非洲茄基因组及重测序

Background: S. aethiopicum is a close relative to S. melongena and has been routinely used to improve disease resistance in S. melongena. However, these efforts have been greatly limited by the lack of a reference genome and the clear understanding of the genes involved during biotic and abiotic stress response. Results: We present here a draft genome assembly of S. aethiopicum of 1.02 Gb in size. Our data shows that 76.2% of the genome is occupied by repetitive sequences, predominantly long terminal repeat elements. We annotated 37,681 gene models including 34,905 protein-coding genes. We observed an expansion of resistance genes through two rounds of amplification of LTRs, which may have occurred around 1.25 and 3.5 million years ago, respectively. The expansion also occurred in gene families related to drought tolerance. Re-sequencing of 65 S. aethiopicum genotypes, 41,046 SNPs are closely linked to resistance genes. The domestication and demographic history inferred a selection of genes involved in drought tolerance in both “Gilo” and “Shum” groups. A pan-genome of S. aethiopicum with a total of 36,250 protein-coding genes was assembled, of which 1,345 genes are missing in the reference genome. Conclusions: Overall, the genome sequence of S. aethiopicum increases our understanding of the genomic mechanisms of its extraordinary disease resistance and drought tolerance. The SNPs identified are available for potential 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.