Technical note

The genus Sorbus consists of approximately 250 species which are spread throughout the northern hemisphere in Asia, North America, Europe and northern Africa (Phipps et al. 1990). One example is wild service tree (Sorbus torminalis [L.] Crantz), which is widely distributed across western, central and southern Europe. However, the species is rare in Britain, Denmark, Germany and Poland, and therefore is being often protected at a local (nature reserves) or national scales (e.g. Poland, Bednorz 2007). Because of its specific features, such as scattered distribution of populations, insect pollination and animal seed dispersal, gametophytic self-incompatibility system, the ability for clonal propagation, and its ecological importance as a driver of biodiversity of forest ecosystems, it has been subjected to research studies often addressing the species gene conservation status (Hoebee et al. 2006; Oddou-Muratorio et al. 2004; Ludwig et al. 2013; Jankowska-Wroblewska et al. 2016). However, genomic resources of S. torminalis, which could further contribute to the advancement of population genetic studies of the species are currently limited. In this report we summarize our work on the S. torminalis chloroplast genome sequencing, assembly and annotation. The annotated sequence has been submitted to GenBank under accession number KY457242.

The individual wild service tree selected for this study was located in the Jamy Forest District (53°35′40′′N, 18°50′59′′E), in the north-central part of Poland, at the north-eastern distribution limits of the species. Fresh leaves were collected in late summer of 2016, stored in the dark at 20 °C for 48 h to reduce the starch levels samples and allowed to dry. The total gDNA was isolated according to Wang et al. (2013) and send to the Macrogen (Macrogen Inc., Seoul, South Korea) in order to perform library preparation and sequencing on the HiSeq X Illumina system. The chloroplast genome was constructed de novo using NOVO Plasty pipeline v. 1.2.3 (Dierckxsens et al. 2016), based on 10% of the initial 242.4 M raw 150 bp pair-end reads dataset. Complete chloroplast genome sequences of Pyrus pyrifolia (GenBank: AP012207) (Terakami et al. 2012) and Malus prunifolia (GenBank: KU851961) (Bao et al. 2016), two closely related species from the Roseaceae family, were used as seed sequences in the assembly, which resulted in exactly the same chloroplast genome assemblies od S. torminalis. The de novo assembly generated a double-stranded 160,390 bp circular genome from 1,618,116 aligned and 372,372 assembled reads, with final 1523x coverage. The genome annotation was performed using Dual Organellar GenoMe Annotator (DOGMA) (Wyman et al. 2004) and Plann software (Huang and Cronk 2015) with manual correction using the AP012207 sequence as a reference. Genome was visualized with OrganellarGenomeDRAW (OGDRAW) (Lohse et al. 2007).

The nucleotide share: 31.35% A, 18.61% C, 17.87% G, 32.12% T and 36.48% GC content is similar to those found in P. pyrifolia (Terakami et al. 2012) and M. prunifolia (Bao et al. 2016). The cpDNA structure is quadripartite and is build by large (LSC, 88,029 bp) and small (SCC, 19,547 bp) singlecopy regions separated by two inverted repeat regions (IRA and IRB, 26,407 bp each) (Fig. 1). The genome contains 127 genes including: protein-coding genes (PCG), transfer RNA (tRNA) and ribosomal RNA (rRNA). PCG group includes 83 genes (77 unique genes), in which 6 of them are in double copies (ndhB, rpl2, rpl23, rps7, rps12, ycf2). Notably, 13 PCGs contain at least one intron (atpF, ndhA, ndhB, petB, petD, clpP, rpoC1, rpl2, rpl16, rps16, rps12, ycf3). The tRNA group includes 36 genes in which 7 of them are in double copies (trnA-UGC, trnI-CAU, trnI-GAU, trnL-CAA, trnN-GUU, trnR-ACG, trnV-GAC), and 6 of them contain at least one intron (trnA-UGC, trnG-UCC, trnI-GAU, trnK-UUU, trnL-UAA, trnV-UAC). In the rRNA group all genes are in double copies (rrn4.5, rrn5, rrn16, rrn23) without introns.

Fig. 1
figure 1

Visualization of the Sorbus torminalis chloroplast genome, with marked genes and transcription directions on the outer circle. The inner circle highlights contents of G+C (dark grey) and A+T (light grey) and show locations of the LSC, SSC, IRA and IRB regions

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In order to determine the phylogenetic position of S. torminalis based on the whole chloroplast genome sequence we have selected 12 available complete genomes from the Maloideae subfamily (Fig. 2). The sequences were aligned using MAFFT software (Katoh and Standley 2013) online server (http://mafft.cbrc.jp/alignment/server/) and a neighborhood-joining (NJ) tree was created using Archeopteryx (Han and Zmasek 2009) integrated with MAFFT server. The resulting phylogenetic tree suggests that S. torminalis is more closely related to the genus Malus than Pyrus, which confirms earlier findings on the phylogeny within Rosaceae family (Campbell et al. 2007).

Fig. 2
figure 2

Phylogenetic relationship within the subfamily Maloideae, calculated based on available complete chloroplast genome sequences using NJ method

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