The complete chloroplast genome and phylogenetic analysis of Potentilla sischanensis Bunge ex Lehm

Abstract

Potentilla sischanensis Bunge ex Lehm. is a widespread perennial herb in north China. The plant has little yellow flowers, and the petioles are white-tomentose and sparsely villous. To determine the chloroplast genome, total genomic DNA was extracted from fresh leaves and sequenced. The complete chloroplast genome was assembled and annotated. The chloroplast genome of this plant is a circular form with a length of 156,240 bp, including a large single-copy region (LSC, 85,748 bp), a small single-copy region (SSC, 18,566 bp), and two inverted repeats (IRs, 25,963 bp). A total of 132 genes were predicted, comprising 87 encoded proteins, 8 rRNAs and 37 tRNAs. The evolutionary history indicates that P. sischanensis was grouped within Potentilla and formed a clade with Potentilla chinensis and Potentilla stolonifera with a 100% bootstrap support value. The complete cp genome can serve as a reference for future studies on molecular biology, evolution, population genetics, taxonomy and resource protection.

Keywords:

• Potentilla sischanensis Bunge ex Lehm.
• chloroplast genome
• phylogenetic analysis

Potentilla sischanensis Bunge ex Lehm., belonging to Rosaceae, is a perennial herb that is 10–330 cm tall with little yellow flowers and petioles that are white-tomentose and sparsely villous. This plant is widespread in northern China (Delectis Florae Reipublicae Popularis Sinicae Agendae Academiae Sinicae Edita 1989). For containing bioactive constituents, most of Potentilla species have therefore been used extensively in traditional medicine. Extracts from these plants have been used to cure toothache, inflammation of the throat, and ulcers of the mouth in Europe and to treat diarrhea, hepatitis, rheuma, scabies and detoxification in China (Tomczyka and Latté 2009). Extracts from some species can also delay the process of carcinogenesis (Ganguly et al. 2019; Kowalik et al. 2020). The extract from Potentilla rugulosa leaves has been identified as a potential functional food supplement for preventing the development of obesity (Choi et al. 2020). Among the many studies that have been performed on Potentilla plants, very few studies have been performed on P. sischanensis, except for one phylogenetic study (Feng et al. 2017). Here, we report the complete chloroplast (cp) genome of P. sischanensis and analyze its phylogenetic relationship with other related species.

Samples were collected from the Qilian Mountains (36°34′21″N, 101°48′44″E) in Qinghai Province. A specimen was deposited at the College of Ecological Environment and Resources, Qinghai Nationalities University (https://shxy.qhmu.edu.cn/, Junqiao Li, email: [email protected]) under voucher number HCEERQNU-20200517001. Total genomic DNA was extracted from the fresh leaves of a sample with a Rapid Plant Genomic DNA Isolation Kit. Paired-end libraries with an average length of 500 bp were constructed and sequenced on the Illumina HiSeq 4000 platform (Sangon Biotech (Shanghai) Co., Ltd.). The complete cp genome was assembled via NOVOPlasty 3.7.2 (Dierckxsens et al. 2017) with Potentilla freyniana Bornm. (GenBank accession no. MK472813.1) as the reference genome. The complete assembled genome was annotated via PGA (Qu et al. 2019).

The complete cp genome of P. sischanensis (GenBank accession no. MW678838.1) has a typical quadripartite form with a length of 156,240 bp and is composed of a large single-copy region (LSC, 85,748 bp), a small single-copy region (SSC, 18,566 bp), and two inverted repeats (IRs, 25,963 bp). The genome has a GC content of 37%. A total of 132 genes were predicted in this cp genome, comprising 87 encoded proteins, 8 rRNAs and 37 tRNAs.

Phylogenetic analysis was performed based on the complete cp genomes of P. sischanensis and 33 other related species in Rosaceae with two species in Rhizophoraceae as outgroup. The genome-wide alignment was constructed by HomBlocks (Bi et al. 2018), the evolutionary history was inferred using the maximum likelihood (ML) method by IQ-TREE 1.6.12 under the GTR + F + R3 model (Nguyen et al. 2015; Kalyaanamoorthy et al. 2017), and the output file was edited in MEGA X (Kumar et al. 2018). Bootstrap (BS) values were calculated by UFBoot2 from 1000 replicates (Hoang et al. 2018). As expected, P. sischanensis was grouped within Potentilla and formed a clade with Potentilla chinensis Ser. and Potentilla stolonifera Lehm. ex Ledeb. with a 100% BS support value (Figure 1). The complete cp genome of P. sischanensis can serve as a reference for future studies on molecular biology, evolution, population genetics, taxonomy and resource protection.

Figure 1. ML phylogenetic tree based on 36 species chloroplast genomes was constructed using IQ-TREE 1.6.12. Numbers on each node are bootstrap support values from 1000 replicates.

Disclosure statement

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

Data availability statement

The genome sequence data that support the findings of this study are openly available in GenBank of NCBI at (https://www.ncbi.nlm.nih.gov/nuccore/MW678838) under the accession no. MW678838.

The associated BioProject, SRA, and Bio-Sample numbers are PRJNA725277, SRR14328193, and SAMN 18875820, respectively.

Additional information

Funding

This work was supported by High-level talent foundation of Qinghai Nationalities University [grant No.2017XJG03].