Browsing by Author "Stomeo, Francesca"

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    Draft genome sequence of Solanum aethiopicum provides insights into disease resistance, drought tolerance, and the evolution of the genome
    (GigaScience, 2019) Song, Bo; Song, Yue; Fu, Yuan; Balyejusa Kizito, Elizabeth; Ndagire Kamenya, Sandra; Nahamya Kabod, Pamela; Liu, Huan; Muthemba, Samuel; Kariba, Robert; Njuguna, Joyce; Maina, Solomon; Stomeo, Francesca; Djikeng, Appolinaire; Hendre, Prasad S.; Chen, Xiaoli; Chen, Wenbin; Li1, Xiuli; Sun, Wenjing; Wang, Sibo; Cheng, Shifeng; Muchugi, Alice; Jamnadass, Ramni; Shapiro, Howard-Yana; Van Deynze, Allen; Yang, Huanming; Wang, Jian; Xu, Xun; Achieng Odeny, Damaris; Liu, Xin
    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.
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    Genomic analysis of Sweet potato feathery mottle virus from East Africa
    (Physiological and Molecular Plant Pathology, 2020) Wokorach, Godfrey; Otima, Geoffrey; Njuguna, Joyce; Edema, Hilary; Njung'e, Vincent; Machuka, Eunice M.; Yaoc, Nasser; Stomeo, Francesca; Echodu, Richard
    Sweet potato feathery mottle virus is a potyvirus that infect sweet potato. The genome of the virus was analysed to understand genetic diversity, evolution and gene flow. Motifs, nucleotide identity and a phylogenetic tree were used to determine phylogroup of the isolates. Gene flow and genetic diversity were tested using DnaSP v.5. Codons evolution were tested using three methods embedded in Datamonkey. The results indicate occurrence of an isolate of phylogroup B within East Africa. Low genetic differentiation was observed between isolates from Kenya and Uganda indicating evidence of gene flow between the two countries. Four genes were found to have positively selected codons bordering or occurring within functional motifs. A motif within P1 gene evolved differently between phylogroup A and B. The evidence of gene flow indicates frequent exchange of the virus between the two countries and P1 gene motif provide a possible marker that can be used for mapping the distribution of the phylogroups.