Phylogenomic relationship and evolutionary insights of sweet potato viruses from the western highlands of Kenya

James M Wainaina; Elijah Ateka; Timothy Makori; Monica A Kehoe; Laura M Boykin

doi:10.7717/peerj.5254

Phylogenomic relationship and evolutionary insights of sweet potato viruses from the western highlands of Kenya

PeerJ. 2018 Jul 19:6:e5254. doi: 10.7717/peerj.5254. eCollection 2018.

Authors

James M Wainaina¹, Elijah Ateka², Timothy Makori², Monica A Kehoe³, Laura M Boykin¹

Affiliations

¹ School of Molecular Sciences/ARC CoE Plant Energy Biology, The University of Western Australia, Crawley, WA, Australia.
² Department of Horticulture, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya.
³ Plant Pathology, Department of Primary Industries and Regional Development Diagnostic Laboratory Service, South Perth, WA, Australia.

Abstract

Sweet potato is a major food security crop within sub-Saharan Africa where 90% of Africa production occurs. One of the major limitations of sweet potato production are viral infections. In this study, we used a combination of whole genome sequences from a field isolate obtained from Kenya and those available in GenBank. Sequences of four sweet potato viruses: Sweet potato feathery mottle virus (SPFMV), Sweet potato virus C (SPVC), Sweet potato chlorotic stunt virus (SPCSV), Sweet potato chlorotic fleck virus (SPCFV) were obtained from the Kenyan sample. SPFMV sequences both from this study and from GenBank were found to be recombinant. Recombination breakpoints were found within the Nla-Pro, coat protein and P1 genes. The SPCSV, SPVC, and SPCFV viruses from this study were non-recombinant. Bayesian phylogenomic relationships across whole genome trees showed variation in the number of well-supported clades; within SPCSV (RNA1 and RNA2) and SPFMV two well-supported clades (I and II) were resolved. The SPCFV tree resolved three well-supported clades (I-III) while four well-supported clades were resolved in SPVC (I-IV). Similar clades were resolved within the coalescent species trees. However, there were disagreements between the clades resolved in the gene trees compared to those from the whole genome tree and coalescent species trees. However the coat protein gene tree of SPCSV and SPCFV resolved similar clades to the genome and coalescent species tree while this was not the case in SPFMV and SPVC. In addition, we report variation in selective pressure within sites of individual genes across all four viruses; overall all viruses were under purifying selection. We report the first complete genomes of SPFMV, SPVC, SPCFV, and a partial SPCSV from Kenya as a mixed infection in one sample. Our findings provide a snap shot on the evolutionary relationship of sweet potato viruses (SPFMV, SPVC, SPCFV, and SPCSV) from Kenya as well as assessing whether selection pressure has an effect on their evolution.

Keywords: Africa; Next-generation sequencing; Plant virus; Recombination; Selective pressure; Smallholder farmer; Smallholder farmers; Sweet potato virus disease.

Grants and funding

James M. Wainaina is supported by an Australian Award Scholarships from the Department of Foreign Affairs and Trade (DFAT), and this work is part of his PhD research. Pawsey Supercomputing Centre provided supercomputer resources for data analysis with funding from the Australian Government and the Government of Western Australia. Laboratory and sequencing cost were paid for through a Rising star grant from the Faculty of Science University of Western Australia to Laura M. Boykin. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.