Dataset on MatK-based intra- and inter-specific genetic relationships among four Solanum L. species from Southwestern Nigeria

Globally, the eggplant clade (<i>Solanum</i> L.) (Solanaceae) is an economically important source of food, nutrition, income, and medicines. Members of the clade are distinctively known for their incompatibility and yet genetically related as a diploid hyper-diverse monophyletic group. The eggplant clade are underutilized, and there are concerns about genetic erosion in Nigeria, primarily attributed to a limited understanding of their genetic diversity. To improve the members of the clade, it is imperative to understand their intra- and inter-specific genetic diversity and relationships for sustainable cultivation, conservation, and genetic improvement. A total of twelve (12) eggplant accessions comprising four (4) accessions of <i>Solanum aethiopicum</i>, three (3) accessions each of <i>S. macrocarpon</i> and <i>S. melongena</i>, and two accessions of <i>S. nigrum</i> obtained from the National Centre for Genetic Resources and Biotechnology (NACGRAB) Ibadan, Oyo state, Nigeria were assessed for their intra- and inter-specific genetic diversity. Genomic DNA was extracted from four-week-old young leaves at the emergence of each accession, followed by Polymerase Chain Reaction (PCR) amplification of the maturase K (MatK) gene. The PCR amplicons were then sequenced using Sanger's technique and the results analysed. The dataset presents intra- and inter-specific diversity and population structure of the studied species. A relatively low level of intraspecific diversity and moderate to high level of interspecific diversity with varying degrees of nucleotide and haplotype diversities were recorded for the dataset. Quite elevated values of 693 total allele sites, 9 haplotypes, 0.96 gene diversity, 100 polymorphic sites, 16 parsimony information sites, and 101 total number of mutations were documented for the sequence dataset. Relatively high gene flow and genetic differentiation (Fst) were observed among the populations of <i>S. aethiopicum</i> and <i>S. nigrum</i> (0.939), <i>S. macrocarpon</i> and <i>S. nigrum</i> (0.833), whereas a moderate Fst was recorded for the populations of <i>S. melongena</i> and <i>S. nigrum</i> (0.254) and <i>S. aethiopicum</i> and <i>S. melongena</i> (0.047), while populations of <i>S. aethiopicum</i> and <i>S. macrocarpon</i> as well as <i>S. macrocarpon</i> and <i>S. melongena</i> showed a low Fst values of -0.129 and 0.014. Genetic distance and phylogenetic relationships showed a closely related taxa of four distinct cluster groups with three groups of mixed species and one unique cluster of <i>S. nigrum</i>. The dataset provides insights into the genetic diversity within and between <i>Solanum</i> species which could be used to inform commercial cultivation, conservation, and breeding efforts, as well as the evolutionary dynamics of the clade.