Accurate Transposable Element Annotation Is Vital When Analyzing New Genome Assemblies.

ABSTRACT: Transposable elements (TEs) are mobile genetic elements with the ability to replicate themselves throughout the host genome. In some taxa TEs reach copy numbers in hundreds of thousands and can occupy more than half of the genome. The increasing number of reference genomes from nonmodel species has begun to outpace efforts to identify and annotate TE content and methods that are used vary significantly between projects. Here, we demonstrate variation that arises in TE annotations when less than optimal methods are used. We found that across a variety of taxa, the ability to accurately identify TEs based solely on homology decreased as the phylogenetic distance between the queried genome and a reference increased. Next we annotated repeats using homology alone, as is often the case in new g

SUBMITTER: Platt RN 

PROVIDER: S-EPMC4779615 | biostudies-literature | 2016 Jan

REPOSITORIES: biostudies-literature