Characteristics, Comparative Analysis, and Phylogenetic Relationships of Chloroplast Genomes of Cultivars and Wild Relatives of Eggplant (<i>Solanum melongena</i>)

The eggplant (<i>Solanum melongena</i>) is a popular vegetable around the world. However, the origin and evolution of eggplant has long been considered complex and unclear, which has become the barrier to improvements in eggplant breeding. Sequencing and comparative analyses of 13 complete chloroplast (cp) genomes of seven <i>Solanum</i> species were performed. Genome sizes were between 154,942 and 156,004 bp, the smallest genome was from <i>S. torvum</i> and the largest from <i>S. macrocapon</i>. Thirteen cp genomes showed highly conserved sequences and GC contents, particularly at the subgenus level. All genes in the 13 genomes were annotated. The cp genomes in this study comprised 130 genes (i.e., 80 protein-coding genes, 8 rRNA genes, and 42 tRNA genes), apart from <i>S. sisymbriifolium</i>, which had 129 (79 protein-coding genes, 8 rRNA genes, and 42 tRNA genes.). The <i>rps16</i> was absent from the cp genome of <i>S. sisymbriifolium</i>, resulting in a nonsense mutation. Twelve hotspot regions of the cp genome were identified, which showed a series of sequence variations and differed significantly in the inverted repeat/single-copy boundary regions. Furthermore, phylogenetic analysis was conducted using 46 cp genomic sequences to determine interspecific genetic and phylogenetic relationships in <i>Solanum</i> species. All species formed two branches, one of which contained all cultivars of the subgenus <i>Leptostemonum</i>. The cp genome data and phylogenetic analysis provides molecular evidence revealing the origin and evolutionary relationships of <i>S. melongena</i> and its wild relatives. Our findings suggest precise intra- and interspecies relatedness within the subgenus <i>Leptostemonum</i>, which has positive implications for work on improvements in eggplant breeding, particularly in producing heterosis, expanding the source of species variation, and breeding new varieties.