome sequences of Diospyros ranged from 157,300 to 157,784 bp in length, presenting a typical quadripartite structure with two inverted repeats each separated by one large and one small single-copy region. For each cp genome, 134 genes were annotated, including 80 protein-coding, 31 tRNA, and 4 rRNA unique genes. In all, 179 repeats and 283 single sequence repeats were identified. Four hypervariable regions, namely, intergenic region of trnQ_rps16, trnV_ndhC, and psbD_trnT, and intron of ndhA, were identified in the Diospyros genomes. Phylogenetic analyses based on the whole cp genome, protein-coding, and intergenic and intron sequences indicated that D. oleifera is closely related to D. kaki and could be used as a model plant for future research on D. kaki; to our knowledge, this is proposed for the first time. Further, these analyses together with two large deletions (301 and 140 bp) in the cp genome of D. ‘Jinzaoshi’, support its placement as a new species in Diospyros. Both maximum parsimony and likelihood analyses for 19 taxa indicated the basal position of Ericales in asterids and suggested that Ebenaceae is monophyletic in Ericales.
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spelling pubmed-49561992016-08-08 Five Complete Chloroplast Genome Sequences from Diospyros: Genome Organization and Comparative Analysis Fu, Jianmin Liu, Huimin Hu, Jingjing Liang, Yuqin Liang, Jinjun Wuyun, Tana Tan, Xiaofeng PLoS One Research Article Diospyros is the largest genus in Ebenaceae, comprising more than 500 species with remarkable economic value, especially Diospyros kaki Thunb., which has traditionally been an important food resource in China, Korea, and Japan. Complete chloroplast (cp) genomes from D. kaki, D. lotus L., D. oleifera Cheng., D. glaucifolia Metc., and Diospyros ‘Jinzaoshi’ were sequenced using Illumina sequencing technology. This is the first cp genome reported in Ebenaceae. The cp genome sequences of Diospyros ranged from 157,300 to 157,784 bp in length, presenting a typical quadripartite structure with two inverted repeats each separated by one large and one small single-copy region. For each cp genome, 134 genes were annotated, including 80 protein-coding, 31 tRNA, and 4 rRNA unique genes. In all, 179 repeats and 283 single sequence repeats were identified. Four hypervariable regions, namely, intergenic region of trnQ_rps16, trnV_ndhC, and psbD_trnT, and intron of ndhA, were identified in the Diospyros genomes. Phylogenetic analyses based on the whole cp genome, protein-coding, and intergenic and intron sequences indicated that D. oleifera is closely related to D. kaki and could be used as a model plant for future research on D. kaki; to our knowledge, this is proposed for the first time. Further, these analyses together with two large deletions (301 and 140 bp) in the cp genome of D. ‘Jinzaoshi’, support its placement as a new species in Diospyros. Both maximum parsimony and likelihood analyses for 19 taxa indicated the basal position of Ericales in asterids and suggested that Ebenaceae is monophyletic in Ericales. Public Library of Science 2016-07-21 /pmc/articles/PMC4956199/ /pubmed/27442423 http://dx.doi.org/10.1371/journal.pone.0159566 Text en © 2016 Fu 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
Fu, Jianmin
Liu, Huimin
Hu, Jingjing
Liang, Yuqin
Liang, Jinjun
Wuyun, Tana
Tan, Xiaofeng
Five Complete Chloroplast Genome Sequences from Diospyros: Genome Organization and Comparative Analysis
title Five Complete Chloroplast Genome Sequences from Diospyros: Genome Organization and Comparative Analysis
title_full Five Complete Chloroplast Genome Sequences from Diospyros: Genome Organization and Comparative Analysis
title_fullStr Five Complete Chloroplast Genome Sequences from Diospyros: Genome Organization and Comparative Analysis
title_full_unstemmed Five Complete Chloroplast Genome Sequences from Diospyros: Genome Organization and Comparative Analysis
title_short Five Complete Chloroplast Genome Sequences from Diospyros: Genome Organization and Comparative Analysis
title_sort five complete chloroplast genome sequences from diospyros: genome organization and comparative analysis
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4956199/
https://www.ncbi.nlm.nih.gov/pubmed/27442423
http://dx.doi.org/10.1371/journal.pone.0159566
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