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Complete chloroplast genome of Prunus emarginata and its implications for the phylogenetic position within Prunus sensu lato (Rosaceae).

ABSTRACT: Prunus emarginata is a species of Prunus native to western North America.We determined the first complete chloroplast genome of P. emarginata using genome skimming approach. The cp genome was 157,458?bp long, with a large single-copy region (LSC) of 85,567?bp and a small single-copy region (SSC) of 19,121?bp separated by a pair of inverted repeats (IRs) of 26,385?bp. It encodes 129 genes, including 84 protein-coding genes, 37 tRNA genes, and 8 ribosomal RNA genes. We also reconstructed the phylogeny of Prunus sensu lato using maximum likelihood (ML) method, including our data and previously reported cp genomes of related taxa. The phylogenetic analysis indicated that P. emarginata is closely related with Prunus subhirtella var. subhirtella and Prunus yedoensis.

SUBMITTER: Chen LX

PROVIDER: S-EPMC7707383 | biostudies-literature | 2019 Oct

REPOSITORIES: biostudies-literature

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Complete chloroplast genome of Prunus emarginata and its implications for the phylogenetic position within Prunus sensu lato (Rosaceae).

Chen Lu-Xi LX Brown Kevin R KR Yi Xian-Gui XG Sun Zhong-Shuai ZS

Mitochondrial DNA. Part B, Resources 20191009 2

Prunus emarginata is a species of Prunus native to western North America.We determined the first complete chloroplast genome of P. emarginata using genome skimming approach. The cp genome was 157,458 bp long, with a large single-copy region (LSC) of 85,567 bp and a small single-copy region (SSC) of 19,121 bp separated by a pair of inverted repeats (IRs) of 26,385 bp. It encodes 129 genes, including 84 protein-coding genes, 37 tRNA genes, and 8 ribosomal RNA genes. We also reconstru ...[more]

PMID: 33366013

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Project description:BackgroundSorbus sensu stricto (Sorbus s.s.) is a genus with important economical values because of its beautiful leaves, and flowers and especially the colorful fruits. It belongs to the tribe Maleae of the family Rosaceae, and comprises about 90 species mainly distributed in China. There is on-going dispute about its infrageneric classification and species delimitation as the species are morphologically similar. With the aim of shedding light on the circumscription of taxa within the genus, phylogenetic analyses were performed using 29 Sorbus s.s. chloroplast (cp) genomes (16 newly sequenced) representing two subgenera and eight sections.ResultsThe 16 cp genomes newly sequenced range between 159,646 bp and 160,178 bp in length. All the samples examined and 22 taxa re-annotated in Sorbus sensu lato (Sorbus s.l.) contain 113 unique genes with 19 of these duplicated in the inverted repeat (IR). Six hypervariable regions including trnR-atpA, petN-psbM, rpl32-trnL, trnH-psbA, trnT-trnL and ndhC-trnV were screened and 44-53 SSRs and 14-31 dispersed repeats were identified as potential molecular markers. Phylogenetic analyses under ML/BI indicated that Sorbus s.l. is polyphyletic, but Sorbus s.s. and the other five segregate genera, Aria, Chamaemespilus, Cormus, Micromeles and Torminalis are monophyletic. Two major clades and four sub-clades resolved with full-support within Sorbus s.s. are not consistent with the existing infrageneric classification. Two subgenera, subg. Sorbus and subg. Albocarmesinae are supported as monophyletic when S. tianschanica is transferred to subg. Albocarmesinae from subg. Sorbus and S. hupehensis var. paucijuga transferred to subg. Sorbus from subg. Albocarmesinae, respectively. The current classification at sectional level is not supported by analysis of cp genome phylogeny.ConclusionPhylogenomic analyses of the cp genomes are useful for inferring phylogenetic relationships in Sorbus s.s. Though genome structure is highly conserved in the genus, hypervariable regions and repeat sequences used are the most promising molecule makers for population genetics, species delimitation and phylogenetic studies.

Dataset Information

Complete chloroplast genome of Prunus emarginata and its implications for the phylogenetic position within Prunus sensu lato (Rosaceae).

Publications

Complete chloroplast genome of <i>Prunus emarginata</i> and its implications for the phylogenetic position within <i>Prunus sensu lato</i> (Rosaceae).

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