The complete chloroplast genome and phylogenetic analysis of Smilax moranensis (Liliales: Smilacaceae)

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.

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 0 N, 111 41 0 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.
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.

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.