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, TriAnnot 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.
Keywords: cluster, gene models, pipeline, plant genome, structural and functional annotation, transposable elements, wheat
Citation: Leroy P, Guilhot N, Sakai H, Bernard A, Choulet F, Theil S, Reboux S, Amano N, Flutre T, Pelegrin C, Ohyanagi H, Seidel M, Giacomoni F, Reichstadt M, Alaux M, Gicquello E, Legeai F, Cerutti L, Numa H, Tanaka T, Mayer K, Itoh T, Quesneville H and Feuillet C (2012) TriAnnot: a versatile and high performance pipeline for the automated annotation of plant genomes. Front. Plant Sci. 3:5. doi: 10.3389/fpls.2012.00005
Received: 02 October 2011; Accepted: 04 January 2012;
Published online: 31 January 2012.
Edited by:Takuji Sasaki, National Institute of Agrobiological Sciences, Japan
Copyright: © 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. This is an open-access article distributed under the terms of the Creative Commons Attribution Non Commercial License, which permits non-commercial use, distribution, and reproduction in other forums, provided the original authors and source are credited.
*Correspondence: Philippe Leroy and Catherine Feuillet, UMR 1095, Genetics, Diversity and Ecophysiology of Cereals, Institut National de la Recherche Agronomique-Université Blaise Pascal, 234 Avenue du Brézet, Domaine de Crouel, F-63000 Clermont-Ferrand, France. e-mail: email@example.com; firstname.lastname@example.org