LTRharvest, an Efficient and Flexible Software for De Novo Detection of LTR Retrotransposons

Overview

Journal BMC Bioinformatics

Publisher Biomed Central

Specialty Biology

Date 2008 Jan 16

PMID 18194517

Citations 720

Authors

David Ellinghaus

Stefan Kurtz

Ute Willhoeft

Affiliations

Soon will be listed here.

Abstract

Background: Transposable elements are abundant in eukaryotic genomes and it is believed that they have a significant impact on the evolution of gene and chromosome structure. While there are several completed eukaryotic genome projects, there are only few high quality genome wide annotations of transposable elements. Therefore, there is a considerable demand for computational identification of transposable elements. LTR retrotransposons, an important subclass of transposable elements, are well suited for computational identification, as they contain long terminal repeats (LTRs).

Results: We have developed a software tool LTRharvest for the de novo detection of full length LTR retrotransposons in large sequence sets. LTRharvest efficiently delivers high quality annotations based on known LTR transposon features like length, distance, and sequence motifs. A quality validation of LTRharvest against a gold standard annotation for Saccharomyces cerevisae and Drosophila melanogaster shows a sensitivity of up to 90% and 97% and specificity of 100% and 72%, respectively. This is comparable or slightly better than annotations for previous software tools. The main advantage of LTRharvest over previous tools is (a) its ability to efficiently handle large datasets from finished or unfinished genome projects, (b) its flexibility in incorporating known sequence features into the prediction, and (c) its availability as an open source software.

Conclusion: LTRharvest is an efficient software tool delivering high quality annotation of LTR retrotransposons. It can, for example, process the largest human chromosome in approx. 8 minutes on a Linux PC with 4 GB of memory. Its flexibility and small space and run-time requirements makes LTRharvest a very competitive candidate for future LTR retrotransposon annotation projects. Moreover, the structured design and implementation and the availability as open source provides an excellent base for incorporating novel concepts to further improve prediction of LTR retrotransposons.

Citing Articles

A near-complete genome assembly of Fragaria iinumae.

Du H, He Y, Chen M, Zheng X, Gui D, Tang J BMC Genomics. 2025; 26(1):253.

PMID: 40087556 DOI: 10.1186/s12864-025-11440-0.

Hordeum I genome unlocks adaptive evolution and genetic potential for crop improvement.

Feng H, Du Q, Jiang Y, Jia Y, He T, Wang Y Nat Plants. 2025; .

PMID: 40087544 DOI: 10.1038/s41477-025-01942-w.

Haplotype-resolved and chromosome-level reference genome assembly of provides insights into the evolution and juvenile growth of persimmon.

Guan C, Liu Y, Li Z, Zhang Y, Liu Z, Zhu Q Hortic Res. 2025; 12(4):uhaf001.

PMID: 40078717 PMC: 11896977. DOI: 10.1093/hr/uhaf001.

The pan-genome of Spodoptera frugiperda provides new insights into genome evolution and horizontal gene transfer.

Huang Y, Rao H, Su B, Lv J, Lin J, Wang X Commun Biol. 2025; 8(1):407.

PMID: 40069391 PMC: 11897360. DOI: 10.1038/s42003-025-07707-7.

Marine vs. terrestrial: links between the environment and the diversity of Copia retrotransposon in metazoans.

Klai K, Farhat S, Lamothe L, Higuet D, Bonnivard E Mob DNA. 2025; 16(1):9.

PMID: 40055832 PMC: 11889832. DOI: 10.1186/s13100-025-00346-z.

References

Xu Z, Wang H . LTR_FINDER: an efficient tool for the prediction of full-length LTR retrotransposons. Nucleic Acids Res. 2007; 35(Web Server issue):W265-8. PMC: 1933203. DOI: 10.1093/nar/gkm286. View

Campagna D, Romualdi C, Vitulo N, Del Favero M, Lexa M, Cannata N . RAP: a new computer program for de novo identification of repeated sequences in whole genomes. Bioinformatics. 2004; 21(5):582-8. DOI: 10.1093/bioinformatics/bti039. View

Jurka J . Repbase update: a database and an electronic journal of repetitive elements. Trends Genet. 2000; 16(9):418-20. DOI: 10.1016/s0168-9525(00)02093-x. View

