Dataset on the genetic diversity and phylogenetic relationships of Irvingia wombolu and Irvingia gabonensis using rbcL markers

Abstract

This dataset provides a comprehensive molecular characterization of Irvingia gabonensis and Irvingia wombolu , two indigenous West and Central Africa tree species vital for food security. Genomic DNA was extracted from 14 accessions, followed by PCR amplification and Sanger sequencing of the rbcL chloroplast gene. The data includes aligned sequences, polymorphism indices, conserved regions, and Relative Synonymous Codon Usage (RSCU) statistics. Analysis identified 593 nucleotide sites, 129 monomorphic sites, three haplotypes, and six mutation sites, with a gene diversity of 0.28. Notably, two highly conserved regions (1–249 bp and 311–408 bp, C = 1.0) were established as reliable reference blocks for the genus. Phylogenetic reconstruction using maximum likelihood (83% bootstrap support) grouped the accessions into two distinct clades, while a synonymous substitution rate ( K s ) of 0.857 confirmed low inter-specific divergence. Codon usage analysis revealed specific preferences, such as ACU (Threonine, RSCU = 2.89). Despite the overall low genetic variability, minor sequence differences identified in accessions PV089637 and PV089642 suggest potential for hybridization. This dataset serves as a foundational genetic resource for conservation planning, germplasm development, and targeted breeding programs to improve these underutilized species.