Análises in silico de genes de vigna unguiculata (l.) walp envolvidos na interação compatível com o Cowpea Severe Mosaic Virus (CPSMV)

Abstract

The cowpea (Vigna unguiculata [L.] Walp.) is one of the most cultivated legume species along the Brazilian territory. Several factors affect the productivity of cowpea, among which pests and pathogens are responsible for large losses of productivity of this crop. Cowpea Severe Mosaic Virus (CPSMV) is the most devastating pathogen of cowpea crops in Brazil. Recent studies on the compatible interaction between V. unguiculata and CPSMV have identified a variety of differentially accumulated proteins in different stages of infection by the virus. A better understanding of the role of the genes coding for these proteins during this interaction is critical for the development of genetic improvement in breeding programs. In this sense, in silico genomic analyses significantly aid the acquisition of relevant structural and functional information regarding genes of interest. The draft genome available for V. unguculata on public databases presents insufficient quality for more solid studies. Thus, this work aims to obtain the structure of the coding regions of differentially expressed genes during the compatible interaction between V. unguiculata and CPSMV, as well as to perform a phylogenetic reconstruction of corresponding amino acid sequences from the orthologous sequences of species phylogenetically closely related to V. unguiculata. For this purpose, four differentially expressed genes during the aforementioned compatible interaction have been selected. Amino acid sequences of orthologous proteins obtained from UniProt databank have been used as reference for obtaining their corresponding genes in Vigna angularis and Phaseolus vulgaris, using the specialized plant databases: Viggs and Phytozome, respectively. V. unguiculata sequence reads archives (SRA) files have been obtained from NCBI SRA database and used to perform mapping the reads onto the coding nucleotide sequences of the reference species. Consensus sequences corresponding to the coding regions of V. unguiculata genes have been obtained as output from those mappings. These consensus sequences have been used for predicting the corresponding amino acid sequences. These amino acid sequences have been used in multiple alignments with orthologous sequences, as well as for the prediction of conserved protein domains. The multiple alignments have been used to reconstruct the evolutionary relationships among the orthologous sequences by Bayesian inference. The analyses have exhibited a high degree of evolutionary divergence among the analyzed proteins, except for the regions corresponding to the conserved protein domains. This work is expected to be the initial step toward the structural and functional study of these four differentially expressed genes in this important pathosystem, aiming for its future application on breeding programs.