Recombination and darwinian selection as drivers of genetic diversity and evolution of sweet potato leaf curl viruses in Tanzania

Abstract

Using High-throughput Sequencing (HTS) and Sanger sequencing techniques, we detected sweet potato leaf curl viruses (SPLCVs; Genus Begomovirus) and determined their genetic diversities, recombination, and evolutionary selection pressure imposed on their genes. Eleven complete (2767–2824 nucleotides) and fifty partial (V1 and C1 proteins) sequences of SPLCVs were generated, and one complete genome of sweet potato pakakuyu virus was also generated. The detected SPLCVs were genetically diverse, with complete nucleotide sequence identities ranging from 78.7 to 100%. These sequences were closely related (>89% identical) to the sweet potato leaf curl virus, the sweet potato Sao Paulo virus, and the sweet potato leaf curl Uganda virus. The diversity of SPLCVs indicated the occurrence of their strains and variants in Tanzania. Intra- and interspecies recombination events were detected in four and two complete and partial sequences of SPLCVs, respectively. The genes of SPLCVs, except the C4 gene, are evolving under purifying selection pressure. In the C4 gene, numerous codon sites are evolving under positive selection pressure. High genetic diversity and diversifying selection imply an increased chance of SPLCVs to interact and adapt to diverse sweet potato genotypes and their wild relatives in Tanzania.