Combined Evidence Annotation of Transposable Elements in Genome Sequences

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.

Genome expansion and lineage-specific genetic innovations in the forest pathogenic fungi Armillaria

“…Consensus sequences were clustered using Piler v1.0 84 , Recon 1.08 85 and Grouper 86 and classified using PASTEC 82 . The resulting consensus sequences were filtered for low-frequency elements, short sequence repeats and sequences that were classified as putative host genes and then clustered into families using Markov clustering 64 .…”

Finding a partner in the ocean: molecular and evolutionary bases of the response to sexual cues in a planktonic diatom

“…The TE denovo pipeline (Flutre et al ., 2011) was used to build a library of consensus sequences of repetitive elements in the genome assembly. The TE annot pipeline (Quesneville et al ., 2005) was employed with default settings using the sequences from the filtered combined library as probes to perform genome annotation.…”

High-quality de novo assembly of the apple genome and methylome dynamics of early fruit development

“…The TEdenovo pipeline 37,77 from the REPET package v2.5 (see URLs) was used to detect TEs in genomic sequences and to provide a consensus sequence for each TE family. Consensus TE sequences were used to annotate the TE copies in the whole genome using the TEannot pipeline 38 from the REPET package v2.5. Consensus sequences that were classified as potential host genes because they contain host gene Pfam domains were kept from this study.…”