Molecular evolution of a mitochondrial polB gene, encoding a family B DNA polymerase, towards the elimination from Agrocybe mitochondrial genomes

Two genes ( Ac-polB O1and Ac-polB O2), each encoding a family B DNA polymerase, were characterized from the mitochondrial genome of the basidiomycete Agrocybe chaxingu. These two polB genes constitute orthologs of the potentially functional Aa-polB gene and its disrupted paralog Aa-polB P1, previously described in the closely related species A. aegerita. Unlike the case in Aa-polB, both gene copies in A. chaxingu are constituted by large but disrupted ORFs, which very probably encode nonfunctional enzymes: Ac-polB O1 has a deletion of 126 bp between the segments encoding the Exo II and Pol I domains and a 78-bp insertion between the Exo II and Exo III domains, whereas Ac-polB O2 has a large deletion of 1208 bp between the Exo II and Pol III domains and a deletion of 54-bp involving the 3′ end of the gene. Hence, rearrangements in the Ac-polB ORFs appear to have led to their functional erosion in the mitochondrial genome in this species. Phylogenetic analysis has shown a close relationship between the mitochondrial polB genes and homologous genes carried by fungal linear plasmids, suggesting that they may have been acquired by the integration of linear plasmids into the mitochondrial genome.