Positive selection, molecular recombination structure and phylogenetic reconstruction of members of the family Tombusviridae: implication in virus taxonomy

A detailed study of putative recombination events and their evolution frequency in the whole genome of the currently known members of the family Tombusviridae, comprising 79 accessions retrieved from the international databases, was carried out by using the RECCO and RDP version 3.31β algorithms. The first program allowed the detection of potential recombination sites in seven out of eight virus genera (Aureusvirus, Avenavirus, Carmovirus, Dianthovirus, Necrovirus, Panicovirus, and Tombusvirus), the second program provided the same results except for genus Dianthovirus. On the other hand, both methods failed to detect recombination breakpoints in the genome of members of genus Machlomovirus. Furthermore, based on Fisher's Exact Test of Neutrality, positive selection exerted on protein-coding genes was detected in 17 accession pairs involving 15 different lineages. Except genera Machlomovirus, and Panicovirus along with unclassified Tombusviridae, all the other taxonomical genera and the unassigned Tombusviridae encompassed representatives under positive selection. The evolutionary history of all members of the Tombusviridae family showed that they segregated into eight distinct groups corresponding to the eight genera which constitute this family. The inferred phylogeny reshuffled the classification currently adopted by the International Committee on Taxonomy of Viruses. A reclassification was proposed

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Not AvailableSugarcane yellow leaf virus (SCYLV) is one of the most widespread virus diseases affecting sugarcane worldwide. The virus has been responsible for drastic economic losses in most sugarcane growing regions and remains a major concern for sugarcane breeders. Symptoms are characterized by intense yellowing of the midrib, which extends to the leaf blade followed by tissue necrosis from the leaf tip towards the leaf base. Such symptomatic leaves are usually characterized by increased respiration, reduced photosynthesis, a change in the ratio of hexose to sucrose, and an increase in starch. Viral infection often affects carbon assimilation and metabolism in host plants. Sugarcane growth is always stunted in severe infections. SCYLV is mainly propagated by planting cuttings from infected stalks. Phylogenetic analyses have confirmed the worldwide distribution of at least eight SCYLV genotypes (BRA, CHN1, CHN3, CUB, HAW, IND, PER, and REU). Evidence of the recombination has been found in the SCYLV genome which contains potential recombination signals in the ORF1/2 and ORF5. This shows that recombination plays an important role in the selection pressure on SCYLVNot Availabl