Complete chloroplast genome of three Solanum species (Solanaceae) from China: genome structure, comparative analysis, and phylogenetic relationships
Rebecca Jia Yinn Ng1, Zhihui Chen2, Lu Tan3, Douglas Law1, Wenbo Liao2, Yangyang Liu4*, Shiou Yih Lee1*
1Faculty of Health and Life Sciences, INTI International University, 71800 Nilai, Negeri Sembilan, Malaysia
2State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, 510275 Guangzhou, Guangdong, China
3Faculty of Liberal Arts, Shinawatra University, Pathum Thani 12160, Thailand
4International Joint Research Center for Quality of Traditional Chinese Medicine, Hainan Branch of the Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, 570311 Haikou, Hainan, China
Received: 29 May 2025 / Accepted: 24 July 2025 / Published Online: 09 August 2025
Abstract
Solanum members are economically important crops worldwide; these species lack molecular information. We assembled and annotated the chloroplast (cp) genomes of three Solanum species: Solanum aculeatissimum, Solanum lasiocarpum, and Soalnum pittosporifolium. Genome comparative analyses characterised these species, and a phylogenetic tree was reconstructed using maximum likelihood and approximate Bayesian inference methods on the complete cp genome sequence without IRA. The cp genomes of S. aculeatissimum, S. lasiocarpum, and S. pittosporifolium displayed a quadripartite circular structure that was 155,821 bp, 155,671 bp, and 155,926 bp in length, respectively. S. aculeatissimum and S. lasiocarpum cp genomes had 131 unique genes, including 86 protein-coding (CDS), 37 transfer RNA, and eight ribosomal RNA genes. S. pittosporifolium had an additional CDS gene, bringing the total to 130. The sequence alignment of 23 Solanum species revealed four highly variable regions in the cp genome: ndhC–trnV-UAC, petD, rpl33–rpl8, and ycf1, when Pi > 0.03. Based on the complete cp genome sequence of 27 Chinese Solanum species, phylogenetic analysis showed a monophyletic relationship. The maximum-likelihood and Bayesian inference methods placed S. aculeatissimum and S. lasiocarpum in the same clade as Solanum capsicoides, while S. pittosporifolium was placed with Solanum dulcamara, Solanum japonense, and Solanum septemlobum.
