Comparative Genomic Characterization and Evolutionary Analysis of PRT Gene Family Members in Plants
Keywords:
Phosphoribosyltransferase, PRT gene family, protein sequence screening, comparative genomics, plant bioinformaticsAbstract
In plants, proteins related to phosphoribosyltransferase participate in metabolic processes, and a wide search of protein databases may yield several families of proteins with the same annotation keywords. A collection of 36 candidates PRT-labelled or PRT associated proteins were characterized in this exploratory analysis from Oryza sativa, Zea mays, Hordeum vulgare, Arabidopsis thaliana and Setaria italica. The parsed candidate amino acid sequences were evaluated using Python scripts for length, molecular weight, theoretical isoelectric point, hydropathy, sequence quality and similarity to three-amino-acid words. A reproducible script was used to generate species level descriptive tables, a pairwise similarity matrix and an exploratory hierarchical clustering visualization. Eight of the rice, seven of the maize, five of the barley, eight of the Arabidopsis and eight of the Setaria candidate proteins were included. There were significant variation in mean protein lengths among the 5 screening groups and 2 candidate records were identified for automatic check. These outputs can be easily used for downstream validation and can serve as a way to assess candidate datasets prior to phylogenetic analysis. The absence of accession supported family validation and the lack of coding DNA sequences and genomic coordinates in the dataset prevents the calculation of gene-family expansion, molecular selection, chromosomal synteny, and natural evolutionary relationship. It is necessary to do additional conserved domain checking and reference genome mapping to form biological conclusions.
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