Abstract
Eleutherococcus trifoliatus (L.) S. Y. Hu is a wild edible plant and widely used in the coastal region of South China. Here, we report the complete chloroplast genome of E. trifoliatus. The length of the cp genome was determined to be 156751 bp with a small single copy (SSC) region of 18316 bp, a large single copy (LSC) region of 86747 bp and two separated inverted region of 25844 bp, respectively. Totally, 132 unique genes were identified of this genome, including 87 protein-coding genes, 37 tRNA genes and eight rRNA genes. The GC contents of this genome is 38%. Chloroplast phylogenomics analysis indicates that E. trifoliatus is closely related to E. gracilistylus (W.W. Sm.) S.Y. Hu.
Keywords: Eleutherococcus trifoliatus, chloroplast genome, wild vegetable, phylogenetic analysis
Eleutherococcus trifoliatus (L.) S. Y. Hu is a commonly used wild vegetable and tea in the coastal region of South China (Wang et al. 2015; Li et al. 2017). It belongs to the ginseng family (Araliaceae) and distributed in South China, India, Japan, Philippines, Thailand and Vietnam (Xiang and Lowry 2007). Eleutherococcus is one of the important medicinal genera of Araliaceae (Wen et al. 2001), but the phylogenetic relationship between Eleutherococcus and its related genera still uncertain (Li and Wen 2016). Thus we sequenced the complete chloroplast (cp) genome of E. trifoliatus to elucidate its phylogenetic relationship in the family.
The total genomic DNA was extracted from silica gel-dried leaf sample following the CTAB method (Doyle and Doyle 1987). Leaf sample of E. trifoliatus was collected from Nan Ao Island in Shantou City, Guangdong Province, China (117°08′10″E, 23°26′29″N). The voucher specimens (accession number: 0849959) was deposited in the herbarium of South China Botanical Garden (IBSC). The genomic library (paired-end, PE = 150 bp) was sequenced on a BGISEQ-500 platform at Beijing Genomics Institute (Shenzhen, China). Totally, 2 Gb sequence reads were obtained and used to assemble the cp genome after filtering and trimming the low quality reads and adaptor sequences. The annotated plastome for Metapanax delavayi was downloaded from GenBank (accession number: NC_022812), and was used as the reference for the complete cp genome assembly and annotation. Reference assembly was executed on NOVOPlasty 2.6.3 (Dierckxsens et al. 2017) with kmer length set to 39 base pairs. Annotation of the cp genome was performed on Geneious version 11.0.3 (Kearse et al. 2012), while the tRNA genes were annotated on ARAGORN (Laslett and Canback 2004).
The complete cp genome of E. trifoliatus (GenBank accession number: MN727298) was 156751 bp in length, which composed of a small single copy region (SSC) of 18316 bp, a large single copy region (LSC) of 86747 bp and a pair of inverted repeats (IRs) of 25844 bp. The genome encodes a total of 132 unique genes, including 87 protein-coding genes, 37 tRNA genes and eight rRNA genes. Among these genes, 17 genes has two copies, which including six protein-coding genes, seven tRNA genes and four rRNA genes. The GC contents of this genome is 38%, while the GC contents of LSC, SSC and IRs are 36.2%, 32.1% and 43.1% respectively.
To clarify the phylogenetic position of E. trifoliatus, we reconstructed the phylogeny of Eleutherococcus-Dendropanax-Schefflera Group of Araliaceae (Wen et al. 2001) based on all of the reported plastomes of this group. The plastomes of the 14 accessions were aligned using MAFFT (Katoh and Standley 2013). Then, the maximum likelihood (ML) tree was reconstructed using RAxML (Stamatakis 2006) with 1000 bootstrap replicates. Based on the topology of the phylogenetic tree (Figure 1), all of the studied Eleutherococcus species form a monophyletic clade. Eleutherococcus trifoliatus is closely related to E. gracilistylus (W.W. Sm.) S.Y. Hu.
Figure 1.
Maximum likelihood tree based on 14 complete chloroplast genomes of Araliaceae. Bootstrap support values are shown at the branches.
Funding Statement
The study was financially supported by the ‘Strategic Priority Research Program’ of the Chinese Academy of Sciences [Grant No. XDA13020602].
Disclosure statement
No potential conflict of interest was reported by the authors.
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