Comparative chloroplast genomes of camellia species.

<h4>Background</h4>Camellia, comprising more than 200 species, is a valuable economic commodity due to its enormously popular commercial products: tea leaves, flowers, and high-quality edible oils. It is the largest and most important genus in the family Theaceae. However, phylogenetic r...

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Autores principales:	Jun-Bo Yang, Shi-Xiong Yang, Hong-Tao Li, Jing Yang, De-Zhu Li
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2013
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/8edb243c4c794848bb0f6580a623d781
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spelling	oai:doaj.org-article:8edb243c4c794848bb0f6580a623d7812021-11-18T08:58:21ZComparative chloroplast genomes of camellia species.1932-620310.1371/journal.pone.0073053https://doaj.org/article/8edb243c4c794848bb0f6580a623d7812013-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/24009730/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203<h4>Background</h4>Camellia, comprising more than 200 species, is a valuable economic commodity due to its enormously popular commercial products: tea leaves, flowers, and high-quality edible oils. It is the largest and most important genus in the family Theaceae. However, phylogenetic resolution of the species has proven to be difficult. Consequently, the interspecies relationships of the genus Camellia are still hotly debated. Phylogenomics is an attractive avenue that can be used to reconstruct the tree of life, especially at low taxonomic levels.<h4>Methodology/principal findings</h4>Seven complete chloroplast (cp) genomes were sequenced from six species representing different subdivisions of the genus Camellia using Illumina sequencing technology. Four junctions between the single-copy segments and the inverted repeats were confirmed and genome assemblies were validated by PCR-based product sequencing using 123 pairs of primers covering preliminary cp genome assemblies. The length of the Camellia cp genome was found to be about 157kb, which contained 123 unique genes and 23 were duplicated in the IR regions. We determined that the complete Camellia cp genome was relatively well conserved, but contained enough genetic differences to provide useful phylogenetic information. Phylogenetic relationships were analyzed using seven complete cp genomes of six Camellia species. We also identified rapidly evolving regions of the cp genome that have the potential to be used for further species identification and phylogenetic resolution.<h4>Conclusions/significance</h4>In this study, we wanted to determine if analyzing completely sequenced cp genomes could help settle these controversies of interspecies relationships in Camellia. The results demonstrate that cp genome data are beneficial in resolving species definition because they indicate that organelle-based "barcodes", can be established for a species and then used to unmask interspecies phylogenetic relationships. It reveals that phylogenomics based on cp genomes is an effective approach for achieving phylogenetic resolution between Camellia species.Jun-Bo YangShi-Xiong YangHong-Tao LiJing YangDe-Zhu LiPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 8, Iss 8, p e73053 (2013)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Jun-Bo Yang Shi-Xiong Yang Hong-Tao Li Jing Yang De-Zhu Li Comparative chloroplast genomes of camellia species.
description	<h4>Background</h4>Camellia, comprising more than 200 species, is a valuable economic commodity due to its enormously popular commercial products: tea leaves, flowers, and high-quality edible oils. It is the largest and most important genus in the family Theaceae. However, phylogenetic resolution of the species has proven to be difficult. Consequently, the interspecies relationships of the genus Camellia are still hotly debated. Phylogenomics is an attractive avenue that can be used to reconstruct the tree of life, especially at low taxonomic levels.<h4>Methodology/principal findings</h4>Seven complete chloroplast (cp) genomes were sequenced from six species representing different subdivisions of the genus Camellia using Illumina sequencing technology. Four junctions between the single-copy segments and the inverted repeats were confirmed and genome assemblies were validated by PCR-based product sequencing using 123 pairs of primers covering preliminary cp genome assemblies. The length of the Camellia cp genome was found to be about 157kb, which contained 123 unique genes and 23 were duplicated in the IR regions. We determined that the complete Camellia cp genome was relatively well conserved, but contained enough genetic differences to provide useful phylogenetic information. Phylogenetic relationships were analyzed using seven complete cp genomes of six Camellia species. We also identified rapidly evolving regions of the cp genome that have the potential to be used for further species identification and phylogenetic resolution.<h4>Conclusions/significance</h4>In this study, we wanted to determine if analyzing completely sequenced cp genomes could help settle these controversies of interspecies relationships in Camellia. The results demonstrate that cp genome data are beneficial in resolving species definition because they indicate that organelle-based "barcodes", can be established for a species and then used to unmask interspecies phylogenetic relationships. It reveals that phylogenomics based on cp genomes is an effective approach for achieving phylogenetic resolution between Camellia species.
format	article
author	Jun-Bo Yang Shi-Xiong Yang Hong-Tao Li Jing Yang De-Zhu Li
author_facet	Jun-Bo Yang Shi-Xiong Yang Hong-Tao Li Jing Yang De-Zhu Li
author_sort	Jun-Bo Yang
title	Comparative chloroplast genomes of camellia species.
title_short	Comparative chloroplast genomes of camellia species.
title_full	Comparative chloroplast genomes of camellia species.
title_fullStr	Comparative chloroplast genomes of camellia species.
title_full_unstemmed	Comparative chloroplast genomes of camellia species.
title_sort	comparative chloroplast genomes of camellia species.
publisher	Public Library of Science (PLoS)
publishDate	2013
url	https://doaj.org/article/8edb243c4c794848bb0f6580a623d781
work_keys_str_mv	AT junboyang comparativechloroplastgenomesofcamelliaspecies AT shixiongyang comparativechloroplastgenomesofcamelliaspecies AT hongtaoli comparativechloroplastgenomesofcamelliaspecies AT jingyang comparativechloroplastgenomesofcamelliaspecies AT dezhuli comparativechloroplastgenomesofcamelliaspecies
_version_	1718421096311554048

Comparative chloroplast genomes of camellia species.

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