Variabilidade genética e estrutura populacional de Macroptilium yellow vein virus em Macroptilium spp. no estado de Alagoas e primeiro relato de Tomato interveinal chlorosis virus em Rhynchosia minima

Abstract

Non-cultivated plants play an important role as a source of begomovirus diversity, being able to contribute to the emergence of new species and also serve as alternative hosts or as a source of inoculum for epidemics in commercial crops. The genus Begomovirus (family Geminiviridae) is an important group of viruses that infect dicotyledons in the most diverse regions of the planet, causing significant economic losses in crop fields. In this context, the present study aimed to evaluate the genetic variability and population structure of Macroptilium yellow vein virus (MacYVV) infecting Macroptilium spp. in the state of Alagoas and the identification of a species of begomovirus infecting Rhynchosia minima. Aiming to evaluate the genetic variability and population structure of MacYVV infecting the non-cultivated plant Macroptilium spp. (Fabaceae family), leaf samples showing symptoms indicative of begomovirus infection were collected in different municipalities in the state of Alagoas in 2019 and 2020. Total DNA was extracted from each sample and served as a template for rolling circle amplification (ACR), followed by digestion with endonucleases and cloning into plasmid vectors that were completely sequenced using the Sanger method. Paired DNA-A sequence comparisons showed that all isolates belong to a single species, Macroptilium yellow vein virus. Phylogenetic analysis showed the division of MacYVV isolates into five subpopulations, which presented low values of nucleotide variability. Recombination and crosslinking analyzes showed evidence of intraspecific recombination events in some MacYVV isolates. Furthermore, strong negative selection pressure was detected acting on the CP and Rep genes of MacYVV. These results suggest a low genetic variability that may have been generated by possible genetic bottlenecks, and that the strong structure of MacYVV subpopulations must be the effect of the low interaction between them, allowing these subpopulations to continue differentiating. To identify the species of begomovirus infecting Rhynchosia minima, total DNA extraction from symptomatic plants was performed. Aliquots of the DNA were used as a template for detection of begomovirus using genus-specific PCR oligonucleotides. PCR-positive samples were used to obtain complete viral genomes via ACR, endonuclease digestion, cloning into plasmid vectors and sequencing. Pairwise sequence comparisons indicated that DNA-A clones (n=4) had 94% nucleotide identity with Macroptilium yellow net virus (MacYNV), which was reclassified as tomato interveinal chlorosis virus (ToICV). Phylogenetic analysis showed that the isolates formed a clade with other ToICV sequences, agreeing with the results of pairwise comparisons. Rhynchosia minima has already been described as a host for begomovirus in countries such as Ecuador, Puerto Rico, the United States, Cuba, Mexico and Pakistan, but it had not yet been reported in Brazil.

Keywords: Geminivirus, Fabaceae, weed.