Combined Evidence Annotation of Transposable Elements in Genome Sequences

By H. Quesneville, Casey M. Bergman, O. Andrieu, D. Autard, D. Nouaud, Michael Ashburner, D. Anxolabéhère. PLoS Comput. Biol., 2005

398 citations recorded by the source corpus.

Transposable elements (TEs) are mobile, repetitive sequences that make up significant fractions of metazoan genomes. Despite their near ubiquity and importance in genome and chromosome biology, most efforts to annotate TEs in genome sequences rely on the results of a single computational program, RepeatMasker. In contrast, recent advances in gene annotation indicate that high-quality gene models can be produced from combining multiple independent sources of computational evidence. To elevate the quality of TE annotations to a level comparable to that of gene models, we have developed a combined evidence-model TE annotation pipeline, analogous to systems used for gene annotation, by integrating results from multiple homology-based and de novo TE identification methods. As proof of principle, we have annotated “TE models” in Drosophila melanogaster Release 4 genomic sequences using the combined computational evidence derived from RepeatMasker, BLASTER, TBLASTX, all-by-all BLASTN, RECON, TE-HMM and the previous Release 3.1 annotation. Our system is designed for use with the Apollo genome annotation tool, allowing automatic results to be curated manually to produce reliable annotations. The euchromatic TE fraction of D. melanogaster is now estimated at 5.3% (cf. 3.86% in Release 3.1), and we found a substantially higher number of TEs (n = 6,013) than previously identified (n = 1,572). Most of the new TEs derive from small fragments of a few hundred nucleotides long and highly abundant families not previously annotated (e.g., INE-1). We also estimated that 518 TE copies (8.6%) are inserted into at least one other TE, forming a nest of elements. The pipeline allows rapid and thorough annotation of even the most complex TE models, including highly deleted and/or nested elements such as those often found in heterochromatic sequences. Our pipeline can be easily adapted to other genome sequences, such as those of the D. melanogaster heterochromatin or other species in the genus Drosophila.

Subfields: Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/d6caeb84c73e3499254e0d9b0689a60bb006d913

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Citations in the corpus

Genome Sequence of the Pea Aphid Acyrthosiphon pisum (2010, methodology): “This pipeline is composed of TE detection software—BLASTER [115], RepeatMasker [121], and Censor [122]—and satellite detection software—RepeatMasker, TRF [123], and Mreps [124].”
Genomic Analysis of the Necrotrophic Fungal Pathogens Sclerotinia sclerotiorum and Botrytis cinerea (2011, methodology): “using the REPET pipeline [30,31] http://urgi.”
Repetitive Elements May Comprise Over Two-Thirds of the Human Genome (2011, background): “, [20,22,27,28,29,30,31,32]), and are based on a diverse set of approaches (see [33,34] for reviews).”