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Open Access Methodology article

De novo identification of LTR retrotransposons in eukaryotic genomes

Mina Rho1, Jeong-Hyeon Choi2, Sun Kim23, Michael Lynch4 and Haixu Tang23*

Author Affiliations

1 Department of Computer Science, Indiana University, Bloomington, IN 47405, USA

2 Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN 47405, USA

3 School of Informatics, Indiana University, Bloomington, IN 47408, USA

4 Department of Biology, Indiana University, Bloomington, IN 47405, USA

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BMC Genomics 2007, 8:90  doi:10.1186/1471-2164-8-90

Published: 3 April 2007

Abstract

Background

LTR retrotransposons are a class of mobile genetic elements containing two similar long terminal repeats (LTRs). Currently, LTR retrotransposons are annotated in eukaryotic genomes mainly through the conventional homology searching approach. Hence, it is limited to annotating known elements.

Results

In this paper, we report a de novo computational method that can identify new LTR retrotransposons without relying on a library of known elements. Specifically, our method identifies intact LTR retrotransposons by using an approximate string matching technique and protein domain analysis. In addition, it identifies partially deleted or solo LTRs using profile Hidden Markov Models (pHMMs). As a result, this method can de novo identify all types of LTR retrotransposons. We tested this method on the two pairs of eukaryotic genomes, C. elegans vs. C. briggsae and D. melanogaster vs. D. pseudoobscura. LTR retrotransposons in C. elegans and D. melanogaster have been intensively studied using conventional annotation methods. Comparing with previous work, we identified new intact LTR retroelements and new putative families, which may imply that there may still be new retroelements that are left to be discovered even in well-studied organisms. To assess the sensitivity and accuracy of our method, we compared our results with a previously published method, LTR_STRUC, which predominantly identifies full-length LTR retrotransposons. In summary, both methods identified comparable number of intact LTR retroelements. But our method can identify nearly all known elements in C. elegans, while LTR_STRUCT missed about 1/3 of them. Our method also identified more known LTR retroelements than LTR_STRUCT in the D. melanogaster genome. We also identified some LTR retroelements in the other two genomes, C. briggsae and D. pseudoobscura, which have not been completely finished. In contrast, the conventional method failed to identify those elements. Finally, the phylogenetic and chromosomal distributions of the identified elements are discussed.

Conclusion

We report a novel method for de novo identification of LTR retrotransposons in eukaryotic genomes with favorable performance over the existing methods.