Complete chloroplast genomes of Sorbus sensu stricto (Rosaceae): comparative analyses and phylogenetic relationships

Abstract

Background Sorbus 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. Results The 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. Conclusion Phylogenomic 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.

Characterization of the Plastid Genomes of Four Caroxylon Thunb. Species from Kazakhstan

“…Similarly, the IRb/SSC boundary was located within the ycf1 gene, while the IRa/SSC boundary was identified within the duplicated copy of the ycf1 gene. These results are in accordance with previous studies conducted on different species [53,54]. Notably, no major changes in the position of IR regions were observed in the studied plastid genomes, suggesting the absence of substantial structural rearrangements [55,56].…”

Complete chloroplast of four Sanicula taxa (Apiaceae) endemic to China: lights into genome structure, comparative analysis, and phylogenetic relationships

“…The structure, gene orders and GC content were highly conserved and nearly similar in the samples of Sanicula analyzed here, and were also identical to other cp genomes in other genera of Apiaceae and other angiosperms [ 2 , 17 , 20 , 21 , 23 – 26 ]. The size of the 13 cp genomes varied from 155,335 ( S. flavovirens ; NC_061752 and OP703176) to 155,764 bp ( S. lamelligera ; OP703174) (Table 1 ).…”

“…Many works proved that the variation of SSRs in cp genomes were widely used in population genetic studies, species identification and evolutionary relationship [ 26 , 34 , 38 ]. In this study, the characteristics of SSRs and short dispersed repeats (SDRs) were also similar among these Sanicula cp genomes.…”

Pollen morphology of Norwegian hybrids of Sorbus

“…is non‐monophyletic in its traditional large circumscription, as evidence in later years has shown that Sorbus s.l. has five main evolutionary branches and is polyphyletic (Lo and Donoghue 2012, Tang et al 2022).…”