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

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dc.contributor.authorBo Song
dc.contributor.authorYue Song
dc.contributor.authorYuan Fu
dc.contributor.authorElizabeth Balyejusa Kizito
dc.contributor.authorSandra Ndagire Kamenya
dc.contributor.authorPamela Nahamya Kabod
dc.contributor.authorHuan Liu
dc.contributor.authorSamuel Muthemba
dc.contributor.authorRobert Kariba
dc.contributor.authorJoyce Njuguna
dc.contributor.authorSolomon Maina
dc.contributor.authorFrancesca Stomeo
dc.contributor.authorAppolinaire Djikeng
dc.contributor.authorPrasad S. Hendre
dc.contributor.authorXiaoli Chen
dc.contributor.authorWenbin Chen
dc.contributor.authorXiuli Li
dc.contributor.authorWenjing Sun
dc.contributor.authorSibo Wang
dc.contributor.authorShifeng Cheng
dc.contributor.authorAlice Muchugi
dc.contributor.authorRamni Jamnadass
dc.contributor.authorAllen Van Deynze
dc.contributor.authorHuanming Yang
dc.contributor.authorJian Wang
dc.contributor.authorXun Xu
dc.contributor.authorDamaris Achieng Odeny
dc.contributor.authorXin Liu
dc.date.accessioned2024-08-31T14:10:51Z
dc.date.available2024-08-31T14:10:51Z
dc.date.issued2019-08
dc.descriptionResearch Paper Published by OXFORD in GigaScience
dc.description.abstractBackground: 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 esequencing 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.
dc.identifier.otherdoi: 10.1093/gigascience/giz115
dc.identifier.urihttp://hdl.handle.net/20.500.11951/1372
dc.language.isoen
dc.publisherOxford
dc.titleDraft genome sequence of solanum aethiopicum provides insights into disease resistance, drought tolerance, and the evolution of the genome
dc.typeResearch article
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