The complete chloroplast genome of Semenovia thomsonii (Tordylieae: Apiaceae), a new record from Xizang, China

Abstract

Semenovia thomsonii is a perennial herb native to India. In this study, we assembled and annotated the complete chloroplast (cp) genome of a specimen collected from Xizang, China, using whole genome next-generation sequencing. The cp genome is circular in structure and 147,137 bp in length, consisting of one large single-copy (LSC) region of 92,885 bp, one small single-copy (SSC) region of 17,448 bp, and a pair of inverted repeat regions of 36,804 bp. The overall GC content of the genome is 37.6%. The cp genome was predicted to contain 129 genes, including 85 protein-coding, 36 tRNA, and eight rRNA. Phylogenetic analysis of S. thomsonii and 21 cp genomes in the Apiaceae fully resolved S. thomsonii in a clade with S. gyirongensis, and S. transiliensis. These genetic data represent the first confirmed report of S. thomsonii from Xizang, China and provide useful information to the phylogenetic history of the genus Semenovia.

Keywords:

• Semenovia thomsonii
• complete chloroplast genome
• phylogenetic analysis

Semenovia thomsonii (C. B. Clarke) Manden (Apiaceae, Apioideae), is naturally distributed in Jammu, Kashmir, Himachal Pradesh and occurs throughout India (Mukherjee and Constance 1993). Examination of specimens from Zhada County, Xizang, we identified S. thomsoni from the collection (8180, KUN; 76-8180, PE; 76-9163, QTPMB). The specimens were misidentified as Heracleum millefolium Diels. In August 2015, we successfully collected the same samples according to the collection records and further confirmed based on morphology, the occurrence of S. thomsonii in China. In the most updated checklist of the Chinese Umbelliferae, S. thomsonii is recognized in China (Pimenov 2017). To confirm the presence of S. thomsonii in China, we performed next-generation sequencing on a specimen from Xizang and compared its genome to previously published species of Semenovia.

The mature leaves of S. thomsonii were collected from a rocky slope near Seerdi village (32°11′58.02″N, 79°10′58.68″E, altitude 4200 m), Qusong country, Zhada County, Xizang, China and preserved them using silica gel for future study. A voucher specimen (voucher number: xqy2015081901) was deposited in the herbarium of the Natural History Museum of Sichuan University (SZ). Herbarium acronyms followed Thiers (2016). Total genomic DNA of S. thomsonii was isolated using the Plant Genomic DNA Kit (TIANGEN Biotech., Beijing, China) and sequenced on an Illumina HiSeq × Ten platform (Illumina, San Diego, CA). Approximately, 5 Gb of raw data were generated through pair-end 150 bp sequencing. Adapters and low-quality reads were removed and high-quality reads were used for the cp genome assembly using SOAPdenovo2 (Luo et al. 2012). The resulting contigs were linked based on overlapping regions after being aligned to S. gyirongensis Q.Y. Xiao & X.J. He (NC_042912) using Geneious version 11.0.4 (Kearse et al. 2012). The complete chloroplast (cp) genome of S. thomsonii was annotated in Geneious and submitted to GenBank (accession number: MW371294). The genome annotation was performed by aligning with the cp genomes of related species.

The cp genome of S. thomsonii exhibited a general quadripartite structure typical of higher plants. The cp genome is 147,137 bp in length and contains a large single-copy region (LSC) of 92,885 bp and a small single-copy region (SSC) of 17,448 bp, separated by two identical inverted repeat regions (IRa and IRb, 18,402 bp). The overall GC content was 37.6% and the plastome contained 129 genes, including 85 protein-coding, eight rRNA, and 36 tRNA.

To confirm the phylogenetic position of S. thomsonii within the family of Apiaceae, a total of 21 complete cp genomes of Apiaceae were obtained from GenBank, designating Bupleurum boissieuanum and B. falcatum as out-groups. The 22 complete cp sequences were aligned using MAFFT version 7 (Katoh and Standley 2013) and maximum likelihood (ML) analysis was conducted using RAxML (Stamatakis 2014) with 1000 bootstraps under the GTRGAMMAI substitution model. The phylogenetic tree (Figure 1) indicated that S. thomsonii was closely related to S. gyirongensis and S. transiliensis Regel & Herder. These results are similar to those found by Logacheva et al. (2010) and Xiao et al. (2018). This analysis represents the first genetic confirmation of S. thomsonii in China and the first published cp genome. The data will provide useful information for phylogenetic studies and conservation genetics in the Apiaceae.

Figure 1. Phylogenetic analysis of S. thomsonii and related Apiaceae based on complete chloroplast genome sequences. Bootstrap values based on 1000 replicates a listed at the nodes and GenBank accession follow the binomials.

Research involving human participants and/or animals

This article does not contain any studies with human participants or animals performed by any of the authors.

Acknowledgments

The authors thank Dr. Xian-Lin Guo for their help in preparing this article.

Disclosure statement

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

Data availability statement

Chloroplast data supporting this study are openly available in GenBank at nucleotide database, https://www.ncbi.nlm.nih.gov/nuccore/MW371294.

Associated BioProject, https://www.ncbi.nlm.nih.gov/bioproject/PRJNA730370, BioSample accession number at https://www.ncbi.nlm.nih.gov/biosample/SAMN19229653 and Sequence Read Archive at https://www.ncbi.nlm.nih.gov/sra/SRR14561442.

Additional information

Funding

This work was supported by the National Specimen Information Infrastructure, specimen platform of China, teaching specimens sub-platform (Web, http://mnh.scu.edu.cn/, 2005DKA21403-JK]; Science and Technology Projects of Guizhou Province, China [No. ZK[2021]090]; Regional First-class Discipline of Ecology in Guizhou Province [No. XKTJ[2020]22]; Innovation Research Project of Coarse Cereals Specialty in Guizhou Province [No. 2019[4012]]; Talents Research Project of Guizhou Provincial Department of Education [No. KY[2018]072]; High-level Innovative Talents Project in Guizhou Province [No. [2016]4]; the National Natural Science Foundation of China [No.31560059].