The first chloroplast and nuclear genome assemblies of Prasoxylon excelsum (Meliaceae) reveal phylogenetics, evolutionary and functional insights

Abstract

Prasoxylon excelsum (Spreng.) Mabb., a medicinal tree of the family Meliaceae, is traditionally used to treat diarrhoea, dysentery, and food poisoning. Despite its ethnobotanical significance, no genomic resources have been available to date. This study presents the first de novo assembly and characterization of both the chloroplast (Cp) and nuclear genomes of P. excelsum. The complete Cp genome spans 160,299 bp and exhibits a typical quadripartite structure, comprising a large single-copy (LSC) region of 87,832 bp, a small single-copy (SSC) region of 18,360 bp, and a pair of inverted repeats (IRs) of 27,054 bp each. The plastome encodes 81 protein-coding genes, 37 transfer RNAs, and eight ribosomal RNAs. A total of 98 simple sequence repeats (SSRs) were identified, predominantly mononucleotide motifs (68). Nucleotide diversity analysis revealed atpB and ycf1 as the most variable regions, suggesting their potential as DNA barcodes. Phylogenetic reconstruction using the maximum-likelihood method confirmed the placement of P. excelsum within the subfamily Melioideae. Molecular dating analysis indicated that P. excelsum diverged during the late Burdigalian age of the Miocene epoch, approximately 16.21 million years ago. The nuclear genome assembly totaled 676.45 Mb with an N50 of 3,686 bp, showing 87.8% BUSCO completeness. Gene prediction identified 44,465 genes, with KEGG analysis indicating enrichment in metabolic pathways. These findings provide a valuable foundation for evolutionary, phylogenomic, and functional studies in Prasoxylon and related Meliaceae species, aiding future research in conservation genomics, phytochemistry, and molecular breeding.

Bangladesh J. Plant Taxon. 32(2): 139-160, 2025 (December)