Sequence exploration reveals information bias among molecular markers used in phylogenetic reconstruction for Colletotrichum species.

ABSTRACT: The Colletotrichum gloeosporioides species complex is among the most destructive fungal plant pathogens in the world, however, identification of isolates of quarantine importance to the intra-specific level is confounded by a number of factors that affect phylogenetic reconstruction. Information bias and quality parameters were investigated to determine whether nucleotide sequence alignments and phylogenetic trees accurately reflect the genetic diversity and phylogenetic relatedness of individuals. Sequence exploration of GAPDH, ACT, TUB2 and ITS markers indicated that the query sequences had different patterns of nucleotide substitution but were without evidence of base substitution saturation. Regions of high entropy were much more dispersed in the ACT and GAPDH marker alignments than fo

SUBMITTER: Rampersad SN 

PROVIDER: S-EPMC4210461 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature