Genomic analysis of Sweet potato feathery mottle virus from East Africa

Godfrey Wokorach; Geoffrey Otim; Joyce Njuguna; Hilary Edema; Vincent Njung'e; Eunice M Machuka; Nasser Yao; Francesca Stomeo; Richard Echodu

doi:10.1016/j.pmpp.2020.101473

Genomic analysis of Sweet potato feathery mottle virus from East Africa

Physiol Mol Plant Pathol. 2020 Apr:110:101473. doi: 10.1016/j.pmpp.2020.101473.

Authors

Godfrey Wokorach¹, Geoffrey Otim^{1

2}, Joyce Njuguna³, Hilary Edema¹, Vincent Njung'e³, Eunice M Machuka³, Nasser Yao³, Francesca Stomeo³, Richard Echodu^{1

2

4}

Affiliations

¹ Biosciences Research Laboratory, Gulu University, P.O. Box 166, Gulu, Uganda.
² Faculty of Agriculture, Gulu University, P.O. Box 166, Gulu, Uganda.
³ Biosciences Eastern and Central Africa, International Livestock Research Institute (BecA-ILRI) Hub, P.O. Box 30709, Nairobi, 00100, Kenya.
⁴ Department of Biology, Faculty of Science, Gulu University, P.O. Box 166, Gulu, Uganda.

Abstract

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.

Keywords: EA, East Africa; East Africa; O, ordinary; Potyvirus; RC, Russet crack; Recombination; SPFMV; SPFMV, Sweet potato feathery mottle virus; Sweet potato.