Dataset Information

The complete chloroplast genome of a Chinese endemic ornamental plant Sorbus unguiculata Koehne (Rosaceae).

ABSTRACT: Sorbus unguiculata is a pinnate-leaved deciduous shrub growing in mixed forests in Sichuan province, China. It is one of the least known species in the genus with high ornamental value. In this study, we firstly assembled and annotated the complete chloroplast genome of the species using the next-generation sequencing method. The results showed that the chloroplast genome size is 159,900?bp, comprising of a large single-copy (LSC) region of 87,888?bp, a small single-copy (SSC) region of 19,256?bp, and a pair of IR regions of 26,378?bp. The whole cp genome predicted 109 genes in total, including 76 protein-coding genes, 29 tRNAs, and 4 tRNAs. The overall GC content of the chloroplast genome is 36.6%. The phylogenetic relationship exhibited that S. unguiculata is closely clustered with S. helenae in Sorbus.

SUBMITTER: Niu Z

PROVIDER: S-EPMC7687415 | biostudies-literature | 2019 Jul

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

The complete chloroplast genome of a Chinese endemic ornamental plant <i>Sorbus unguiculata</i> Koehne (Rosaceae).

Niu Zhengyang Z Xiong Zhongren Z Xi Lianlian L Chen Xin X

Mitochondrial DNA. Part B, Resources 20190711 2

<i>Sorbus unguiculata</i> is a pinnate-leaved deciduous shrub growing in mixed forests in Sichuan province, China. It is one of the least known species in the genus with high ornamental value. In this study, we firstly assembled and annotated the complete chloroplast genome of the species using the next-generation sequencing method. The results showed that the chloroplast genome size is 159,900 bp, comprising of a large single-copy (LSC) region of 87,888 bp, a small single-copy (SSC) region of 1 ...[more]

PMID: 33365486

Similar Datasets

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

The complete chloroplast genome of a Chinese endemic ornamental plant Sorbus unguiculata Koehne (Rosaceae).

Publications

The complete chloroplast genome of a Chinese endemic ornamental plant <i>Sorbus unguiculata</i> Koehne (Rosaceae).

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets