The web pages of the TriAnnot pipeline has not been updated since 2014, we apologize ...

Unfortunately, the TriAnnot pipeline is not anymore available at INRAE URGI

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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.

References

Cuello C, Baldy A, Brunaud V, Joets J, Delannoy E, Jacquemot M-P, Botran L, Griveau Y, Guichard C, Soubigou-Taconnat L, Martin-Magniette M-L, Leroy P, Méchin V, Reymond M, Coursol S (2019) A systems biology approach uncovers a gene co-expression network associated with cell wall degradability in maize. Plos ONE 14:e0227011 - PMID: 31891625

Tulpová Z, Toegelová H, Lapitan NLV, Peairs FB, Macas J, Novák P, Lukaszewski AJ, Kopecký D, Mazáčová M, Vrána J, Holušová K, Leroy P, Doležel J, Šimková H (2019) Accessing a Russian Wheat Aphid Resistance Gene in Bread Wheat by Long-Read Technologies. Plant Genome 12:1-11 - PMID: 31290924

International Wheat Genome Sequencing Consortium (IWGSC) et al. (2018) Shifting the limits in wheat research and breeding using a fully annotated reference genome.  Science 361:eaar7191 - PMID: 30115783

Munhoz CF, Costa ZP, Cauz-Santos LA, Reátegui ACE, Rodde N, Cauet S, Dornelas MC, Leroy P, de Mello Varani A, Bergès H, Carneiro Vieira ML (2018) A gene-rich fraction analysis of the Passiflora edulis genome reveals highly conserved microsyntenic regions with two related Malpighiales species.  Nature Scientific Reports 8:13024 - PMID: 30158558

Keeble-Gagnère G, Rigault P, Tibbits J, Pasam R, Hayden M, Forrest K, Frenkel Z, Korol A, Huang BE, Cavanagh C, Taylor J, Abrouk M, Sharpe A, Konkin D, Sourdille P, Darrier B, Choulet F, Bernard A, Rochfort S, Dimech A, Watson-Haigh N, Baumann U, Eckermann P, Fleury D, Juhasz A, Boisvert S, Nolin MA, Doležel J, Šimková H, Toegelová H, Šafář J, Luo MC, Câmara F, Pfeifer M, Isdale D, Nyström-Persson J, Iwgsc, Koo DH, Tinning M, Cui D, Ru Z, Appels R (2018) Optical and physical mapping with local finishing enables megabase-scale resolution of agronomically important regions in the wheat genome. Genome Biology 19:112 - PMID: 30115128

Luo M-C, QG Yong, Puiu D, Wang Hao, Twardziok SO, Deal KR, Huo N, Zhu T, Wang L, Wang Y, McGuire PE, Liu S, Long H, Ramasamy RK, Rodriguez JC, Van SL, Yuan L, Wang Z, Xia Z, Xiao L, Anderson OD, Ouyang S, Liang Y, Zimin AV, Pertea G, Qi P, Bennetzen JL, Dai X, Dawson MW , Müller H-G, Kugler K, Rivarola-Duarte L, Spannagl M, Mayer KFX, Lu F-H, Bevan MW, Leroy P, Li P, You FM, Sun Q, Liu Z, Lyons E, Wicker T, Salzberg SL, Devos KM, Dvořák J (2017) Genome sequence of the progenitor of the wheat D genome Aegilops tauschii. Nature 551:498-502 - PMID: 29143815

Holtz Y, Ardisson M, Ranwez V, Besnard A, Leroy P, Poux G, et al. (2016) Genotyping by Sequencing Using Specific Allelic Capture to Build a High-Density Genetic Map of Durum Wheat. PLoS ONE 115:e0154609 - PMID: 27171472

Yeo FK, Wang Y, Vozabova T, Huneau C, Leroy P, Chalhoub B, Qi XQ, Niks RE, Marcel TC (2015) Haplotype divergence and multiple candidate genes at Rphq2, a partial resistance QTL of barley to Puccinia hordei. Theor Appl Genet 129:289-304 –  PMID: 26542283

Helguera M, Rivarola M, Clavijo B, Martis MM, Vanzetti LS, Gonzalez S, Garbus I, Leroy P, Hana S, Valarik M, Caccamo M, Dolezel D, Mayer KF, Feuillet C, Tranquilli G, Paniego N, Echenique VC (2015) New insights into the wheat chromosome 4D structure and virtual gene order, revealed by survey pyrosequencing. Plant Science 233:200-212 – PMID: 25711827

Choulet F, Caccamo M, Wright J, Alaux M, Simkova H, Safar J, Leroy P, Dolezel J, Rogers J, Eversole K, Feuillet C (2014) The wheat black jack: Advances towards sequencing the 21 chromosomes of bread wheat. In: Tuberosa R, Graner A & Frison Eds, Genomics of Plant Genetic Resources Vol1. Managing, Sequencing and Mining Genetic Resources. Springer Science+Business Media Dordrecht pp 406-438

Choulet C, Alberti A, Theil S, Glover N, Barbe V, Daron J, Pingault L, Sourdille P, Couloux A, Paux E, Leroy P, Mangenot S, Guilhot N, Le Gouis J, Balfourier F, Alaux M, Jamilloux V, Poulain J, Durand C, Bellec A, Gaspin C, Safar J, Dolezel J, Rogers J, Vandepoele K, Aury J-M, Mayer K, Berges H, Quesneville H, Wincker P, Feuillet C (2014) Structural and functional partitioning of bread wheat chromosome 3B. Science 345:1249721 - PMID: 25035497

Raats D, Frenkel Z, Krugman T, Dodek I, Sela H, Simková H, Magni F, Cattonaro F, Vautrin S, Bergès H, Wicker T, Keller B, Leroy P, Philippe R, Paux E, Dolezel J, Feuillet C, Korol A, Fahima T (2013) The physical map of wheat chromosome 1BS provides insights into its gene space organization and evolution. Genome Biology 14:R138 – PMID: 24359668

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 (2012) TriAnnot: a versatile and high performance pipeline for the automated annotation of plant genomes. Frontiers in Plant Sciences 3:1-14 – PMID: 22645565

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. Plant Cell 22:1686-1701 – PMID: 20581307

Sabot F, Guyot R, Wicker T, Chantret N, Laubin 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 Gen Genomics 274:119-130 – PMID: 16034625

The TriAnnot pipeline has been presented at several international congresses as poster, talk or invited talk.
Link to presentation in congress list.

Intellectual Property

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).