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. 2019 Feb 13:7:e6297.
doi: 10.7717/peerj.6297. eCollection 2019.

Evolutionary insights of Bean common mosaic necrosis virus and Cowpea aphid-borne mosaic virus

James M Wainaina  1 , Laura Kubatko  2 , Jagger Harvey  3 , Elijah Ateka  4 , Timothy Makori  4 , David Karanja  5 , Laura M Boykin  1 , Monica A Kehoe  6
Affiliations
Free PMC article

Evolutionary insights of Bean common mosaic necrosis virus and Cowpea aphid-borne mosaic virus

James M Wainaina et al. PeerJ. .
Free PMC article

Abstract

Plant viral diseases are one of the major limitations in legume production within sub-Saharan Africa (SSA), as they account for up to 100% in production losses within smallholder farms. In this study, field surveys were conducted in the western highlands of Kenya with viral symptomatic leaf samples collected. Subsequently, next-generation sequencing was carried out to gain insights into the molecular evolution and evolutionary relationships of Bean common mosaic necrosis virus (BCMNV) and Cowpea aphid-borne mosaic virus (CABMV) present within symptomatic common bean and cowpea. Eleven near-complete genomes of BCMNV and two for CABMV were obtained from western Kenya. Bayesian phylogenomic analysis and tests for differential selection pressure within sites and across tree branches of the viral genomes were carried out. Three well-supported clades in BCMNV and one supported clade for CABMNV were resolved and in agreement with individual gene trees. Selection pressure analysis within sites and across phylogenetic branches suggested both viruses were evolving independently, but under strong purifying selection, with a slow evolutionary rate. These findings provide valuable insights on the evolution of BCMNV and CABMV genomes and their relationship to other viral genomes globally. The results will contribute greatly to the knowledge gap involving the phylogenomic relationship of these viruses, particularly for CABMV, for which there are few genome sequences available, and inform the current breeding efforts towards resistance for BCMNV and CABMV.

Keywords: Genomics; Kenya; Next-generation sequencing (NGS); Phylogenomics of BCMNV and CABMV; Smallholder farmer; Virus evolution.

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Conflict of interest statement

Laura M. Boykin is an Academic Editor for PeerJ.

Figures

Figure 1
Figure 1. Bayesian analysis of near complete genome of Bean common mosaic necrosis virus (BCMNV) and Cowpea aphid-borne mosaic virus (CABMV) with nodes in each branch labeled with posterior probabilities.
Bean common mosaic virus (BCMV) was used as the out group to root the tree (B) Bayesian analysis of near complete genome of Bean common mosaic necrosis virus (BCMNV) with nodes in each branch labeled with posterior probabilities. (C) Bayesian analysis of near complete genome of Cowpea aphid-borne mosaic virus (CABMV) with nodes in each branch labeled with posterior probabilities. The scale indicates the nucleotides substitutions per every 100 sites across the near complete genome trees. Tip labels contains information on: virus, country of sample collection, isolation source, GenBank and/or field identification and year of sampling.
Figure 2
Figure 2. Consensus trees sampled in a Bayesian analysis of Bean common mosaic necrosis virus (BCMNV) and Cowpea aphid-borne mosaic virus (CABMV) (A), coat protein (CP) (B) CI (C) Nlb (D) PI (E) Hc-Pro (F) P3 (G) Nla-Pro (H) Nla-Vpg (I) 6K2 (J) 6K1.
The scale bar represents the nucleotide substitution per every 100 sites within each gene. Tip labels contain information on: virus, country of sample collection, isolation source, GenBank and/or field identification and year of sampling.
Figure 3
Figure 3. Selection pressure within sites across the viral gene fragments was determined by assessing the average synonymous and non-synonymous (dN/dS) across the coding region using SNAP and SLAC that were plotted against each gene.
Confidence interval of the dN/dS ratio are provided. All sites are under strong purifying selection with dN/dS values < 1 (A) Comparison of the average synonymous (dS) and non-synonymous (dN) sites across the coding region of each gene in bean common mosaic necrosis virus (BCMNV) near complete genome using SNAP. (B) Comparison of the average synonymous (dS) and non-synonymous (dN) across the coding region of each gene cowpea aphid-borne mosaic necrosis virus (CABMV) near complete genome using SNAP. The dots on the graph represent the average dN/dS in each codon of the gene fragment.
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References

    1. Aberer AJ, Kobert K, Stamatakis A. ExaBayes: massively parallel bayesian tree inference for the whole-genome era. Molecular Biology and Evolution. 2014;31:1–8. doi: 10.1093/molbev/msu236. - DOI - PMC - PubMed
    1. Alicai T, Ndunguru J, Sseruwagi P, Tairo F, Okao-Okuja G, Nanvubya R, Kiiza L, Kubatko L, Kehoe MA, Boykin LM. Cassava brown streak virus has a rapidly evolving genome: implications for virus speciation, variability, diagnosis and host resistance. Scientific Reports. 2016;6:36164. doi: 10.1038/srep36164. - DOI - PMC - PubMed
    1. Almakarem ASA, Heilman KL, Conger HL, Shtarkman YM, Rogers SO. Extraction of DNA from plant and fungus tissues in situ. BMC Research Notes. 2012;5:266. doi: 10.1186/1756-0500-5-266. - DOI - PMC - PubMed
    1. Blawid R, Silva JMF, Nagata T. Discovering and sequencing new plant viral genomes by next-generation sequencing: description of a practical pipeline. Annals of Applied Biology. 2017;170:301–314. doi: 10.1111/aab.12345. - DOI
    1. Boni MF, Posada D, Feldman MW. An exact nonparametric method for inferring mosaic structure in sequence triplets. Genetics. 2007;176:1035–1047. doi: 10.1534/genetics.106.068874. - DOI - PMC - PubMed

Grants and funding

Laboratory consumables were purchased through the Rising Star grants by the faculty of Science University of Western Australia to Laura M Boykin. Pawsey supercomputing Centre provided supercomputer resources for data analysis with funding from the Australian Government and the Government of Western Australia. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.