The complete chloroplast genome of Drymocallis saviczii (Rosaceae: Potentilleae)

Abstract

The complete chloroplast genome of Drymocallis saviczii was reported in the present study. The chloroplast genome of D. saviczii was a circular DNA molecule with a size of 154,487 bp in length. The genome had a typical quadripartite structure composed of a pair of inverted repeats (IRa and IRb) of 25,991 bp separated by a large single-copy (LSC) region of 84,332 bp and a small single-copy (SSC) region of 18,173 bp. The genome encoded a set of 129 genes, comprising 84 protein-coding genes, 37 tRNA genes, and eight rRNA genes. Phylogenetic analysis demonstrated that D. saviczii was closer to D. glandulosa in current sampling.

Keywords:

• Chloroplast genome
• Drymocallis saviczii
• Potentilleae
• Rosaceae

Drymocallis saviczii (Schischk. et Kom.) Soják [synonym: Potentilla saviczii Schischk. et Kom.] belongs to the family Rosaceae Juss., subfamily Rosoideae (Juss.) Arn., tribe Potentilleae Sweet. This species is distributed in the eastern half of Siberia in the Russian Far East and adjacent parts of north-eastern China (Soják 2004, 2007, 2011, 2012). The complete chloroplast (cp) genome of D. saviczii was reported and characterized herein, which provides significant information for further studies on its taxonomy and population genetics.

Fresh leaves of D. saviczii were collected from Arxan, Nei Mongol, China. Voucher specimen (no. Li QQ 20170822002) was deposited in the herbarium of Inner Mongolia Normal University (NMTC). Total genomic DNA was extracted using the method of Doyle and Doyle (1987). Short-insert library (insert size, 300 bp) was prepared and then sequenced using the Illumina HiSeq platform in Novogene (Nanjing, China). A total of 36,860,588-bp raw reads were generated by Illumina paired-end sequencing after removing adapters. The raw reads were used to assemble the cp genome in NOVOPlasty (Dierckxsens et al. 2017), with ribulose-1, 5-bisphosphate carboxylase/oxygenase (rbcL) gene from D. glandulosa (GenBank accession no. KY420015) as the seed sequence. Chloroplast genome annotation was conducted using transferring annotations in Geneious Prime (Kearse et al. 2012), with the complete cp genome of Farinopsis salesoviana (Steph.) Chrtek et Soják (GenBank accession no. MT017928) as the reference. Where necessary, gene boundaries were manually corrected to match the start and stop codons and intron/exon boundaries. The annotated complete cp genome of D. saviczii was submitted to GenBank with the accession no. MT178809. The complete cp genome of D. saviczii was a circular DNA molecule with a size of 154,487 bp in length. The genome had a typical quadripartite structure, which composed of two copies of inverted repeats (IRa and IRb: 25,991 bp) separated by two regions: the large single-copy region (LSC: 84,332 bp) and the small single-copy region (SSC: 18,173 bp). The total GC content was 37.2%, and those of the LSC, SSC and each IR were 35.1%, 30.9%, and 42.8%, respectively. The cp genome encoded a set of 129 genes, comprising 84 protein-coding genes, 37 tRNA genes, and eight rRNA genes.

To examine the phylogenetic position of D. saviczii, the cp genome sequences of D. saviczii and 31 related species in Potentilleae plus four Rosa species were aligned by MAFFT version 7.450 (Katoh and Standley 2013) and trimmed properly using trimAL version 1.4 (Capella-Gutiérrez et al. 2009). The maximum likelihood (ML) tree was inferred using RAXML version 8 (Stamatakis 2014), with the combined rapid bootstrap analysis (1000 replicates) and search for best-scoring ML tree (the ‘-f a’ option). The GTRGAMMA model was used in the analysis. Phylogenetic tree demonstrated that D. saviczii was closer to D. glandulosa than to other species in current sampling (Figure 1).

Figure 1. Maximum likelihood (ML) tree based on the cp genome sequences of Drymocallis saviczii and related species plus four Rosa species as outgroups. Values along branches correspond to ML bootstrap percentages (only values <100% are shown).

Disclosure statement

No potential conflict of interest was reported by the author(s).

Data availability statement

The authors confirm that the data supporting the finding of this study are available within its supplementary material.

Additional information

Funding

This work was supported by the National Natural Science Foundation of China [Grant no. 31460051] and the Natural Science Foundation of Inner Mongolia, China [Grant no. 2018MS03039].