The complete chloroplast genome of mock strawberry, Duchesnea indica (Andrews) Th.Wolf (Rosoideae)

Abstract

Duchesnea indica (Andrews) Th.Wolf is a species of genus Duchesnea which is nested in Potentilla clade. Its fruit is developed enough to be compared with strawberry, which is a significant key to be independent genus Potentilla. In this study, we presented the first complete chloroplast genome of D. indica which length is 156,050 bp long and has four sub-regions: 85,352 bp of large single copy (LSC) and 18,572 bp of small single copy (SSC) regions are separated by 26,063 bp of inverted repeat (IR) regions including 129 genes (84 protein-coding genes, 8 rRNAs, and 37 tRNAs). The overall GC contents of the chloroplast genome are 37.0% and in the LSC, SSC, and IR regions are 34.9%, 30.6%, and 42.7%, respectively.

Keywords:

• Duchesnea indica
• chloroplast genome
• Rosaceae
• Duchesnea
• Potentilla

Genus Duchesnea belonging to subtribe Potentillinae, tribe Potentilleae has a swollen receptacle, red insipid fruit, 3–5 foliolate leaf blades, and yellow petals (Rydberg 1898). This fruit type is a unique feature inside subtribe Potentillinae, which is similar to that of genus Fragaria included in subtribe Fragariinae. Based on recent molecular phylogenetic studies, genus Duchesnea is nested within Potentilla clade of subtribe Potentillinae and clustered into the same clade with Potentilla reptans which is a type species of genus Potentilla (Eriksson et al. 1998; Eriksson et al. 2003; Kurtto and Eriksson 2003; Töpel et al. 2011). Genus Duchesnea was classified into the section Tomentilae covering Potentilla reptans, Potentilla flagellaris, and Potentilla tormentilla based on morphological classification (Wolf 1908).

To understand phylogenetic position of genus Duchesnea with whole chloroplast genomes, we sequenced complete chloroplast genome of Deuchesnea indica (Andrews) Th.Wolf (Voucher in InfoBoss Cyber Herbarium (IN); K-I. Heo; IB-00571). Total DNA was extracted from fresh leaves of D. indica by using a DNeasy Plant Mini kit (QIAGEN, Hilden, Germany). Genome sequencing was performed using HiSeq2000 at Macrogen Inc., Korea and de novo assembly was done by Velvet 1.2.10 (Zerbino and Birney 2008), gap was filled by SOAPGapCloser 1.12 (Zhao et al. 2011) and assembled sequences were confirmed by BWA 0.7.17 (Li 2013) and SAMtools 1.9 (Li et al. 2009). Geneious R11 11.0.5 (Biomatters Ltd., Auckland, New Zealand) was used for chloroplast genome annotation based on Potentilla purpurea chloroplast partial genome (KY419953.1; Zhang et al. 2017).

The chloroplast genome of D. indica (Genbank accession is MK134678) is 156,050 bp and has four sub-regions: 85,352 bp of large single copy (LSC) and 18,572 bp of small single copy (SSC) regions are separated by 26,063 bp of inverted repeat (IR). It contained 129 genes (84 protein-coding genes, 8 rRNAs, and 37 tRNAs); 18 genes (7 protein-coding genes, 4 rRNAs, and 7 tRNAs) are duplicated in IR regions. The overall GC content of D. indica is 37.0% and in the LSC, SSC, and IR regions were 34.9%, 30.6%, and 42.7%, respectively.

One complete chloroplast genome of Potentilla, Potentilla micrantha (HG931056; Ferrarini et al. 2013), and several partial chloroplast genomes (Zhang et al. 2017) are available. In total, nine chloroplast genomes of Rosaceae including D. indica complete or selected partial chloroplast genomes were aligned by MAFFT 7.388 (Katoh and Standley 2013) for constructing neighbor joining phylogenetic tree under MEGA X (Kumar et al. 2018). The tree shows that genus Duchesnea is nested in Potentilla chloroplast genomes; which is the same result in molecular phylogeny of Potentilla and Duchesnea genera (Heo et al., in preparation; Figure 1).

Figure 1. Neighbor joining phylogenetic tree (bootstrap repeat is 10,000) of nine Rosaceae partial or complete chloroplast genomes: Duchesnea indica (MK134678; this study), Potentilla tilingii (KY420028; partial genome), Potentilla lancinata (KY419968; partial genome), Potentilla purpurea (KY419953; partial genome), Potentilla micrantha (HG931056), Dasiphora fruticosa (NC 036423), Fragaria x ananassa cultivar Benihoppe (NC_035961), Fragaria vesca subsp. vesca (NC_015206), and Rubus crataegifolius (MG189543). The numbers above branches indicate bootstrap support values of the neighbor joining tree.

Disclosure statement

The authors declare that they have no competing interests.

Additional information

Funding

This work was supported by InfoBoss Research Grant [IBG-0005].