Draft genome sequence of Solanum aethiopicum provides insights into disease resistance, drought tolerance, and the evolution of the genome

Bo Song, Yue Song, Yuan Fu, Elizabeth Balyejusa Kizito, Sandra Ndagire Kamenya, Pamela Nahamya Kabod, Huan Liu, Samuel Muthemba, Robert Kariba, Joyce Njuguna, Solomon Maina, Francesca Stomeo, Appolinaire Djikeng, Prasad S. Hendre, Xiaoli Chen, Wenbin Chen, Xiuli Li, Wenjing Sun, Sibo Wang, Shifeng ChengAlice Muchugi, Ramni Jamnadass, Howard Yana Shapiro, Allen Van Deynze, Huanming Yang, Jian Wang, Xun Xu, Damaris Achieng Odeny*, Xin Liu

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review


Background: The African eggplant (Solanum aethiopicum) is a nutritious traditional vegetable used in many African countries, including Uganda and Nigeria. It is thought to have been domesticated in Africa from its wild relative, Solanum anguivi. S. aethiopicum has been routinely used as a source of disease resistance genes for several Solanaceae crops, including Solanum melongena. A lack of genomic resources has meant that breeding of S. aethiopicum has lagged behind other vegetable crops. Results: We assembled a 1.02-Gb draft genome of S. aethiopicum, which contained predominantly repetitive sequences (78.9%). We annotated 37,681 gene models, including 34,906 protein-coding genes. Expansion of disease resistance genes was observed via 2 rounds of amplification of long terminal repeat retrotransposons, which may have occurred ∼1.25 and 3.5 million years ago, respectively. By resequencing 65 S. aethiopicum and S. anguivi genotypes, 18,614,838 single-nucleotide polymorphisms were identified, of which 34,171 were located within disease resistance genes. Analysis of domestication and demographic history revealed active selection for genes involved in drought tolerance in both "Gilo" and "Shum" groups. A pan-genome of S. aethiopicum was assembled, containing 51,351 protein-coding genes; 7,069 of these genes were missing from the reference genome. Conclusions: The genome sequence of S. aethiopicum enhances our understanding of its biotic and abiotic resistance. The single-nucleotide polymorphisms identified are immediately available for use by breeders. The information provided here will accelerate selection and breeding of the African eggplant, as well as other crops within the Solanaceae family.

Original languageEnglish
Article numbergiz115
Issue number10
Publication statusPublished - 1 Oct 2019


  • African eggplant
  • biotic stress
  • drought tolerance
  • LTR-Rs
  • Solanum aethiopicum
  • Solanum anguivi


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