De novo identification of LTR retrotransposons in eukaryotic genomes

Rho, Mina; Choi, Jeong Hyeon; Kim, Sun; Lynch, Michael; Tang, Haixu

doi:10.1186/1471-2164-8-90

Cited by 74 publications

(71 citation statements)

References 34 publications

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“…For comparison, we chose four of the most widely used LTR-searching methods, LTR_STRUC (McCarthy and McDonald, 2003), MGEScan-LTR (Rho et al, 2007), LTR_finder (Xu and Wang, 2007), and LTRharvest (Ellinghaus et al, 2008), for performance benchmarks. As LTRharvest is the most flexible program, with more than 20 modifiable parameters, we optimized some of the most influential parameters, including LTR identity (-similar), alignment seed length (-seed), and TSD search range (-vic).…”

Section: Comparison Of Performance With Other Ltr Identification Toolsmentioning

confidence: 99%

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LTR_retriever: A Highly Accurate and Sensitive Program for Identification of Long Terminal Repeat Retrotransposons

2017

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Long terminal repeat retrotransposons (LTR-RTs) are prevalent in plant genomes. The identification of LTR-RTs is critical for achieving high-quality gene annotation. Based on the well-conserved structure, multiple programs were developed for the de novo identification of LTR-RTs; however, these programs are associated with low specificity and high false discovery rates. 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 (Oryza sativa). LTR_retriever is also compatible with long sequencing reads. With 40k self-corrected PacBio reads equivalent to 4.53 genome coverage in Arabidopsis (Arabidopsis thaliana), the constructed LTR library showed excellent sensitivity and specificity. In addition to canonical LTRRTs with 59-TG.CA-39 termini, LTR_retriever also identifies noncanonical LTR-RTs (non-TGCA), which have been largely ignored in genome-wide studies. We identified seven types of noncanonical LTRs from 42 out of 50 plant genomes. The majority of noncanonical 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 their potential as mutagenesis tools.

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Section: Comparison Of Performance With Other Ltr Identification Toolsmentioning

confidence: 99%

“…Nevertheless, these programs suffer from reporting large numbers of false positives (Lerat, 2010). MGEScan-LTR is another early development of LTR-searching programs (Rho et al, 2007). Its recent update on the Web-based platform allows wider usage (Lee et al, 2016), but it is still associated with the issue of false identifications.…”

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confidence: 99%

LTR_retriever: A Highly Accurate and Sensitive Program for Identification of Long Terminal Repeat Retrotransposons

2017

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“…In the euchromatin, 235 sequences exhibited a similarity $98%. Twenty-one of these sequences corresponded to solo LTRs, whereas the remaining 214 were associated by pairs at distances ranging from 1000 to 20,000 bp, indicating that they belonged to the same TE element (Rho et al 2007). This would imply that in situ analysis using an internal probe (as in previous studies for MA1 ;Maside et al 2001;Vázquez 2006) should detect 214 2 ¼ 107 bands in the release 5.1 genome, while our LTR probe would be expected to detect a number 19.6% larger ( 214 2 1 21 ¼ 128 bands).…”

Section: Preliminary Informationmentioning

confidence: 99%

The Dynamics of therooTransposable Element In Mutation-Accumulation Lines and Segregating Populations ofDrosophila melanogaster

et al. 2007

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We estimated the number of copies for the long terminal repeat (LTR) retrotransposable element roo in a set of long-standing Drosophila melanogaster mutation-accumulation full-sib lines and in two large laboratory populations maintained with effective population size $500, all of them derived from the same isogenic origin. Estimates were based on real-time quantitative PCR and in situ hybridization. Considering previous estimates of roo copy numbers obtained at earlier stages of the experiment, the results imply a strong acceleration of the insertion rate in the accumulation lines. The detected acceleration is consistent with a model where only one (maybe a few) of the $70 roo copies in the ancestral isogenic genome was active and each active copy caused new insertions with a relatively high rate ($10 À2 ), with new inserts being active copies themselves. In the two laboratory populations, however, a stabilized copy number or no accelerated insertion was found. Our estimate of the average deleterious viability effects per accumulated insert ½E(s) , 0.003 is too small to account for the latter finding, and we discuss the mechanisms that could contain copy number.

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“…Several programs have been released for identifying full-length or intact LTRs, such as LTR_STRUCT [3], LTR_PAR [4], FIND_LTR [5], LTR_FINDER [6] and LTR harvest [7]. These tools take into account several major characteristics of LTRs such as the size range of intact LTRs, the distances between two LTRs of intact elements, the presence of target site duplications (TSDs) at each terminal region, the presence of critical sites for reversing transcribing elements for transposition such as the primer binding site (PBS) and the poly purine tract (PPT), and the identity percentage between two LTRs.…”

Section: Introductionmentioning

confidence: 99%

LTR Annotator: Automated Identification and Annotation of LTR Retrotransposons in Plant Genomes

You¹,

Cloutier²,

Shan³

et al. 2015

IJBBB

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Long Terminal Repeat transposable element (LTR) is a major type of mobile elements ubiquitous in eukaryotic genomes. They account for a major proportion of many plant genomes and have a prominent impact on the evolution of genome size, structure and function. Although some bioinformatics tools for de novo LTR identification from genome sequences have been developed, an automated and standardized software tool for both LTR identification and annotation would be valuable and essential for comparative analysis of sequenced plant genomes. We present here a Java-based pipeline tool, called LTR Annotator, for automatically and consistently performing genome-wide de novo identification and annotation of LTRs of plant genome sequences. The pipeline first identifies LTRs using both LTR_FINDER and LTR harvest, then performs intensive annotations, and finally sweeps out potentially false-positive LTRs. The pipeline was evaluated using the well curated Arabidopsis genome. High sensitivity (>0.9) was obtained by using LTR harvest or LTR harvest+LTR_FINDER. Ten potentially new intact LTRs were detected. This pipeline provides a comprehensive tool to perform comparative analysis of LTRs for plant genomes, delivering annotated genomic resources for epigenetic and other studies. LTR Annotator is free and available upon request.

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De novo identification of LTR retrotransposons in eukaryotic genomes

Cited by 74 publications

References 34 publications

LTR_retriever: A Highly Accurate and Sensitive Program for Identification of Long Terminal Repeat Retrotransposons

LTR_retriever: A Highly Accurate and Sensitive Program for Identification of Long Terminal Repeat Retrotransposons

The Dynamics of therooTransposable Element In Mutation-Accumulation Lines and Segregating Populations ofDrosophila melanogaster

LTR Annotator: Automated Identification and Annotation of LTR Retrotransposons in Plant Genomes

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