Abstract Detail



Comparative Genomics/Transcriptomics

Ou, Shujun [1], Jiang, Ning [2].

LTR_retriever: a highly accurate and sensitive program for identification of LTR retrotransposons.

Long terminal-repeat retrotransposons (LTR-RTs) are prevalent in plant genomes. Identification of LTR-RTs is critical for achieving high-quality gene annotation. Based on the well-conserved structure, multiple programs were developed for de novo identification of LTR-RTs; however, these programs are associated with low specificity and high false discovery rate (FDR). Here we report LTR_retriever, a multithreading empowered Perl program that identifies LTR-RTs and generates high-quality LTR libraries from genomic sequences. LTR_retriever demonstrated significant improvements by achieving high levels of sensitivity (91%), specificity (97%), accuracy (96%), and precision (90%) in rice. LTR_retriever is also compatible with long sequencing reads. With 40k self-corrected PacBio reads equivalent to 4.5X genome coverage in Arabidopsis, the constructed LTR library showed excellent sensitivity and specificity.  In addition to canonical LTR-RTs with 5'-TG…CA-3' termini, LTR_retriever also identifies non-canonical LTR-RTs (non-TGCA), which have been largely ignored in genome-wide studies. We identified seven types of non-canonical LTRs from 42 out of 50 plant genomes. The majority of non-canonical LTRs are Copia elements, with which the LTR is four times shorter than that of other Copia elements, which may be a result of their target specificity. Strikingly, non-TGCA Copia elements are often located in genic regions and preferentially insert nearby or within genes, indicating their impact on the evolution of genes and potential as mutagenesis tools.


Related Links:
Link to the software download (GitHub)
The paper published in Plant Physiology


1 - Michigan State University, 1066 Bogue St, Room A326, East Lansing, MI, 48823, United States
2 - Michigan State University, 1066 Bogue St, Room A330, East Lansing, MI, 48823, United States

Keywords:
LTR retrotransposon
LTR_retriever
transposable element
genome annotation
Evolution.

Presentation Type: Poster
Number: PGT012
Abstract ID:652
Candidate for Awards:Genetics Section Poster Award


Copyright © 2000-2018, Botanical Society of America. All rights reserved