Compensatory Base Changes and Varying Phylogenetic Effects on Angiosperm ITS2 Genetic Distances.

ABSTRACT: A compensatory base change (CBC) that coevolves in the secondary structure of ribosomal internal transcribed spacer 2 (ITS2) influences the estimation of genetic distance and thus challenges the phylogenetic use of this most popular genetic marker. To date, however, the CBC effect on ITS2 genetic distance is still unclear. Here, ITS2 sequences of 46 more recent angiosperm lineages were screened from 5677 genera and phylogenetically analyzed in sequence-structure format, including secondary structure prediction, structure-based alignment and sequence partition of paired and unpaired regions. ITS2 genetic distances were estimated comparatively by using both conventional DNA substitution models and RNA-specific models, which were performed in the PHASE package. Our results showed that the exi

SUBMITTER: Cao R 

PROVIDER: S-EPMC9003356 | biostudies-literature | 2022 Mar

REPOSITORIES: biostudies-literature