New version v4.3 online
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, Feuillet C (2011) TriAnnot: a versatile and high performance pipeline for the automated annotation of plant genomes. Frontiers in Plant Science 3:1-14 .
Genome sequences hold the key for understanding the molecular basis of phenotypic traits and variation and provide a framework for rapid varietal development through the utilization of marker-assisted selection, marker-assisted recurrent selection, genome wide selection, and molecular breeding. Despite the recognition that genome sequencing is critical for crop improvement, the size and complexity of the wheat genome (17 Gb, hexaploid AABBDD, >80% of TEs) has been perceived as an obstacle for the efficient development of genome sequencing projects. However, the convergence of technological advances in recent years (e.g., BAC library construction from different wheat genomes and from individual wheat chromosomes; and the revolution in genome sequencing technologies) offer the prospects of tractable large-scale programs that can deliver much-needed sequence based resources for wheat.
The International Wheat Genome Sequencing Consortium (IWGSC) was launched in 2005 with the aim of advancing agricultural research for wheat production and utilization by developing DNA-based tools and resources that result from sequencing the wheat genome.
In this context, the UMR 1095 INRA-UBP Génétique, Diversité & Ecophysiologie des Céréales in Clermont-Ferrand (France) in collaboration with the Institute of Experimental Botany in the Czech Republic, confirmed the concept that the hexaploid wheat genome can be approached chromosome by chromosome by constructing the first physical map of chromosome 3B (Paux et al. 2008 ). In 2010, a project funded by the ANR and FranceAgrimer , was initiated to sequence the Minimal Tiling Path of chromosome 3B using Next Generation Sequencing technologies (3BSEQ ). Other projects for the other 20 chromosomes are now underway within the IWGSC .
To provide the wheat community with an online resource for efficient and accurate BAC or contigs sequence annotation, INRA GDEC and URGI in collaboration with colleagues from the NIAS have developed TriAnnot, a semi-automated pipeline. The pipeline is organized in 5 panels for TEs, genes, other features annotation and for markers development.
If you want to use the TriAnnot pipeline, you will need first to obtain an account with a login/password. Please click here for more details.
The code of TriAnnot is available upon request (firstname.lastname@example.org ) and groups can choose to install the program in-house instead of running the analysis on the URGI server. However, such installation may require extensive skills in informatics and bioinformatics. INRA will not be able to provide any technical support for the installation except in the framework of formal collaborations.
Version 3.5 of the TriAnnot pipeline has been described in:
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, Feuillet C (2011) TriAnnot: a versatile and high performance pipeline for the automated annotation of plant genomes. Frontiers in Plant Science 3:1-14
Marcelo Helguera, Máximo Rivarola, Bernardo Clavijo, Mihaela M. Martis, Leonardo S. Vanzetti, Sergio González, Ingrid Garbus, Phillippe Leroy, Hana Šimková, Miroslav Valárik, Mario Caccamo, Jaroslav Doležel, Klaus F.X. Mayer, Catherine Feuillet, Gabriela Tranquilli, Norma Paniego, Viviana Echenique (2014) New insights into the wheat chromosome 4D structure and virtual gene order, revealed by survey pirosequencing. Plant Scidoi.org/10.1016/j.plantsci.2014.12.004
Frédéric Choulet, Adriana Alberti, Sébastien Theil, Natasha Glover, Valérie Barbe, Josquin Daron, Lise Pingault, Pierre Sourdille, Arnaud Couloux, Etienne Paux, Philippe Leroy, Sophie Mangenot, Nicolas Guilhot, Jacques Le Gouis, Francois Balfourier, Michael Alaux, Véronique Jamilloux, Julie Poulain, Céline Durand, Arnaud Bellec, Christine Gaspin, Jan Safar, Jaroslav Dolezel, Jane Rogers, Klaas Vandepoele, Jean-Marc Aury, Klaus Mayer, Hélène Berges, Hadi Quesneville, Patrick Wincker, Catherine Feuillet (2014) Structural and Functional Partitioning of Bread Wheat Chromosome 3B. Science Vol. 345 no. 6194 DOI: 10.1126/science.1249721
Choulet F, Wicker T, Rustenholz C, Paux E, Salse J, Leroy P, Schlub S, Le Paslier M-C, Magdelenat G, Gonthier C, Couloux A, Budak H, Breen J, Pumphrey M, Liu S, Kong X, Jia J, Gut M, Brunel D, Anaderson JA, Gill BS, Appels R, Keller B, Feuillet C (2010) Megabase level sequencing reveals contrasted organization and evolution patterns of the wheat gene and transposable element spaces.The Plant Cell 22:1686-1701
Sabot F, Guyot R, Wicker T, Chantret N, aubin B, Chalhoub B, Leroy P, Sourdille P, Bernard M (2005) Updating of transposable element annotations from large wheat genomic sequences reveals diverse activities and gene associations. Mol Gene Genomics 274:119-130
The TriAnnot pipeline has been presented at several international congresses as poster, talk or invited talk.
Link to presentation in congress list.
Version 1 of TriAnnot was deposited on January 31, 2006, in the French APP ("Agence pour la Protection des Programmes") repository for intellectual property (APP # IDDN.FR.001.05008.000.R.C.2006.000.31235).
We welcome comments and suggestions on the system and if you want to participate to the TriAnnot pipeline improvement, please contact us at email@example.com