Patterns of Spontaneous Nucleotide Substitutions in Grape Processed Pseudogenes

Abstract

Pseudogenes are dead copies of genes. Owing to the absence of functional constraint, all nucleotide substitutions that occur in these sequences are selectively neutral, and thus represent the spontaneous pattern of substitution within a genome. Here, we analysed the patterns of nucleotide substitutions in Vitis vinifera processed pseudogenes. In total, 259 processed pseudogenes were used to compile two datasets of nucleotide substitutions. The ancestral states of polymorphic sites were determined based on either parsimony or site functional constraints. An overall tendency towards an increase in the pseudogene A:T content was suggested by all of the datasets analysed. Low association was seen between the patterns and rates of substitutions, and the compositional background of the region where the pseudogene was inserted. The flanking nucleotide significantly influenced the substitution rates. In particular, we noted that the transition of G→A was influenced by the presence of C at the contiguous 5′ end base. This finding is in agreement with the targeting of cytosine to methylation, and the consequent methyl-cytosine deamination. These data will be useful to interpret the roles of selection in shaping the genetic diversity of grape cultivars.