Comparative analysis of the chloroplast genomes of three Populus species: Insights into genetic relationships, evolution and classification

Abstract

Background: Natural hybridisation is prevalent among Populus species in the Hengduan Mountains. Clarifying their interrelationships and hybrid formation mechanisms is critical for taxonomic classification and breeding of the genus. Methods: This study sequenced the complete chloroplast genomes of three Populus species – P. lasiocarpa Oliv. (Sect. Leucoides Spach), P. gonggaensis N. Chao & J.R. He (Sect. Leucoides Spach), and P. cathayana Rehd. (Sect. Tacamahaca Spach) - to investigate their genetic relationships and evolutionary patterns. Results: The chloroplast genome lengths were 156,554 bp (P. lasiocarpa), 156,494 bp (P. gonggaensis), and 156,812 bp (P. cathayana), with all sharing a 37% GC content and conserved quadripartite structure (large/small single-copy regions plus two inverted repeats). They contained 130 or 131 genes (85 or 86 protein-coding, 37 tRNA, 8 rRNA) and 129-142 simple sequence repeat (SSR) loci (primarily adenine/thymine-dominated mononucleotide repeats). Phylogenetic analysis revealed the three species form a monophyletic clade, with P. gonggaensis and P. cathayana showing close affinity. Conclusions: Chloroplast evidence indicated that P. gonggaensis is maternally closely related to P. cathayana, supporting its maternal lineage from P. cathayana. Further nuclear genome evidence is needed to confirm the hybrid origin of this species.