Supporting data for "Draft genome sequence of Solanum aethiopicum provides insights into disease resistance, drought tolerance and the evolution of the genome".

The African eggplant (<i>Solanum aethiopicum</i>) is a nutritious traditional vegetable used in many African countries, including Uganda and Nigeria. It is believed to have been domesticated in Africa from its wild relative, <i>Solanum anguiv</i>i. <i>S. aethiopicum</i> has been routinely used as a source of disease resistance genes for several Solanaceae crops including <i>Solanum melongena</i>. Breeding of <i>S. aethiopicum</i> has lagged behind due to lack of genomic resources. <br>We assembled a 1.02 Gb draft genome of <i>S. aethiopicum</i>, which contained predominantly repetitive sequences (76.2%). We annotated 37,681 gene models including 34,906 protein-coding genes. We observed an expansion of disease resistance genes through two rounds of amplification of long terminal repeat retrotransposons (LTR-Rs), which may have occurred around 1.25 and 3.5 million years ago, respectively. We identified 14,995,740 SNPs by re-sequencing 65 <i>S. aethiopicum</i> and <i>S. anguiv</i>i genotypes, of which 41,046 SNPs were closely linked to disease resistance genes. The domestication and demographic history analysis revealed the active selection for genes involved in drought tolerance in both Gilo and Shum groups. A pan-genome of <i>S. aethiopicum</i> with a total of 51,351 protein-coding genes was assembled, 7,069 genes of which are missing in the reference genome. <br> The genome sequence of <i>S. aethiopicum</i> enhances our understanding of its extraordinary biotic and abiotic resistance nature. The SNPs identified will be available for immediate use by breeders. The information provided here will greatly accelerate the selection and breeding of the African eggplant as well as other crops within the Solanaceae family.