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Chloroplast genome for Crataegus pinnatifida (Rosaceae) and phylogenetic analyses with its coordinal species.

ABSTRACT: Crataegus pinnatifida is an important medicinal and edible plant. Now, the complete chloroplast (cp) genome of C. pinnatifida was assembled and annotated. The cp genome of C. pinnatifida was 159,898 bp and contained two short inverted repeat regions (26,540 bp) which were separated by a small single copy region (19,219 bp) and a large single copyregion (87,599 bp). The cp genome encodes 109 unique genes, including 75 protein-coding genes, 30 transfer RNA genes and 4 ribosomal RNA genes. The topology of the phylogenetic tree showed that C. pinnatifida has a close relationship with species Eriobotrya, Sorbus, Pyrus, Mulus, and Chaenomeles.

SUBMITTER: He SL

PROVIDER: S-EPMC7510473 | 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 for Crataegus pinnatifida (Rosaceae) and phylogenetic analyses with its coordinal species.

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