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

, , , ,
1 School of Molecular Sciences/ARC CoE Plant Energy Biology, The University of Western Australia, Crawley, 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, Australia
DOI
10.7287/peerj.preprints.26909v1
Published
Accepted
Subject Areas
Agricultural Science, Evolutionary Studies, Genomics
Keywords
recombination, next-generation sequencing, Sweet potato virus disease, smallholder farmers, selective pressure, Africa, smallholder farmer
Copyright
© 2018 Wainaina et al.
Licence
This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ Preprints) and either DOI or URL of the article must be cited.
Cite this article
Wainaina JM, Ateka E, Makori T, Kehoe MA, Boykin LM. 2018. Phylogenomic relationship and evolutionary insights of sweet potato viruses from the western highlands of Kenya. PeerJ Preprints 6:e26909v1

Abstract

Sweet potato is a major food security crop within sub-Saharan Africa where 90 % of Africa’s sweet potato 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 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 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 the 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. In addition, we reveal their phylogenomic relationships and provide evolutionary insights into these viruses. Our findings demonstrate the need for clean planting materials as the first line of control for these viruses, in particular for smallholder farmers within eastern Africa region.

Author Comment

This is a submission to PeerJ for review.

Supplemental Information

Additional Information

Competing Interests

The authors declare that they have no competing interests.

Author Contributions

James M Wainaina conceived and designed the experiments, performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft.

Elijah Ateka performed the experiments, contributed reagents/materials/analysis tools, authored or reviewed drafts of the paper, approved the final draft.

Timothy Makori performed the experiments, contributed reagents/materials/analysis tools, authored or reviewed drafts of the paper, approved the final draft.

Monica A Kehoe conceived and designed the experiments, performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft.

Laura M Boykin conceived and designed the experiments, performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft.

Field Study Permissions

The following information was supplied relating to field study approvals (i.e., approving body and any reference numbers):

Ethical approval to conduct this study was obtained from the University of Western Australia (RA/4/1/7475). In addition, permission to access all privately owned farms was obtained through signed consent forms by the head of each household. Sweet potato samples were collected as part of a larger field survey in the western highlands of Kenya over two cropping seasons (2015 and 2016) during the long season (Wainaina et al., 2018).

DNA Deposition

The following information was supplied regarding the deposition of DNA sequences:

GenBank with the accession numbers: SPVC (MH264531), SPCSV (RNA1 MH264532), SPCSV (RNA2, MH264533), SPCFV (MH264534), and SPFMV (MH264535).

Data Deposition

The following information was supplied regarding data availability:

Sequences are uploaded to GenBank.

Funding

JMW is supported by the Australian Award Scholarships from
the Department of Foreign Affairs and Trade (DFAT), and this work is part of his PhD research. Fieldwork activities were coordinated through Cassava Diagnostics Project Kenyan node. Pawsey Supercomputing Centre provided supercomputer resources for data analysis with funding from the Australian Government and the Government of Western Australia. LMB was awarded a UWA Rising Star award which funded this work. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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