Complete chloroplast genome of Ixora finlaysoniana: comparative analysis and phylogenetic insights into Ixoroideae (Rubiaceae)

Ixora finlaysoniana , a shrub and small tree found in pantropical rain forests, is a member of the tribe Ixoreae (subfamily Ixoroideae, family Rubiaceae). However, genetic information on the genus Ixora , particularly its chloroplast (cp) genomes, remains poorly known, which hinders our understanding of the evolution of the species. In this study, we sequenced and characterized the complete cp genome of I. finlaysoniana and conducted the comparative analyses with other species in the Ixoroideae subfamily. The I. finlaysoniana cp genome was 154,869 bp in length and contained 113 unique genes, including 79 protein-coding genes, 30 transfer RNA genes, and four ribosomal RNA genes. Comparative analysis of eight Ixoroideae cp genomes revealed high conversion in genome structure, gene content, and inverted repeats/single-copy junctions, with five divergent hotspot regions ( matK-rps16, rps1 6-psbK , psbE-petG, ndhF, and ycf1 ) identified as potential molecular markers. The phylogenetic analyses based on 79 protein-coding genes revealed that Ixora species form a distinct monophyletic group, with I. finlaysoniana showing the closest relationship to Ixora hookeri . This study represents the first comprehensive analysis of I. finlaysoniana cp genome, providing a valuable resource for future research on species identification, population genetics, and the evolutionary relationships between I. finlaysoniana and other members of the Rubiaceae family.