Deciphering the complete plastid genome of an endemic monotypic species Kostermansia malayana (Malvaceae) from Peninsular Malaysia: structural comparative genomics and phylogenomic placement

Abstract

Kostermansia malayana Soegeng, a species of Malvaceae endemic to the Malay Peninsula, is threatened by its rare flowering rate and habitat loss due to agriculture land conversion. The species is currently listed as “Vulnerable” on the International Union for Conservation of Nature Red List of Threatened Species. To expand genomic information, the study characterised its plastid genome (plastome) and conducted genome comparative and phylogenetic analyses with other selected species of Malvaceae. The quadripartite-structured plastome was 161 750 bp long and contained 83 protein-coding genes (PCGs), 37 tRNA genes, and eight rRNA genes. The overall GC content was 36.3%. Repeat analyses revealed 49 large repeats and 205 simple sequence repeats. A high preference for A/U-ended amino acids was found. Eight and nine PCGs were positively selected when compared to Coelostegia griffithii Benth. & Hook.f. and Reevesia thyrsoidea Lindl., respectively. A notable degree of collinearity was identified between the plastomes of K. malayana and six selected taxa of Helicteroideae. The phylogenetic tree reconstruction based on the concatenated PCG dataset showed a nearly well-resolved relationship within Malvaceae, with K. malayana placed under the Helicteroideae clade. The genomic data will provide a basis for future studies on the genetic conservation, phylogenetics, and evolutionary patterns of Durioneae and Malvaceae.