First chloroplast genome of Scleropyrum wallichianum (Cervantesiaceae) insights into phylogeny and conservation

THUY LIEN BUI (Hanoi Pedagogical University 2. Nguyen Van Linh Street, Xuan Hoa 280000, Phu Tho Province, Vietnam)
LINYUE HE (State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University. 222 Tianshui South Rd., Lanzhou 730000, China)
WYCKLIFFE OMONDI OMOLLO (National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agricultural University. No. 1 Shizishan St., Wuhan 430070, China)
SHENGDAN WU (State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University. 222 Tianshui South Rd., Lanzhou 730000, China)
BA CUONG CAO (Hanoi Pedagogical University 2. Nguyen Van Linh Street, Xuan Hoa 280000, Phu Tho Province, Vietnam)
XUAN THANH NGUYEN (Hanoi Pedagogical University 2. Nguyen Van Linh Street, Xuan Hoa 280000, Phu Tho Province, Vietnam)
XUAN THANH TRINH (Institute of Biology, Vietnam Academy of Science and Technology. 18 Hoang Quoc Viet St., Nghia Do, Cau Giay, Hanoi, Vietnam)
PHI BANG CAO (Faculty of Natural Sciences, Hung Vuong University. Nguyen Tat Thanh St., Viet Tri 35120, Phu Tho, Vietnam)
NGAN THI LU (Vietnam National Museum of Nature, Vietnam Academy of Science and Technology. 18 Hoang Quoc Viet St., Cau Giay, Hanoi, Vietnam)
CHI TOAN LE (Hanoi Pedagogical University 2. Nguyen Van Linh Street, Xuan Hoa 280000, Phu Tho Province, Vietnam)

Biodiversitas Journal of Biological Diversity
Vol. 26 No. 11 (2025)

Abstract. Bui TL, He L, Omollo WO, Wu S, Cao BC, Nguyen XT, Trinh XT, Cao PB, Lu NT, Le CT. 2025. First chloroplast genome of Scleropyrum wallichianum (Cervantesiaceae) insights into phylogeny and conservation. Biodiversitas 26: 5763-5769. Scleropyrum wallichianum, a member of the family Cervantesiaceae (order Santalales), is distributed across Southeast Asia and China. The species is economically significant due to its seed oil, which is used in the production of lubricants and soap. In this study, the complete chloroplast genome of S. wallichianum was sequenced and analyzed to clarify its phylogenetic position within Santalales and to support conservation efforts. A leaf sample was collected from the Me Linh Station for Biodiversity in northern Vietnam. The genome was sequenced using the DNBSEQ-T7 platform, assembled with GetOrganelle, and annotated with CPGAVAS2, with manual correction of ambiguous regions performed in Apollo. The circular plastome was visualized using OrganellarGenomeDRAW. The assembled chloroplast genome, representing the first complete sequence reported for S. wallichianum, provides a valuable genomic resource for molecular systematics, evolutionary genomics, and conservation genetics of Cervantesiaceae and the order Santalales. The plastome exhibits a typical quadripartite structure with a total length of 149,066 bp and a GC content of 38.3%, comprising a Large Single-Copy (LSC) region of 85,000 bp, a Small Single-Copy (SSC) region of 18,500 bp, and two Inverted Repeats (IRs) of 22,783 bp each. Phylogenomic reconstruction based on 80 shared coding genes strongly supports S. wallichianum as a distinct clade within Cervantesiaceae, sister to Opiliaceae. This newly characterized plastome enriches the genomic resources available for the genus Scleropyrum and enhances understanding of the evolutionary history, taxonomy, and conservation genetics of Cervantesiaceae and related parasitic lineages within Santalales.