Title
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.
Year
DOI
Venue
2005
10.1371/journal.pcbi.0010022
PLOS COMPUTATIONAL BIOLOGY
Keywords
Field
DocType
genomics,sequence analysis,nucleotides,proof of principle,transposable element,sequence alignment,genome sequence,genome annotation
Genome,Sequence alignment,Annotation,Biology,Genome project,Transposable element,Genomics,Bioinformatics,Genetics,Gene Annotation,Sequence analysis
Journal
Volume
Issue
ISSN
1
2
1553-734X
Citations 
PageRank 
References 
13
1.46
12
Authors
7
Name
Order
Citations
PageRank
Hadi Quesneville1587.12
Casey M Bergman243233.52
Olivier Andrieu3785.75
Delphine Autard4131.46
Danielle Nouaud5131.46
Michael Ashburner639939.94
Dominique Anxolabéhère7272.65