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Chloroplast genome features and phylogenomic placement of Sorbus hupehensis var. paucijuga (Rosaceae).

ABSTRACT: The complete chloroplast genome of Sorbus hupehensis var. paucijuga was sequenced with Illumina HiSeq 2000 platform. It was a typical quadruple structure as other plants of Sorbus with 160,050 bp in length, including a large single-copy (LSC: 87,905 bp) region and a small single-copy (SSC: 19,325 bp) which were separated by a pair of inverted repeats (IRa, b: 26,410 bp) region. The overall GC content is 36.5%. A total of 130 genes was annotated which contained 85 protein-coding genes including the Trans splicing gene of rps12, 37 tRNA genes, and 8 rRNA genes. ML phylogenetic analysis compared with 7 expressed chloroplast genomes of Rosaceae revealed that S. hupehensis var. paucijuga was a sister to other Sorbus species. Six species of Sorbus were divided into two groups, the species of group one is distributed in Asia and the species of group two distributed in Europe. Among group one, S. hupehensis var. paucijuga had the closest genetic relationship with S. ulleungensis which is a New Endemic Species on Ulleung Island of Korea, and followed by S. setschwanensis which is only distributed in Sichuan and Guizhou of China. Sorbus hupehensis var. paucijuga has a relatively close relationship with the other three species of Sorbus in the group two. And, it has a relatively distant from other genera of Prunus mongolica and Rosa rugosa.

SUBMITTER: Liu D

PROVIDER: S-EPMC7995867 | biostudies-literature |

REPOSITORIES: biostudies-literature

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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.

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Chloroplast genome features and phylogenomic placement of Sorbus hupehensis var. paucijuga (Rosaceae).

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