COMPARATIVE PLASTOME STRUCTURE REVEALS TAXONOMIC INCONSISTENCIES IN THE CURRENT SECTIONAL DELIMITATIONS IN RUBROSHOREA

Abstract

Rubroshorea (Meijer) P.S.Ashton & J.Heck. is a genus comprising 71 species with Borneo recognised as the center of species diversity for this genus, hosting 64 species, including 44 endemic species. In Borneo, several species of Rubroshorea and a species of Shorea are known for their non-timber value, via the nut oils, and are collectively locally known as Engkabang species. However, only a few Engkabang species have been included in previous phylogenetic studies, leaving their taxonomic placement at both generic and intrageneric levels insufficiently resolved understood. In this study, we conducted sequencing and assembly of the plastid genomes (plastomes) of 27 Rubroshorea accessions (representing 18 Bornean species) and nine Shorea accessions (representing seven species). The Rubroshorea plastid genome exhibits typical quadripartite structure and encodes 110–112 unique genes, comprising 77–78 protein-coding genes (PCGs), 29–30 tRNAs, and 4 rRNAs. Sliding-window analyses identified five highly variable regSliding-window analyses identified five highly variable regions, including rps16-trnQ-UUG, ClpP1, rps15-ycf1, rpl32-trnL-UAG, and trnG-GCCtrnM-CAU within Rubroshorea and a species of Shorea, representing promising molecular markers for future taxonomic and population genetic studies. Our phylogenomic analysis established a well-resolved and strongly supported phylogenetic framework for Rubroshorea but did not support the currently recognized sectional classification. By expanding plastid genomic data for Bornean endemics, this study provides new insights into the evolutionary relationships and taxonomy of Rubroshorea taxonomic clarity with practical conservation, securing the future of a genus integral to both biodiversity and human economies.