Zhang Z, Schwartz S, Wagner L, Miller W . A greedy algorithm for aligning DNA sequences. J Comput Biol. 2000; 7(1-2):203-14. DOI: 10.1089/10665270050081478. View

McCarthy E, Liu J, Lizhi G, McDonald J . Long terminal repeat retrotransposons of Oryza sativa. Genome Biol. 2002; 3(10):RESEARCH0053. PMC: 134482. DOI: 10.1186/gb-2002-3-10-research0053. View

Kalyanaraman A, Aluru S . Efficient algorithms and software for detection of full-length LTR retrotransposons. J Bioinform Comput Biol. 2006; 4(2):197-216. DOI: 10.1142/s021972000600203x. View

Quesneville H, Bergman C, Andrieu O, Autard D, Nouaud D, Ashburner M . Combined evidence annotation of transposable elements in genome sequences. PLoS Comput Biol. 2005; 1(2):166-75. PMC: 1185648. DOI: 10.1371/journal.pcbi.0010022. View

Franchini L, Ganko E, McDonald J . Retrotransposon-gene associations are widespread among D. melanogaster populations. Mol Biol Evol. 2004; 21(7):1323-31. DOI: 10.1093/molbev/msh116. View

Kaminker J, Bergman C, Kronmiller B, Carlson J, Svirskas R, Patel S . The transposable elements of the Drosophila melanogaster euchromatin: a genomics perspective. Genome Biol. 2003; 3(12):RESEARCH0084. PMC: 151186. DOI: 10.1186/gb-2002-3-12-research0084. View

10.

McCarthy E, McDonald J . Long terminal repeat retrotransposons of Mus musculus. Genome Biol. 2004; 5(3):R14. PMC: 395764. DOI: 10.1186/gb-2004-5-3-r14. View

11.

Altschul S, Gish W, Miller W, Myers E, Lipman D . Basic local alignment search tool. J Mol Biol. 1990; 215(3):403-10. DOI: 10.1016/S0022-2836(05)80360-2. View

12.

Waterston R, Lindblad-Toh K, Birney E, Rogers J, Abril J, Agarwal P . Initial sequencing and comparative analysis of the mouse genome. Nature. 2002; 420(6915):520-62. DOI: 10.1038/nature01262. View

13.

Kapitonov V, Jurka J . Molecular paleontology of transposable elements in the Drosophila melanogaster genome. Proc Natl Acad Sci U S A. 2003; 100(11):6569-74. PMC: 164487. DOI: 10.1073/pnas.0732024100. View

14.

Rho M, Choi J, Kim S, Lynch M, Tang H . De novo identification of LTR retrotransposons in eukaryotic genomes. BMC Genomics. 2007; 8:90. PMC: 1858694. DOI: 10.1186/1471-2164-8-90. View

15.

Kim J, Vanguri S, Boeke J, Gabriel A, Voytas D . Transposable elements and genome organization: a comprehensive survey of retrotransposons revealed by the complete Saccharomyces cerevisiae genome sequence. Genome Res. 1998; 8(5):464-78. DOI: 10.1101/gr.8.5.464. View

16.

McCarthy E, McDonald J . LTR_STRUC: a novel search and identification program for LTR retrotransposons. Bioinformatics. 2003; 19(3):362-7. DOI: 10.1093/bioinformatics/btf878. View

17.

Bao Z, Eddy S . Automated de novo identification of repeat sequence families in sequenced genomes. Genome Res. 2002; 12(8):1269-76. PMC: 186642. DOI: 10.1101/gr.88502. View

18.

Lerat E, Rizzon C, Biemont C . Sequence divergence within transposable element families in the Drosophila melanogaster genome. Genome Res. 2003; 13(8):1889-96. PMC: 403780. DOI: 10.1101/gr.827603. View

19.

Kurtz S, Choudhuri J, Ohlebusch E, Schleiermacher C, Stoye J, Giegerich R . REPuter: the manifold applications of repeat analysis on a genomic scale. Nucleic Acids Res. 2001; 29(22):4633-42. PMC: 92531. DOI: 10.1093/nar/29.22.4633. View

20.

Polavarapu N, Bowen N, McDonald J . Identification, characterization and comparative genomics of chimpanzee endogenous retroviruses. Genome Biol. 2006; 7(6):R51. PMC: 1779541. DOI: 10.1186/gb-2006-7-6-r51. View