Detectable episodic positive selection in the virion strand A-strain maize streak virus genes may have a role in its host adaptation

Abstract

Maize streak virus (MSV) has only three genes : cp encoding the coat protein, mp encoding the movement protein and rep/repA encoding two distinct replication associated proteins from an alternatively spliced transcript. These genes have roles in encapsidation, movement, replication and interactions with the external environment and are thus prone to stimuli-driven molecular adaptation. We accomplished selection studies for these publicly available curated, recombination-free complete coding sequences for representative A-strain maize streak virus (MSV-A) cp and mp genes. We found evidence of gene-wide selection in these two MSV genes at specific sites within the genes (cp 1.23% and mp 0.99%). Positively selected sites have amino acids that are 60% hydrophilic and 40% hydrophobic in nature. We found significant evidence of positive selection at branches (cp: 0.76 and mp :1.66%) representing the diversity of MSV-A strain in South Africa that is closely related to the MSV-Mat-A isolate (GenBank accession number: AF329881) that is well disseminated and adapted to the maize plant in the sub-Saharan Africa. While in the mp gene, selection significantly intensified for the overall diversities of the MSV-A sequences, and those that are closely related to the MSV-Mat-A isolate. These findings have revealed that these genes, despite mostly undergoing non-diversifying selection, the detectable diversifying positive selection observed could have a major role in MSV-A host adaptive evolution that has over time, ensured a degree of pathogenicity that is sufficient for onward transmission rather than killing its host.