ArticleBMC genomics2007
De novo identification of LTR retrotransposons in eukaryotic genomes.
Article in BMC genomics, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
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Who cites it
41 citing papers in PubMed.
- Chromosome-level genome assembly of Dynastes reidi reveals structural evolution of autosomes and the sex chromosomes in Hercules beetles.G3 (Bethesda, Md.) · 2025Article
- DANTE and DANTE_LTR: lineage-centric annotation pipelines for long terminal repeat retrotransposons in plant genomes.NAR genomics and bioinformatics · 2024Article
- Repetitive DNA sequence detection and its role in the human genome.Communications biology · 2023Review
- Finding and Characterizing Repeats in Plant Genomes.Methods in molecular biology (Clifton, N.J.) · 2022Article
- A sensitive repeat identification framework based on short and long reads.Nucleic acids research · 2021Article
- Human Endogenous Retrovirus K (HERV-K) can drive gene expression as a promoter in Caenorhabditis elegans.BMB reports · 2020Article
- Comparative Study of Pine Reference Genomes Reveals Transposable Element Interconnected Gene Networks.Genes · 2020Article
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- The quail genome: insights into social behaviour, seasonal biology and infectious disease response.BMC biology · 2020Article
- Benchmarking transposable element annotation methods for creation of a streamlined, comprehensive pipeline.Genome biology · 2019Article
- Retrotransposons in Plant Genomes: Structure, Identification, and Classification through Bioinformatics and Machine Learning.International journal of molecular sciences · 2019Review
- LtrDetector: A tool-suite for detecting long terminal repeat retrotransposons de-novo.BMC genomics · 2019Article
- LTR_retriever: A Highly Accurate and Sensitive Program for Identification of Long Terminal Repeat Retrotransposons.Plant physiology · 2018Article
- A New Reference Genome Assembly for the MicrocrustaceanG3 (Bethesda, Md.) · 2017Article
- Insertion Polymorphisms of Mobile Genetic Elements in Sexual and Asexual Populations of Daphnia pulex.Genome biology and evolution · 2017Article
- A New Chicken Genome Assembly Provides Insight into Avian Genome Structure.G3 (Bethesda, Md.) · 2017Article
- LTRtype, an Efficient Tool to Characterize Structurally Complex LTR Retrotransposons and Nested Insertions on Genomes.Frontiers in plant science · 2017Article
- A new look at the LTR retrotransposon content of the chicken genome.BMC genomics · 2016Article
- LINE-1-like retrotransposons contribute to RNA-based gene duplication in dicots.Scientific reports · 2016Article
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Authors and funding
5 authors.
Funding
Abstract
backgroundLTR 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.
resultsIn 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.
conclusionWe report a novel method for de novo identification of LTR retrotransposons in eukaryotic genomes with favorable performance over the existing methods.
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