Accurate Transposable Element Annotation Is Vital When Analyzing New Genome Assemblies

Genome Biology and Evolution
Roy N PlattDavid A Ray

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 genome analyses, and a combination of homology and de novo methods as well as an additional manual curation step. Reannotation using these methods identified a substantial number of new TE subfamilies in previously characterized genomes, recognized a higher proportion of the genome as repetitive, and decreased the average genetic distance within TE families, implying recent TE accumulation. Finally, these finding-increased recognition of younge...Continue Reading

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Dec 21, 2016·Annals of the New York Academy of Sciences·Aurélie Kapusta, Alexander Suh
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Software Mentioned

RepeatMasker
RepeatScout
LTR
BLAST
calcDivergenceFromAlign
TimeTree
R
finder
RepeatModeler
UCSC Genome Browser

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