http://orcid.org/0000-0003-0786-4701
Abstract
Selaginella tamariscina (Beauv.) Spring distributed in East Asia region including Korea used as traditional medicine. We completed chloroplast genome of Korean S. tamariscina. Its length is 126,368 bp and has four subregions: 53,213 bp of large single-copy and 47,560 bp of small single-copy regions are separated by 12,796 bp of direct repeat regions including 80 genes (61 protein-coding genes, 8 rRNAs, and 9 tRNAs). Phylogenetic trees show that Korean S. tamariscina is clustered with that of China species and 1,213 single nucleotide polymorphisms and 1,641 insertions and deletions are identified against Chinese S. tamariscina.
Selaginella tamariscina (Beauv.) Spring (Selaginellaceae) possesses extreme drought tolerance (Giarola et al. Citation2017), distributing in Russia (Siberia), China, Korea, Japan, Philippines, Taiwan, northern Thailand, and India. It has long been used as a beneficial traditional medicine in Korea. Since it contains Selaginellin (Cheng et al. Citation2008), flavonoids (Zheng, Zhang, et al. Citation2011), and sumaflavone (Yang et al. Citation2006), it also presented anti-cancer (Yang et al. Citation2007), inhibition of immediate allergic reactions (Dai et al. Citation2005), and antihyperglycemic activities (Zheng, Li, et al. Citation2011).
Total DNA of S. tamariscina collected in Wolsong-ri, Jijeong-myeon, Wonju-si, Korea (Voucher in InfoBoss Cyber Herbarium (IN); K. Lee, IB-01028; 37.442160 N, 127.824103E) was extracted from fresh leaves by using a DNeasy Plant Mini Kit (QIAGEN, Hilden, Germany). Genome was sequenced using HiSeqX at Macrogen Inc., Korea, and de novo assembly was done by Velvet 1.2.10 (Zerbino and Birney Citation2008) and SOAPGapCloser 1.12 (Zhao et al. Citation2011) and confirmed by BWA 0.7.17 (Li Citation2013) and SAMtools 1.9 (Li et al. Citation2009). Geneious R11 11.0.5 (Biomatters Ltd, Auckland, New Zealand) was used for chloroplast genome annotation based on the Chinese S. tamariscina chloroplast (NC_041646; Xu et al. Citation2018).
The chloroplast genome of Korean S. tamariscina (GenBank accession is MN894555) is 126,368 bp (GC ratio: 54.0%) and has four subregions: 53,213 bp of large single copy (53.4%) and 47,560 bp of small single copy (54.0%) regions are separated by 12,796 bp of direct repeat regions (55.3%). It contains 80 genes (61 protein-coding genes, 8 rRNAs, 9 tRNAs, and 2 pseudogenes); 7 genes (2 protein-coding genes, 4 rRNAs, and 1 tRNA) are duplicated in direct repeat regions. One pseudogene, chlN, is truncated by one SNP at 103,153 bp on chloroplast genome, which occurred in common ancestor of angiosperm (Jansen et al. Citation2007).
Alignment of two S. tamariscina chloroplast genomes presents 1,213 single nucleotide polymorphisms (SNPs) and 1,641 insertions and deletions (INDELs) are identified, higher than those of Selaginella uncinate between Japan (Tsuji et al. Citation2007) and China (Zhang et al. Citation2019; 525 SNPs and 602 INDELs). It is similar level to Goodyera schlechtendaliana (711 to 2,889 variations; Oh et al. Citation2019a, Citation2019b) and higher than Pyrus ussuriensis (121 SNPs and 781 INDELs; Cho et al. Citation2019), Camellia japonica (78 SNPs and 643 INDELs; Park et al. Citation2019), and Marchantia polymorpha (69 SNPs and 660 INDELs; Kwon et al. Citation2019). Proportion of variations on the chloroplast genome of S. tamariscina is 2.26%, which is between G. schlechtendaliana (1.95%; Oh et al. Citation2019a, Citation2019b) and Gastrodia electa (3.04%; Park et al. Citation2020).
Fifteen chloroplast genomes of Selaginella including two S. tamariscina chloroplasts and one outgroup species, Isoetes yunguiensis (Zhou et al. Citation2016), were used for constructing neighbor joining (bootstrap repeat is 10,000) and maximum likelihood phylogenic trees (bootstrap repeat is 1,000) using MEGA X (Kumar et al. Citation2018) after concatenating alignments of 44 conserved genes by MAFFT 7.450 (Katoh and Standley Citation2013) under the environment of Plant Chloroplast Database (http://www.cp-genome.net/). Phylogenetic trees show that Korean S. tamariscina is clustered with that of China ().
Figure 1. Neighbor joining (bootstrap repeat is 10,000) and maximum likelihood (bootstrap repeat is 1,000) phylogenetic tree of 44 conserved genes from 15 Selagenella and outgroup species chloroplast genomes: Selaginella tamariscina (MN894555 in this study, NC_041646), S. bisulcata (NC_041640), S. doederleinii (NC_041641), S. hainanensis (NC_041642), S. indica (NC_041098), S. lyallii (NC_041556), two S. moellendorffii (HM173080 and MG272484), S. pennata (NC_041643), S. remotifolia (NC_041644), S. sanguinolenta (NC_041645), two S. uncinata (NC_041575 and AB197035), S. vardei (NC_041099), and outgroup species, Isoetes yunguiensis (NC_041146). The numbers above branches indicate bootstrap support values of maximum likelihood and neighbor joining phylogenetic trees, respectively.
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References
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