Evolutionary insights into Bean common mosaic necrosis virus and Cowpea aphid borne mosaic virus using global isolates and thirteen new near complete genomes from Kenya

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. The main aim was to gain insights into the selection pressure and evolutionary relationships of Bean common mosaic necrosis virus (BCMNV) and Cowpea aphid-borne mosaic virus (CABMV), within symptomatic common beans and cowpeas. Eleven near complete genomes of BCMNV and two for CABMV sequences were obtained from SSA. Bayesian phylogenomic analysis and tests for differential selection pressure within sites and across tree branches of the viral genomes was carried out. Three distinct well-supported clades were identified across the whole genome tree, and were 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. These results will contribute greatly to the knowledge gap surrounding the phylogenomic relationship of these viruses, particularly for CABMV, for which there are few genome sequences available, and support the current breeding efforts towards resistance for BCMNV and CABMV.

Peer Review #1 of "Phylogenomic relationship and evolutionary insights of sweet potato viruses from the western highlands of Kenya (v0.1)"

“…It is therefore likely that within the agro-ecosystems of western Kenya, there is heavy infestation of both aphids and whitefly vectors. Previous studies have reported aphid and whitefly-transmitted viruses in crops within the western region (Legg et al, 2006;Mangeni et al, 2014;Legg et al, 2014;Wainaina et al, 2018) and the Lake Victoria region (Tugume et al, 2010a;Adikini et al, 2015;Adikini et al, 2016). Moreover, farming practices within smallholder farms, which include partial harvesting of mature sweet potato, are thought to help maintain the virus within the agro-ecosystem.…”

“…Within the Potyviridae, recombination is highly prevalent (Varsani et al, 2008;Elena et al, 2014 ;Ndunguru et al, 2015;Tugume et al, 2016;Wainaina et al, 2018). Moreover, co-infection of multiple viruses, in particular within sweet potato, can result in well-adapted viruses and has been adversely reported in other countries (Tugume et al, 2010a;Maina et al, 2017;Maina et al, 2018).…”

“…They are flexuous, non-enveloped, rod-shaped particles that are 680-900 nm long and 11-15 nm wide (Urcuqui-inchima & Haenni, 2001). They contain a single open reading frame that is approximately 10,000 nucleotides nt and transcribes ten genes with varying functions (Urcuqui-inchima & Haenni, 2001;Wainaina et al, 2018). On the other hand, SPCSV genus Crinivirus, family Closteroviridae has a non-enveloped bipartite genome (Karasev, 2000).…”

“…It is suspected that a whitefly vector is associated with the transmission of SPCFV (Aritua et al, 2007), however, vector transmission studies on this are yet to confirm this (Aritua et al, 2007;Tugume et al, 2016). The agro-ecosystems in the western highlands of Kenya are characterised by a heterogeneous cropping system (Tittonell et al, 2007;Wainaina et al, 2018), which allow for virus movement between crops during the growing season. To date, there have been limited efforts to identify the diversity and phylogenomic relationships of plant viruses in this system.…”

Phylogenetic relationships of endornaviruses in common bean from the western highlands of Kenya and global sequences

“…We then sampled symptomatic 77 common bean (Phaseolus vulgaris) leaves from the western highlands of Kenya as part of a larger 78 surveillance study on the heterogeneous cropping system in the western highlands of Kenya. RNA 79 extraction, cDNA library preparation and subsequent RNA sequencing on the Illumina Hiseq 2500 80 were carried out as previously described (Wainaina et al, 2018).…”