Combined evidence annotation of transposable elements in genome sequences - PubMed (original) (raw)

Combined evidence annotation of transposable elements in genome sequences

Hadi Quesneville et al. PLoS Comput Biol. 2005 Jul.

Abstract

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.

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Conflict of interest statement

Competing interests. The authors have declared that no competing interests exist.

Figures

Figure 1

Figure 1. Schematic of Our TE Annotation Pipeline

The pipeline is composed of (i) known TE family detection methods such as BLRn, RM, and RMBLR; (ii) satellite detection software such as RM, TRF, and Mreps; (iii) anonymous TE detection methods such BLRa, TE-HMM, RECON, and BLRtx; and (iv) a MySQL database called REPET to manage the results and the annotations. GAME-XML files are then generated from the results stored in the database and loaded into the Apollo genome annotation tool, allowing automatic results to be manually curated to produce a reliable annotation. To facilitate manual curation, we automatically promoted RMBLR results to be the candidate annotation.

Figure 2

Figure 2. Screenshot of an Apollo View for a Peri-Centromeric Region with Extreme TE Density

Curated annotations on both forward strand (top) and reverse strand (bottom) are displayed in the light blue panels. Evidence tiers are shown in the black panels: TE-HMM (yellow), RECON (light purple), BLRa (violet), BLRtx (red), BLRn (teal), RM (blue), RMBLR (light green), and Release 3.1 FlyBase annotations (peach).

Figure 3

Figure 3. Categories of Possible Boundary Comparisons between Predictions and Reference Annotations

The different cases taken into account can be grouped according to one-to-one (1-to-1), one-to-many (1-to-n), many-to-one (_n_-to-1), or many-to-many (_n_-to-n) relationships.

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