Dataset Information

Complete sequence of Cynanchum rostellatum (Apocynaceae: Asclepiadoideae) chloroplast genome and its phylogenetic analysis.

ABSTRACT: Cynanchum rostellatum (Turcz.) Liede and Khanum 2016 is a perennial herbaceous twining vine that is widely distributed in Japan, South Korea, the United States of America, and China. In this study, the complete chloroplast (cp) genome of C. rostellatum was sequenced using the Illumina platform and assembled for the first time. This plastome has a circular structure with a length of 160,641 bp. The GC content of the plastome was 37.82%. The cp genome contained 113 unique genes, including 79 protein-coding, 30 transfer RNA, and four ribosomal RNA genes. Phylogenetic analysis based on the complete cp genome sequences of the Asclepiadoideae subfamily showed that C. rostellatum was closely related to C. bungei in the genus Cynanchum. These results provide useful information for both phylogenetic research and the utilization of C. rostellatum.

SUBMITTER: Pei L

PROVIDER: S-EPMC9341368 | biostudies-literature | 2022

REPOSITORIES: biostudies-literature

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Complete sequence of Cynanchum rostellatum (Apocynaceae: Asclepiadoideae) chloroplast genome and its phylogenetic analysis.

Pei Lixin L Shu Shengnan S Ji Baoyu B Cui Ning N

Mitochondrial DNA. Part B, Resources 20220729 7

Cynanchum rostellatum (Turcz.) Liede and Khanum 2016 is a perennial herbaceous twining vine that is widely distributed in Japan, South Korea, the United States of America, and China. In this study, the complete chloroplast (cp) genome of C. rostellatum was sequenced using the Illumina platform and assembled for the first time. This plastome has a circular structure with a length of 160,641 bp. The GC content of the plastome was 37.82%. The cp genome contained 113 unique genes, incl ...[more]

PMID: 35923636

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Project description:Cynanchum belongs to the Apocynaceae family and is a morphologically diverse genus that includes around 200 shrub or perennial herb species. Despite the utilization of CPGs, few molecular phylogenetic studies have endeavored to elucidate infrafamilial relationships within Cynanchum through extensive taxon sampling. In this research, we constructed a phylogeny and estimated divergence time based on the chloroplast genomes (CPGs) of nine Cynanchum species. We sequenced and annotated nine chloroplast (CP) genomes in this study. The comparative analysis of these genomes from these Cynanchum species revealed a typical quadripartite structure, with a total sequence length ranging from 158,283 to 161,241 base pairs (bp). The CP genome (CPG) was highly conserved and moderately differentiated. Through annotation, we identified a total of 129-132 genes. Analysis of the boundaries of inverted repeat (IR) regions showed consistent positioning: the rps19 gene was located in the IRb region, varying from 46 to 50 bp. IRb/SSC junctions were located between the trnN and ndhF genes. We did not detect major expansions or contractions in the IR region or rearrangements or insertions in the CPGs of the nine Cynanchum species. The results of SSR analysis revealed a variation in the number of SSRs, ranging from 112 to 150. In five types of SSRs, the largest number was mononucleotide repeats, and the smallest number was hexanucleotide repeats. The number of long repeats in the cp genomes of nine Cynanchum species was from 35 to 80. In nine species of Cynanchum, the GC3s values ranged from 26.80% to 27.00%, indicating a strong bias towards A/U-ending codons. Comparative analyses revealed four hotspot regions in the CPG, ndhA-ndhH, trnI-GAU-rrn16, psbI-trnS-GCU, and rps7-ndhB, which could potentially serve as molecular markers. In addition, phylogenetic tree construction based on the CPG indicated that the nine Cynanchum species formed a monophyletic group. Molecular dating suggested that Cynanchum diverged from its sister genus approximately 18.87 million years ago (Mya) and species diversification within the Cynanchum species primarily occurred during the recent Miocene epoch. The divergence time estimation presented in this study will facilitate future research on Cynanchum, aid in species differentiation, and facilitate diverse investigations into this economically and ecologically important genus.

Dataset Information

Complete sequence of Cynanchum rostellatum (Apocynaceae: Asclepiadoideae) chloroplast genome and its phylogenetic analysis.

Publications

Complete sequence of <i>Cynanchum rostellatum</i> (Apocynaceae: Asclepiadoideae) chloroplast genome and its phylogenetic analysis.

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