Complete chloroplast genome sequences of Lilium: insights into evolutionary dynamics and phylogenetic analyses

Abstract Lilium is a large genus that includes approximately 110 species distributed throughout cold and temperate regions of the Northern Hemisphere. The species-level phylogeny of Lilium remains unclear; previous studies have found universal markers but insufficient phylogenetic signals. In this s...

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Autores principales:	Yun-peng Du, Yu Bi, Feng-ping Yang, Ming-fang Zhang, Xu-qing Chen, Jing Xue, Xiu-hai Zhang
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2017
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/f6dad06884b64e9ab8f90bee371d24a4
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spelling	oai:doaj.org-article:f6dad06884b64e9ab8f90bee371d24a42021-12-02T11:51:04ZComplete chloroplast genome sequences of Lilium: insights into evolutionary dynamics and phylogenetic analyses10.1038/s41598-017-06210-22045-2322https://doaj.org/article/f6dad06884b64e9ab8f90bee371d24a42017-07-01T00:00:00Zhttps://doi.org/10.1038/s41598-017-06210-2https://doaj.org/toc/2045-2322Abstract Lilium is a large genus that includes approximately 110 species distributed throughout cold and temperate regions of the Northern Hemisphere. The species-level phylogeny of Lilium remains unclear; previous studies have found universal markers but insufficient phylogenetic signals. In this study, we present the use of complete chloroplast genomes to explore the phylogeny of this genus. We sequenced nine Lilium chloroplast genomes and retrieved seven published chloroplast genomes for comparative and phylogenetic analyses. The genomes ranged from 151,655 bp to 153,235 bp in length and had a typical quadripartite structure with a conserved genome arrangement and moderate divergence. A comparison of sixteen Lilium chloroplast genomes revealed ten mutation hotspots. Single nucleotide polymorphisms (SNPs) for any two Lilium chloroplast genomes ranged from 8 to 1,178 and provided robust data for phylogeny. Except for some of the shortest internodes, phylogenetic relationships of the Lilium species inferred from the chloroplast genome obtained high support, indicating that chloroplast genome data will be useful to help resolve the deeper branches of phylogeny.Yun-peng DuYu BiFeng-ping YangMing-fang ZhangXu-qing ChenJing XueXiu-hai ZhangNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 7, Iss 1, Pp 1-10 (2017)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Yun-peng Du Yu Bi Feng-ping Yang Ming-fang Zhang Xu-qing Chen Jing Xue Xiu-hai Zhang Complete chloroplast genome sequences of Lilium: insights into evolutionary dynamics and phylogenetic analyses
description	Abstract Lilium is a large genus that includes approximately 110 species distributed throughout cold and temperate regions of the Northern Hemisphere. The species-level phylogeny of Lilium remains unclear; previous studies have found universal markers but insufficient phylogenetic signals. In this study, we present the use of complete chloroplast genomes to explore the phylogeny of this genus. We sequenced nine Lilium chloroplast genomes and retrieved seven published chloroplast genomes for comparative and phylogenetic analyses. The genomes ranged from 151,655 bp to 153,235 bp in length and had a typical quadripartite structure with a conserved genome arrangement and moderate divergence. A comparison of sixteen Lilium chloroplast genomes revealed ten mutation hotspots. Single nucleotide polymorphisms (SNPs) for any two Lilium chloroplast genomes ranged from 8 to 1,178 and provided robust data for phylogeny. Except for some of the shortest internodes, phylogenetic relationships of the Lilium species inferred from the chloroplast genome obtained high support, indicating that chloroplast genome data will be useful to help resolve the deeper branches of phylogeny.
format	article
author	Yun-peng Du Yu Bi Feng-ping Yang Ming-fang Zhang Xu-qing Chen Jing Xue Xiu-hai Zhang
author_facet	Yun-peng Du Yu Bi Feng-ping Yang Ming-fang Zhang Xu-qing Chen Jing Xue Xiu-hai Zhang
author_sort	Yun-peng Du
title	Complete chloroplast genome sequences of Lilium: insights into evolutionary dynamics and phylogenetic analyses
title_short	Complete chloroplast genome sequences of Lilium: insights into evolutionary dynamics and phylogenetic analyses
title_full	Complete chloroplast genome sequences of Lilium: insights into evolutionary dynamics and phylogenetic analyses
title_fullStr	Complete chloroplast genome sequences of Lilium: insights into evolutionary dynamics and phylogenetic analyses
title_full_unstemmed	Complete chloroplast genome sequences of Lilium: insights into evolutionary dynamics and phylogenetic analyses
title_sort	complete chloroplast genome sequences of lilium: insights into evolutionary dynamics and phylogenetic analyses
publisher	Nature Portfolio
publishDate	2017
url	https://doaj.org/article/f6dad06884b64e9ab8f90bee371d24a4
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_version_	1718395201767079936

Complete chloroplast genome sequences of Lilium: insights into evolutionary dynamics and phylogenetic analyses

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