Abstract
Smilax moranensis M.Martens & Galeotti 1842 is an important medicinal plant widely distributed in warm and temperate climates. In this paper, the complete chloroplast (cp) genome of S. moranensis was sequenced using the Illumina platform and assembled for the first time. This plastome is a circular structure of 157,907 bp in length. The GC content of the plastome was 37.16%. A total of 112 unique genes in this genome have been annotated, including 78 protein-coding genes, 30 transfer RNA genes, and four ribosomal RNA genes. Phylogenetic analysis based on complete cp genome sequences of Smilacaceae family showed that Smilax is monophyletic. The position of S. moranensis was positioned as the sister to the other seven Smilax species. These results provide an important basis for future species identification and taxonomic determinations, as well as the phylogenetic reconstruction of the family Smilacaceae.
Keywords: Smilax moranensis, chloroplast genome, phylogeny
The genus Smilax (Smilacaceae) comprises about 370 species, which are predominantly distributed in the tropical and temperate zones throughout the world, especially East Asia and North America (Plants of the World Online 2022). Smilax moranensis M.Martens & Galeotti 1842 is a woody vine with stems covered in spikes and is widely distributed in warm and temperate climates between 600 and 2000 m above sea level (Rosas-Ramirez et al. 2020). Several reports about the root of S. moranensis detail its pharmacological activities for treating rheumatic joint pain (Xu et al. 2014; Shu et al. 2017; Rosas-Ramirez et al. 2020). Despite the fact that S. moranensis has significant medicinal value, its research in genetics and evolution is still extremely rare. In this study, we reported the chloroplast (cp) genome of S. moranensis and examined its phylogenetic position within the family Smilacaceae. It is expected to lay the foundation for further molecular study and utilization of S. moranensis.
Fresh leaves of S. moranensis were collected from Xixia County, Nanyang City, Henan Province (33°38′N, 111°41′E). No permission was necessary for the S. moranensis collection, which is widely distributed in North China and is not listed as a national key protected plant. The specimen and DNA were deposited at the herbarium of Henan University of Traditional Chinese Medicine, Henan, China (contact person: Lixin Pei, xlpxlp@aliyun.com), under the voucher number HNPS2020-12-059. Total genomic DNA was extracted by using a Dneasy Plant MiniKit (Qiagen, Valencia, CA) according to the manufacturer’s instructions. Guided by our previous research basis (Cui et al. 2020), the DNA sample pretreatment, whole genome sequencing, cp genome assembly, junction validation, and cp genome annotation were performed in turn. The cp genome assembled and annotated here was submitted to the NCBI database (www.ncbi.nlm.nih.gov) with the GenBank accession number of OL693684.
The cp genome of S. moranensis was circular double-stranded DNA and displayed a typical quadripartite structure, including a pair of inverted repeat (IR) regions with lengths of 27,157 bp, separated by a large single-copy (LSC) region of 85,039 bp and a small single-copy (SSC) region of 18,554 bp. The GC content of the plastome was 37.16%. The genome harbored a set of 133 genes, of which 112 were unique genes. Totally, 85 protein-coding genes (78 unique genes) were annotated, which were mainly involved in processes related to photosynthesis and gene expression. Eleven protein-coding genes (rps16, atpF, rpoC1, petB, petD, rpl16, rpl2, ndhA, ndhB, ndhB, and rpl2) and eight tRNA genes (trnK-UUU, trnG-UCC, trnL-UAA, trnV-UAC, trnI-GAU, trnA-UGC, trnA-UGC, and trnI-GAU) contained one intron, and two genes (ycf3 and clpP) contained two introns.
In order to reveal the evolutionary relationship of S. moranensis, the cp genomes of nine Smilax species were downloaded from the NCBI GenBank database. We aligned the plastomes using MAFFT and constructed a maximum-likelihood (ML) tree (Figure 1) by using RAxML 8.2.9 under the GTRGAMMA model with 1000 rapid bootstrap replicates (Cui et al. 2020). The ML tree indicated that the Smilax genus is monophyletic. S. moranensis was sister to the clade consisting of S. microphylla (NC056390), S. nipponica (NC049024), S. riparia (NC062359), S. china (NC049022 and HM536959), S. sp. (MW890012), S. glycophylla (NC049023), and S. glabra (NC058534 and MZ442610) with a bootstrap support value of 100%. The cp genome of S. moranensis will provide a theoretical basis to further understand the evolution of the family Smilacaceae and improve our understanding of its taxonomic classification.
Figure 1.
Phylogenetic tree constructed by using the whole chloroplast genome sequences of Smilax species with the maximum-likelihood method. Numbers near each branch are the bootstrap values.
Author contributions
N. Cui designed and conceived this work; L.X. Pei collected the samples and carried out the experiment; B.Y. Ji analyzed the data and wrote the first version of the manuscript. All authors read, revised, and approved the final manuscript.
Ethical approval
No permission was necessary in this study for the sample collection. Smilax moranensis is widely distributed in North China and is not listed as a national key protected plant.
Funding Statement
This work was supported by the Research Incubation Fund Project of Shandong Academy of Chinese Medicine [2021SACM-3], Medical and Health Science and Technology Development Project of Shandong Province [202102041135], ‘National Survey of Traditional Chinese Medicine Resources’, a special subsidy program for United States Public Health Service of traditional Chinese medicine in 2017 [caishe[2017] No. 66], and ‘National Survey of Traditional Chinese Medicine Resources’, a special subsidy program for United States Public Health Service of traditional Chinese medicine in 2018 [caishe[2017] No.183].
Disclosure statement
The authors declare that there is no potential conflict of interest exists.
Data availability statement
The complete chloroplast genome sequence of Smilax moranensis was deposited in the GenBank database (https://www.ncbi.nlm.nih.gov/genbank, OL693684). Raw sequencing reads used in this study have been deposited in the SRA database (https://www.ncbi.nlm.nih.gov/sra). The associated BioProject, SRA, and Bio-Sample numbers are PRJNA785329, SRR17085809, and SAMN23553129, respectively.
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Associated Data
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Data Availability Statement
The complete chloroplast genome sequence of Smilax moranensis was deposited in the GenBank database (https://www.ncbi.nlm.nih.gov/genbank, OL693684). Raw sequencing reads used in this study have been deposited in the SRA database (https://www.ncbi.nlm.nih.gov/sra). The associated BioProject, SRA, and Bio-Sample numbers are PRJNA785329, SRR17085809, and SAMN23553129, respectively.