Song, B and Song, Y and Fu, Y and Kizito, E B and Kamenya, S N and Kabod, P N and Liu, H and Muthemba, S and Kariba, R and Njuguna, J and Maina, S and Stomeo, F and Djikeng, A and Hendre, P S and Chen, X and Chen, W and Li, X and Sun, W and Wang, W and Cheng, S and Muchugi, A and Jamnadass, R and Shapiro, H Y and Van Deynze, A and Yang, H and Wang, J and Xu, X and Odeny, D A and Liu, X (2019) Draft genome sequence of Solanum aethiopicum provides insights into disease resistance, drought tolerance, and the evolution of the genome. GigaScience (TSI), 8 (10). pp. 1-16. ISSN 2047-217X
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Abstract
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.
| Item Type: | Article |
|---|---|
| Divisions: | Research Program : East & Southern Africa |
| CRP: | UNSPECIFIED |
| Uncontrolled Keywords: | Solanum aethiopicum, African eggplant, Solanum anguivi, LTR-Rs, biotic stress, drought tolerance |
| Subjects: | Others > Biotic Stress Others > Drought Tolerance Others > Vegetable and Field crops Others > Genetics and Genomics |
| Depositing User: | Mr Arun S |
| Date Deposited: | 18 Mar 2020 10:02 |
| Last Modified: | 18 Mar 2020 10:05 |
| URI: | http://oar.icrisat.org/id/eprint/11406 |
| Official URL: | https://doi.org/10.1093/gigascience/giz115 |
| Projects: | UNSPECIFIED |
| Funders: | UNSPECIFIED |
| Acknowledgement: | We acknowledge Uganda Christian University for providing seeds of the African eggplant. |
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