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The complete genome sequence of Sorbus insignis (Rosaceae: Amygdaloideae), an epiphytic shrub in this genus.

ABSTRACT: Sorbus insignis (Hook. f.) Hedl., belonging to S. sect. Multijugae Yu is an epiphytic shrub. Its phylogenetic position is still poorly understood. In this study, we assembled its complete chloroplast genome from whole-genome high-throughput sequencing data. The chloroplast genome was 159, 993 bp in length, with a large single-copy (LSC) region of 87, 932 bp, a small single-copy (SSC) region of 19, 255 bp, separated by two inverted repeat (IR) regions of 26, 403 bp each. It was predicted to contain a total of 132 genes, with an overall GC content of 36.56%. Phylogenetic analysis suggested S. insignis belongs to S. L. sensu stricto and closest to S. prattii Koehne among the published chloroplast genome.

SUBMITTER: Tan J

PROVIDER: S-EPMC7782918 | biostudies-literature | 2020 Aug

REPOSITORIES: biostudies-literature

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The complete genome sequence of Sorbus insignis (Rosaceae: Amygdaloideae), an epiphytic shrub in this genus.

Tan Jing J Wang Yi Y Wu Wei W Li Yongquan Y Zhao Wanyi W Liao Wenbo W Fan Qiang Q Liao Boyong B

Mitochondrial DNA. Part B, Resources 20200826 3

Sorbus insignis (Hook. f.) Hedl., belonging to S. sect. Multijugae Yu is an epiphytic shrub. Its phylogenetic position is still poorly understood. In this study, we assembled its complete chloroplast genome from whole-genome high-throughput sequencing data. The chloroplast genome was 159, 993 bp in length, with a large single-copy (LSC) region of 87, 932 bp, a small single-copy (SSC) region of 19, 255 bp, separated by two inverted repeat (IR) regions of 26, 403 bp each. It was pred ...[more]

PMID: 33458123

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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

The complete genome sequence of Sorbus insignis (Rosaceae: Amygdaloideae), an epiphytic shrub in this genus.

Publications

The complete genome sequence of <i>Sorbus insignis</i> (Rosaceae: Amygdaloideae), an epiphytic shrub in this genus.

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