Dataset Information

The complete chloroplast genome sequence of Heteropolygonatum ginfushanicum (Asparagaceae) and phylogenetic analysis.

ABSTRACT: Heteropolygonatum ginfushanicum is an endemic epiphytic herb in China. The complete chloroplast (cp) genome of H. ginfushanicum is reported in this study. The total length of the cp genome is 155,508 bp with a typical quadripartite structure consisting of a large single copy region (LSC) of 84,552 bp and a small single copy region (SSC) of 18,528 bp, separated by a pair of 26,214 bp inverted repeats (IRs). It encodes a total of 113 unique genes, including 79 protein-coding, 30 tRNA, and four rRNA genes. Phylogenetic analysis indicated that H. ginfushanicum is sister to Heteropolygonatum marmoratum within subfamily Nolinoideae.

SUBMITTER: Gu L

PROVIDER: S-EPMC8168753 | biostudies-literature | 2021 May

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

The complete chloroplast genome sequence of Heteropolygonatum ginfushanicum (Asparagaceae) and phylogenetic analysis.

Gu Li L Su Ting T Luo Guang-Ling GL Hu Guo-Xiong GX

Mitochondrial DNA. Part B, Resources 20210531 7

Heteropolygonatum ginfushanicum is an endemic epiphytic herb in China. The complete chloroplast (cp) genome of H. ginfushanicum is reported in this study. The total length of the cp genome is 155,508 bp with a typical quadripartite structure consisting of a large single copy region (LSC) of 84,552 bp and a small single copy region (SSC) of 18,528 bp, separated by a pair of 26,214 bp inverted repeats (IRs). It encodes a total of 113 unique genes, including 79 protein-coding, 30 tRNA ...[more]

PMID: 34104777

Similar Datasets

Project description:Polygonatum Miller belongs to the tribe Polygonateae of Asparagaceae. The horizontal creeping fleshy roots of several species in this genus serve as traditional Chinese medicine. Previous studies have mainly reported the size and gene contents of the plastomes, with little information on the comparative analysis of the plastid genomes of this genus. Additionally, there are still some species whose chloroplast genome information has not been reported. In this study, the complete plastomes of six Polygonatum were sequenced and assembled, among them, the chloroplast genome of P. campanulatum was reported for the first time. Comparative and phylogenetic analyses were then conducted with the published plastomes of three related species. Results indicated that the whole plastome length of the Polygonatum species ranged from 154,564 bp (P. multiflorum) to 156,028 bp (P. stenophyllum) having a quadripartite structure of LSC and SSC separated by two IR regions. A total of 113 unique genes were detected in each of the species. Comparative analysis revealed that gene content and total GC content in these species were highly identical. No significant contraction or expansion was observed in the IR boundaries among all the species except P. sibiricum1, in which the rps19 gene was pseudogenized owing to incomplete duplication. Abundant long dispersed repeats and SSRs were detected in each genome. There were five remarkably variable regions and 14 positively selected genes were identified among Polygonatum and Heteropolygonatum. Phylogenetic results based on chloroplast genome strongly supported the placement of P. campanulatum with alternate leaves in sect. Verticillata, a group characterized by whorled leaves. Moreover, P. verticillatum and P. cyrtonema were displayed as paraphyletic. This study revealed that the characters of plastomes in Polygonatum and Heteropolygonatum maintained a high degree of similarity. Five highly variable regions were found to be potential specific DNA barcodes in Polygonatum. Phylogenetic results suggested that leaf arrangement was not suitable as a basis for delimitation of subgeneric groups in Polygonatum and the definitions of P. cyrtonema and P. verticillatum require further study.

Dataset Information

The complete chloroplast genome sequence of Heteropolygonatum ginfushanicum (Asparagaceae) and phylogenetic analysis.

Publications

The complete chloroplast genome sequence of <i>Heteropolygonatum ginfushanicum</i> (Asparagaceae) and phylogenetic analysis.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets