TriAnnot: A versatile and high performance pipeline for the automated annotation of plant genomes
Journal
Frontiers in Plant Science
Journal Volume
3
Journal Issue
JAN
Date Issued
2012-01-31
Author(s)
Leroy, Philippe
Guilhot, Nicolas
Sakai, Hiroaki
Bernard, Aurélien
Choulet, Frédéric
Theil, Sébastien
Reboux, Sébastien
Amano, Naoki
Flutre, Timothée
Pelegrin, Céline
Ohyanagi, Hajime
Seidel, Michael
Giacomoni, Franck
Reichstadt, Mathieu
Alaux, Michael
Gicquello, Emmanuelle
Legeai, Fabrice
Cerutti, Lorenzo
Numa, Hisataka
Tanaka, Tsuyoshi
Mayer, Klaus
Quesneville, Hadi
Feuillet, Catherine
Abstract
In support of the international effort to obtain a reference sequence of the bread wheat genome and to provide plant communities dealing with large and complex genomes with a versatile, easy-to-use online automated tool for annotation, we have developed the TriAnnot pipeline. Its modular architecture allows for the annotation and masking of transposable elements, the structural, and functional annotation of protein-coding genes with an evidence-based quality indexing, and the identification of conserved non-coding sequences and molecular markers. The TriAnnot pipeline is parallelized on a 712 CPU computing cluster that can run a 1-Gb sequence annotation in less than 5 days. It is accessible through a web interface for small scale analyses or through a server for large scale annotations. The performance of TriAnnot was evaluated in terms of sensitivity, specificity, and general fitness using curated reference sequence sets from rice and wheat. In less than 8 h, Tri- Annot was able to predict more than 83% of the 3,748 CDS from rice chromosome 1 with a fitness of 67.4%. On a set of 12 reference Mb-sized contigs from wheat chromosome 3B, TriAnnot predicted and annotated 93.3% of the genes among which 54% were perfectly identified in accordance with the reference annotation. It also allowed the curation of 12 genes based on new biological evidences, increasing the percentage of perfect gene prediction to 63%. TriAnnot systematically showed a higher fitness than other annotation pipelines that are not improved for wheat. As it is easily adaptable to the annotation of other plant genomes,TriAnnot should become a useful resource for the annotation of large and complex genomes in the future. © 2012 Leroy, Guilhot, Sakai, Bernard, Choulet, Theil, Reboux, Amano, Flutre, Pelegrin, Ohyanagi, Seidel, Giacomoni, Reichstadt, Alaux, Gicquello, Legeai, Cerutti, Numa, Tanaka, Mayer, Itoh, Quesneville and Feuillet.
Subjects
Cluster | Gene models | Pipeline | Plant genome | Structural and functional annotation | Transposable elements | Wheat
Type
journal article