LTR_retriever: a highly accurate and sensitive program for identification of long terminal-repeat retrotransposons

Transposable elements are a major part of plant genomes. Long-terminal repeat retrotransposons (LTR (LTR-RTs) alone make up 78% of the maize genome (retrotransposons use a “copy and paste” transposition method meaning that a single source element can generate numerous clones of itself, leading to tremendous amplification).  In the absence of selection, LTR-RTs are particularly subject to mutation, meaning that there is considerable variation in their structure and sequence. Therefore, efforts to sequence and annotate genomes will be greatly enhanced by the ability to reliably and sensitively recognize LTR-RTs. Ou and Jiang have developed a program, LTR_retriever, to annotate LTR-RTs in plant genomes, and demonstrated its effectiveness in several monocot and dicot genomes. (Summary by Mary Williams) Plant Physiol. 10.1104/pp.17.01310