The use of RelocaTE and unassembled short reads to produce high-resolution snapshots of transposable element generated diversity in rice.

ABSTRACT: Transposable elements (TEs) are dynamic components of genomes that often vary in copy number among members of the same species. With the advent of next-generation sequencing TE insertion-site polymorphism can be examined at an unprecedented level of detail when combined with easy-to-use bioinformatics software. Here we report a new tool, RelocaTE, that rapidly identifies specific TE insertions that are either polymorphic or shared between a reference and unassembled next-generation sequencing reads. Furthermore, a novel companion tool, CharacTErizer, exploits the depth of coverage to classify genotypes of nonreference insertions as homozygous, heterozygous or, when analyzing an active TE family, as rare somatic insertion or excision events. It does this by comparing the numbers of RelocaTE

SUBMITTER: Robb SM 

PROVIDER: S-EPMC3689806 | biostudies-literature | 2013 Jun

REPOSITORIES: biostudies-literature