Abstract
Sinolimprichtia alpina var. dissecta is a plant variety which is characterized from S. alpina var. alpina in possessing characteristic, highly dissected bracteoles. In the current study, we have sequenced the complete chloroplast genome of S. alpina var. dissecta using the Illumina sequencing platform. The chloroplast genome is 156,719 bp in length, consisting of a LSC region of 95,625 bp, a SSC region of 10,500 bp, and a pair of inverted repeats (IR) regions of 25,297 bp. The GC content was 37.7%. A total of 126 unique genes were identified, including 81 protein-coding genes, 37 tRNA genes and 8 rRNA genes. Phylogenetic analysis based on 28 chloroplast genomes indicates that S. alpina var. dissecta is most closely related to Pterygopleurum neurophyllum.
Keywords: Sinolimprichtia alpina var. dissecta, alpine plants endemism chloroplast genome sequence
Sinolimprichtia alpina var. dissecta is a plant variety which is characterized from S. alpina var. alpina in possessing characteristic, highly dissected bracteoles. This species is distributed in Qinghai, SW Sichuan, SE Xizang, NW Yunnan occurring at altitudes from 3300 to 5000 meters above sea level. We report the first complete chloroplast genome of S. alpina var. dissecta using Illumina sequencing and resolve the phylogenetic position and characterize the genomic structure.
The plant sample of S. alpina var. dissecta used for sequencing was collected from Ganzi County, Ganzi Tibetan Autonomous Prefecture, Sichuan Province, China (31°49′16.94″N, 100°15′45.41″E). The voucher specimens are archived at the Herbarium of Kunming Institute of Botany, Chinese Academy of Sciences (KUN, KUN1490887). Total genomic DNA was extracted to construct a library for sequencing by using Illumina sequencing methods at the Beijing Novogene Bioinformatics Technology Center. The clean data of S. alpina var. dissecta was de novo assembled using NOVOPlasty v3.1 (Dierckxsens et al. 2017) and GetOrganelle pipeline (Jin et al. 2018). Then, the resulting contigs were identified and rearranged by mapping to reference genome Pleurospermum camtschaticum. Assembled plastid genome annotation was conducted using Geseq in Chlorobox web service (Tillich et al. 2017), with manual corrections for start and stop codons using Geneious v.9.0.2 (Kearse et al. 2012). The annotated plastid genome sequence was submitted to Genbank (MW221263).
The complete chloroplast genome of S. alpina var. dissecta is 156,719 bp in length, with a typical quadripartite structure, and contains a large single-copy (LSC) region of 95,625 bp, a small single-copy (SSC) region of 10,500 bp, a pair of inverted repeats (IR) regions of 25,297 bp. The overall GC content was 37.7%. A total of 126 unique genes, containing 81 protein-coding genes, 37 tRNA genes and eight rRNA genes.
We conducted a phylogenetic analysis to investigate the phylogenetic relationships among the whole chloroplast genome sequence of S. alpina var. dissecta and that of other 27 species of Apioideae in the NCBI GenBank database. We used maximum likelihood (ML) in RAxML8.0 with 1000 bootstrap replicates to construct a phylogenetic tree (Stamatakis 2014). In the ML tree, our results showed that S. alpina var. dissecta was most closely related to P. neurophyllum with strong support (Figure 1). The chloroplast genome of S. alpina var. dissecta will provide useful genomic information for future studies on genetic diversity in this group of rarely studied plants.
Figure 1.
Maximum-likelihood phylogenetic tree based on the chloroplast genome sequences. Numbers at nodes represent bootstrap support values.
Funding Statement
This study was supported by the CAS “Light of West China” Program (Zhilin Jiang), the Fund for Reserve Talents of Young and Middle-aged Academic and Technical Leaders of Yunnan Province [Grant 2014HB027], and Bio-safety and Bio-industry Innovation Team Project of Puer University [CXTD005].
Disclosure statement
No potential conflict of interest was reported by the author(s).
Data availability statement
The data that support the findings of this study are available in [GeneBank] at [heeps:www.ncbi.nlm.nih.gov/genbank/], reference number [MW033345], and the SRA data can be cited for in [GeneBank] at [https://www.ncbi.nlm.nih.gov/sra/PRJNA675925], reference number [PRJNA675925].
References
- Dierckxsens N, Mardulyn P, Smits G.. 2017. NOVOPlasty: de novo assembly of organelle genomes from whole genome data. Nucleic Acids Res. 45(4):e18. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Jin JJ, Yu WB, Yang JB, Song Y, Yi TS, Li DZ.. 2018. GetOrganelle: a simple and fast pipeline for de novo assembly of a complete circular chloroplast genome using genome skimming data. bioRxiv. 256479. [Google Scholar]
- Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, Sturrock S, Buxton S, Cooper A, Markowitz S, Duran C, et al. 2012. Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics. 28(12):1647–1649. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Stamatakis A. 2014. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics. 30(9):1312–1313. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Tillich M, Lehwark P, Pellizzer T, Ulbricht-Jones ES, Fischer A, Bock R, Greiner S.. 2017. GeSeq - versatile and accurate annotation of organelle genomes. Nucleic Acids Res. 45(W1):W6–W11. [DOI] [PMC free article] [PubMed] [Google Scholar]
Associated Data
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Data Availability Statement
The data that support the findings of this study are available in [GeneBank] at [heeps:www.ncbi.nlm.nih.gov/genbank/], reference number [MW033345], and the SRA data can be cited for in [GeneBank] at [https://www.ncbi.nlm.nih.gov/sra/PRJNA675925], reference number [PRJNA675925].