The complete chloroplast genome sequence of the Chinese endemic species Sorbus setschwanensis (Rosaceae) and its phylogenetic analysis

Abstract

Sorbus setschwanensis Koehne is a pinnate‐leaved Sorbus s.str. species endemic to China with narrow distribution and intriguing phylogeny that needs wider attention. In this paper, the complete chloroplast (cp) genome of S. setschwanensis is reported, and its phylogenetic position is analyzed. The complete cp genome of S. setschwanensis is 160 064 bp in size with 36.50% GC content. It has a typical quadripartite structure including a pair of inverted repeat regions (IRs) of 26 378 bp that separates a large single copy (LSC) region of 86 013 bp and a small single copy (SSC) region of 19 295 bp. The cp genome encodes 108 genes, comprising 76 protein‐coding genes, 28 tRNA genes and 4 rRNA genes. Additionally, 52 simple sequence repeats (SSRs) and 43 dispersed repeats were identified. Comparison of the whole cp genome with those of other Sorbus species showed an overall high degree of sequence similarity, but there are six highly variable regions (trnR‐atpA, petN‐psbM, ndhC‐trnV, trnE‐trnT, trnT‐trnL and rpl32‐trnL) located in intergenic spacers that may be useful as molecular markers in future population genetic and phylogenetic studies in the genus. Phylogenetic analyses based on 108 coding genes from 25 species in Rosaceae revealed that S. setschwanensis is nested within Sorbus sect. Sorbus together with other pinnately leaved species, but does not form a sister lineage to S. rufopilosa belonging to the same series Multijugae. Thus, the systematic position of S. setschwanensis and relationships with other species in the genus needs to be further studied.

Phylogeny of Maleae (Rosaceae) Based on Complete Chloroplast Genomes Supports the Distinction of Aria, Chamaemespilus and Torminalis as Separate Genera, Different from Sorbus sp.

“…The new assembly of the chloroplast genome of S. aucuparia obtained in this study extends the list of the available cpDNA genomes of the species belonging to the Maleae tribe, enabling a closer look into its phylogeny. The chloroplast genome of S. aucuparia assembled in this study is similar to other chloroplast genomes of the representatives of the Maleae tribe in terms of genome size, quadripartite structure and gene content [8,13,15,17].…”

“…In this study, we present a new assembly of the complete chloroplast genome of Sorbus aucuparia L., another representative of Sorbus s.s. Given the availability of complete chloroplast genomes of several Maleae species assembled recently by various research groups [8,[13][14][15][16][17][18], we attempted to reconstruct the phylogeny of the Maleae tribe based on complete chloroplast genomes, with a special focus on the relationships among the genera formerly assigned to Sorbus s.l.…”

Comparison among the chloroplast genomes of five species of Chamaerhodos (Rosaceae: Potentilleae): phylogenetic implications

“…These cp genomes have a conserved typically quadripartite structure, in which two inverted repeats (IRs) are separated by a large single‐copy region (LSC) and a small single‐copy region (SSC) (Palmer 1985, Wicke et al 2011). Due to its uniparental inheritance, conserved gene content and structure characteristics (Palmer 1985, Palmer et al 1988, Raubeson and Jansen 2005, Wicke et al 2011), the cp genome is valuable for studies on phylogeny, population genetics and species identification (Korpelainen 2004, Moore et al 2007, Ravi et al 2008, Liu et al 2019, Park et al 2019, Silva et al 2019, Asaf et al 2020, She et al 2020, Wang et al 2020).…”

Initial Complete Chloroplast Genomes of Alchemilla (Rosaceae): Comparative Analysis and Phylogenetic Relationships

“…The advent of the next-generation DNA sequencing technology ( Shendure and Ji, 2008 ) has magnified the rate of cp genome sequencing reports since the process is simpler, cost-effective and fast, resulting in the expansion of the cp genetics and genomics ( Daniell et al, 2016 ). Since the report of the first cp genome sequence of tobacco ( Nicotiana tabacum ) ( Shinozaki et al, 1986 ), several species in the Rosaceae have had their complete cp genome deposited to the National Center for Biotechnology Information (NCBI) organelle genome database 1 ( Salamone et al, 2013 ; Zhao Y. et al, 2018 ; Wang et al, 2020 ). However, none of the Alchemilla species genome has been sequenced to date.…”