Comparative analysis of morphology and chloroplast genomes in endangered plant Madhuca pasquieri and two congeneric plants: revealing phylogenetic relationships

Background This study addresses the taxonomic ambiguity impeding the conservation of Madhuca pasquieri — an endangered tree species classified as vulnerable on the International Union for Conservation of Nature (IUCN) Red List and listed as a national second-class protected plant in China — by integrating morphological comparison with complete chloroplast genome analysis of three Madhuca species. Methods We sequenced and assembled the complete chloroplast genomes of three Madhuca species from Illumina data. Genome annotation, codon usage, repeat elements, and comparative genomics analyses were performed using standard bioinformatic tools. Phylogenetic relationships were reconstructed with 69 orthologous genes using maximum likelihood. Results Despite high morphological similarity among M. pasquieri and its congener M. hainanensis and M. longifolia , their highly conserved chloroplast genomes (159,613-159,726 bp, 131 genes) yielded critical molecular resources. We identified hypervariable intergenic spacers (e.g., trnK-atpH) and simple sequence repeats (SSRs) as candidate markers for species discrimination. Phylogenetic reconstruction strongly supported M. pasquieri and M. hainanensis as a sister clade, with M. longifolia as an earlier‑diverging lineage. Discussion/Conclusion These findings offer a preliminary molecular framework to aid species identification and provide valuable genomic resources for the conservation of M. pasquier