Abstract
The first complete chloroplast genome (cp) sequences of Silene jenisseensis were reported in this study. The S. jenisseensis cp genome was 150,299 bp in size, with two inverted repeat (IR) regions of 25,384 bp, the large single-copy (LSC) region of 82,153 bp, and the small single-copy (SSC) region of 17,378 bp. The cp genome of this species contained 111 genes, including 77 protein-coding genes, 4 ribosomal RNA, and 30 transfer RNA genes. The overall GC content was 36.4%. Phylogenetic analysis of the cp genomes within the Caryophyllaceae family suggests that S. jenisseensis is closer to the clade formed by S. capitata and S. aprica.
Keywords: Caryophyllaceae, chloroplast genome, phylogenetic analysis, Silene jenisseensis
Silene jenisseensis Willdenow is perennials of the Caryophyllaceae family and broadly distributed in forest and meadow communities of Russian, Mongolia, China, and Korea (Zhou et al. 2001). The root of this species is well known in traditional Chinese medicine as a substitute for the Chinese drug Yin-Chai-Hu (root of Stellaria dichotoma Linnaeus var. lanceolata Bge) and it is utilized to treat fever due to Yin-deficiency and fever in infant malnutrition (Chinese Pharmacopoeia 1990). Phytochemical studies have reported that ecdysteroids, flavonoids, triterpene glycosides, and sterols are the major characterized constituents of this plant (Darmograi 1977; Cui and Qiao 1995; Lacaille-Dubois et al. 1995; Olennikov and Kashchenko 2017). Here, we characterized the complete chloroplast (cp) genome of S. jenisseensis based on the Illumina sequencing technology to understand its genetic background and to explore its phylogenetic placement.
The specimen (CaoW5049) of S. jenisseensis was collected from Fengcheng, Liaoning, China (N40°22′52″, E124°5′1″, 110 m) and deposited in the herbarium of Kunming Institute of Botany, CAS (KUN). The total DNA was extracted and used for sequencing as previously described (Zhang et al. 2019). The 2 Gb raw data were generated and used for de novo cp genome assembly with SPAdes (Bankevich et al. 2012) and all predicted genes were annotated using PGA (Qu et al. 2019). The complete cp genome sequence of S. jenisseensis was deposited in GenBank database under the accession number MN723869.
The complete cp genome of S. jenisseensis is 150,299 bp in length and shows the GC content of 36.4%. The cp genome of this species displays a typical quadripartite structure, two copies of inverted repeats (IRs, 25,384 bp each) segregated by a large single-copy (LSC, 82,153 bp) region and a small single-copy (SSC, 17,378 bp) region. In addition, a total of 111 unique genes were encoded, including 77 protein-coding genes (PCGs), 30 transfer RNA (tRNA) genes, and 4 ribosomal RNA (rRNA) genes. Of them, five PCGs (ndhB, rpl2, rps12, rps7, and ycf2), four rRNAs (rrn16, rrn23, rrn4.5, and rrn5), and seven tRNAs (trnA-UGC, trnI-CAU, trnI-GAU, trnL-CAA, trnN-GUU, trnR-ACG, and trnV-GAC) have two copies. Fourteen genes (atpF, ndhA, ndhB, petB, petD, rpl16, rpoC1, rps16, trnA-UGC, trnG-UCC, trnI-GAU, trnK-UUU, trnL-UAA, and trnV-UAC) contain one intron and three genes (clpP, rps12, and ycf3) have two introns.
To determine the phylogenetic position of S. jenisseensis, a phylogenetic analysis was carried out with the maximum likelihood (ML) method (Stamatakis 2014). Agrostemma githago from the Caryophyllaceae family was used as outgroup. The cp genomes of S. jenisseensis and previously published other species from the genus Silene were used for phylogenetic analysis in this study. The GenBank accession numbers of all the species used were provided in Figure 1. The phylogenetic tree showed that S. jenisseensis is more closely related to the clade formed by S. aprica and S. capitate (Figure 1). The S. jenisseensis cp genome reported in this study may provide useful resources for the development of medical value as well as robust phylogenetic study at deep level of Silene in the future.
Figure 1.
The maximum likelihood (ML) tree of Silene inferred from the complete chloroplast genome sequences. Numbers at nodes correspond to ML bootstrap percentages (1000 replicates).
Funding Statement
This work was supported by Project on the Integration of Industry, Education and Research of Liupanshui [52020-2018-02-17]; Scientific Elitists Project of Ordinary Colleges and Universities of Guizhou Province [QJH KY [2019] 061]; and Science and Technology Platform and Talent Team Project of Science and Technology Department of Guizhou Province [QKH Platform & Talent [2017] 5721].
Disclosure statement
No potential conflict of interest was reported by the authors.
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