Comparative analysis and phylogenetic investigation of Hong Kong Ilex chloroplast genomes

Abstract Ilex is a monogeneric plant group (containing approximately 600 species) in the Aquifoliaceae family and one of the most commonly used medicinal herbs. However, its taxonomy and phylogenetic relationships at the species level are debatable. Herein, we obtained the complete chloroplast genom...

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Autores principales:	Bobby Lim-Ho Kong, Hyun-Seung Park, Tai-Wai David Lau, Zhixiu Lin, Tae-Jin Yang, Pang-Chui Shaw
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/6dc12132c730468489b5782a2deaa8e0
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spelling	oai:doaj.org-article:6dc12132c730468489b5782a2deaa8e02021-12-02T13:20:01ZComparative analysis and phylogenetic investigation of Hong Kong Ilex chloroplast genomes10.1038/s41598-021-84705-92045-2322https://doaj.org/article/6dc12132c730468489b5782a2deaa8e02021-03-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-84705-9https://doaj.org/toc/2045-2322Abstract Ilex is a monogeneric plant group (containing approximately 600 species) in the Aquifoliaceae family and one of the most commonly used medicinal herbs. However, its taxonomy and phylogenetic relationships at the species level are debatable. Herein, we obtained the complete chloroplast genomes of all 19 Ilex types that are native to Hong Kong. The genomes are conserved in structure, gene content and arrangement. The chloroplast genomes range in size from 157,119 bp in Ilex graciliflora to 158,020 bp in Ilex kwangtungensis. All these genomes contain 125 genes, of which 88 are protein-coding and 37 are tRNA genes. Four highly varied sequences (rps16-trnQ, rpl32-trnL, ndhD-psaC and ycf1) were found. The number of repeats in the Ilex genomes is mostly conserved, but the number of repeating motifs varies. The phylogenetic relationship among the 19 Ilex genomes, together with eight other available genomes in other studies, was investigated. Most of the species could be correctly assigned to the section or even series level, consistent with previous taxonomy, except Ilex rotunda var. microcarpa, Ilex asprella var. tapuensis and Ilex chapaensis. These species were reclassified; I. rotunda was placed in the section Micrococca, while the other two were grouped with the section Pseudoaquifolium. These studies provide a better understanding of Ilex phylogeny and refine its classification.Bobby Lim-Ho KongHyun-Seung ParkTai-Wai David LauZhixiu LinTae-Jin YangPang-Chui ShawNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-13 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Bobby Lim-Ho Kong Hyun-Seung Park Tai-Wai David Lau Zhixiu Lin Tae-Jin Yang Pang-Chui Shaw Comparative analysis and phylogenetic investigation of Hong Kong Ilex chloroplast genomes
description	Abstract Ilex is a monogeneric plant group (containing approximately 600 species) in the Aquifoliaceae family and one of the most commonly used medicinal herbs. However, its taxonomy and phylogenetic relationships at the species level are debatable. Herein, we obtained the complete chloroplast genomes of all 19 Ilex types that are native to Hong Kong. The genomes are conserved in structure, gene content and arrangement. The chloroplast genomes range in size from 157,119 bp in Ilex graciliflora to 158,020 bp in Ilex kwangtungensis. All these genomes contain 125 genes, of which 88 are protein-coding and 37 are tRNA genes. Four highly varied sequences (rps16-trnQ, rpl32-trnL, ndhD-psaC and ycf1) were found. The number of repeats in the Ilex genomes is mostly conserved, but the number of repeating motifs varies. The phylogenetic relationship among the 19 Ilex genomes, together with eight other available genomes in other studies, was investigated. Most of the species could be correctly assigned to the section or even series level, consistent with previous taxonomy, except Ilex rotunda var. microcarpa, Ilex asprella var. tapuensis and Ilex chapaensis. These species were reclassified; I. rotunda was placed in the section Micrococca, while the other two were grouped with the section Pseudoaquifolium. These studies provide a better understanding of Ilex phylogeny and refine its classification.
format	article
author	Bobby Lim-Ho Kong Hyun-Seung Park Tai-Wai David Lau Zhixiu Lin Tae-Jin Yang Pang-Chui Shaw
author_facet	Bobby Lim-Ho Kong Hyun-Seung Park Tai-Wai David Lau Zhixiu Lin Tae-Jin Yang Pang-Chui Shaw
author_sort	Bobby Lim-Ho Kong
title	Comparative analysis and phylogenetic investigation of Hong Kong Ilex chloroplast genomes
title_short	Comparative analysis and phylogenetic investigation of Hong Kong Ilex chloroplast genomes
title_full	Comparative analysis and phylogenetic investigation of Hong Kong Ilex chloroplast genomes
title_fullStr	Comparative analysis and phylogenetic investigation of Hong Kong Ilex chloroplast genomes
title_full_unstemmed	Comparative analysis and phylogenetic investigation of Hong Kong Ilex chloroplast genomes
title_sort	comparative analysis and phylogenetic investigation of hong kong ilex chloroplast genomes
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/6dc12132c730468489b5782a2deaa8e0
work_keys_str_mv	AT bobbylimhokong comparativeanalysisandphylogeneticinvestigationofhongkongilexchloroplastgenomes AT hyunseungpark comparativeanalysisandphylogeneticinvestigationofhongkongilexchloroplastgenomes AT taiwaidavidlau comparativeanalysisandphylogeneticinvestigationofhongkongilexchloroplastgenomes AT zhixiulin comparativeanalysisandphylogeneticinvestigationofhongkongilexchloroplastgenomes AT taejinyang comparativeanalysisandphylogeneticinvestigationofhongkongilexchloroplastgenomes AT pangchuishaw comparativeanalysisandphylogeneticinvestigationofhongkongilexchloroplastgenomes
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Comparative analysis and phylogenetic investigation of Hong Kong Ilex chloroplast genomes

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