Symbiose Project Team - INRIA/Irisa © 2007 - 2008


Fabrice LEGEAI

Title Engineer
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Address Symbiose
  INRIA/Irisa - Campus de Beaulieu
  35042 RENNES Cedex - France
Tel +33 2 99 84 71 18
Fax +33 2 99 84 71 71
Current position INRA Bioinformaticist



Current Scientific Interest

Setup a bioinformatics platform dedicated to insect pest genomics using open-source software. Its main goals are to supply the needs on automatically or manually annotation, genome browsing or genome comparative analyses as well as to write sophisticated procedures such as ontology driven annotation pipelines and help and teach users and curators by organizing workshop and seminars

 

Support to various genomics research activities (genome annotation, physical and genetic maps, miRNA identification, comparative genomics and evolution)


Work experience


Since 2007 : bioinformaticist and software ingeneer at INRA's BiO3P laboratory (Rennes, France) in the genomics group leaded by Denis Tagu, but detached in the GenOuest group of the INRIA's Symbiose project leaded by J. Nicolas.


From 2000 to 2007 : bioinformaticist and software ingeneer at INRA's URGI laboratory (Versailles, France, leaded by Hadi Quesneville) in charge of the development and maintenance of annotation pipelines, physical mapping data management, web services, software maintenance and installation, projects support...


From 1998 to 2000 : bioinformaticist at Aventis Pharma (Evry and Vitry sur Seine, France)

Teaching


since 2002 : Perl, perl-object and bioperl for biologist at Evry university, INSERM, CNRS, INRIA


from 2003 to 2006 : curation and assembly of genomic sequences with the Phred-Phrap-Consed Package at Evry university


Publications



Jaquiéry J, Stoeckel S, Nouhaud P, Mieuzet L, Mahéo F, Legeai F, Bernard N, Bonvoisin A, Vitalis R, Simon JC. Genome scans reveal candidate regions involved in the adaptation to host plant in the pea aphid complex. Mol Ecol. 2012 Nov;21(21):5251-64.


Le Trionnaire G, Jaubert-Possamai S, Bonhomme J, Gauthier JP, Guernec G, Le Cam A, Legeai F, Monfort J, Tagu D. Transcriptomic profiling of the reproductive mode switch in the pea aphid in response to natural autumnal photoperiod. J Insect Physiol. 2012 Dec;58(12):1517-24.


Jacquin-Joly E, Legeai F, Montagné N, Monsempes C, François MC, Poulain J,Gavory F, Walker WB 3rd, Hansson BS, Larsson MC. Candidate chemosensory genes in female antennae of the noctuid moth Spodoptera littoralis. Int J Biol Sci.2012;8(7):1036-50.


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. TriAnnot: A Versatile and High Performance Pipeline for the Automated Annotation of Plant Genomes. Front Plant Sci. 2012;3:5. .


Ollivier M, Gabaldón T, Poulain J, Gavory F, Leterme N, Gauthier JP, Legeai F,Tagu D, Simon JC, Rispe C. Comparison of gene repertoires and patterns of evolutionary rates in eight aphid species that differ by reproductive mode. Genome Biol Evol. 2012;4(2):155-67.


Dubois A, Remay A, Raymond O, Balzergue S, Chauvet A, Maene M, Pécrix Y, Yang SH, Jeauffre J, Thouroude T, Boltz V, Martin-Magniette ML, Janczarski S, Legeai F, Renou JP, Vergne P, Le Bris M, Foucher F, Bendahmane M. Genomic approach to study floral development genes in Rosa sp. PLoS One. 2011;6(12


Jaquiéry J, Stoeckel S, Rispe C, Mieuzet L, Legeai F, Simon JC. Accelerated evolution of sex chromosomes in aphids, an x0 system. Mol Biol Evol. 2012 Feb;29(2):837-47.


Vialette-Guiraud AC, Alaux M, Legeai F, Finet C, Chambrier P, Brown SC, Chauvet A, Magdalena C, Rudall PJ, Scutt CP. Cabomba as a model for studies of early angiosperm evolution. Ann Bot. 2011 Sep;108(4):589-98.


Legeai F, Malpel S, Montagné N, Monsempes C, Cousserans F, Merlin C, François MC, Maïbèche-Coisné M, Gavory F, Poulain J, Jacquin-Joly E. An Expressed Sequence Tag collection from the male antennae of the Noctuid moth Spodoptera littoralis: a resource for olfactory and pheromone detection research. BMC Genomics. 2011 Jan 29;12:86.


Volkoff AN, Jouan V, Urbach S, Samain S, Bergoin M, Wincker P, Demettre E, Cousserans F, Provost B, Coulibaly F, Legeai F, Béliveau C, Cusson M, Gyapay G, Drezen JM. Analysis of virion structural components reveals vestiges of the ancestral ichnovirus genome. PLoS Pathog. 2010 May 27;6(5)


d’Alençon, E, Sezutsu H, Legeai F, Permal, E, Bernard-Samain, S., Gimeneza, S., Gagneur, C., Cousserans, F., Shimomura, M., Brun-Barale, A., Flutre, T., Couloux, A., East, P., Gordong, K., Mita, K., Quesneville, H., Fournier P., Feyereisen, R. Extensive synteny conservation of holocentric chromosomes in Lepidoptera despite high rates of local genome rearrangements, (2010) PNAS  Apr 27;107(17):7680-5.


Volkoff, A-N, Jouan, V., Urbach, S., Samain, S., Bergoin, M., Wincker, P., Demettre, E., Cousserans, F., Provost, B., Fasseli
Coulibaly, F., Legeai, F., Béliveau, C., Cusson, M., Gyapay, G., Drezen, J-M, (2010) Analysis of Virion Structural Components Reveals Vestiges of the Ancestral Ichnovirus Genome.PLoS Pathogens in press

International Aphid Genomics Consortium. Genome sequence of the pea aphid Acyrthosiphon pisum. PLoS Biol. 2010 Feb 23;8(2)


Legeai F, Shigenobu S, Gauthier JP, Colbourne J, Rispe C, Collin O, Richards S, Wilson ACC, Tagu D (2010) AphidBase: A centralized bioinformatic resource for annotation of the pea aphid genome. Insect Molecular Biology vol19,0,5-12


Ollivier M., Legeai F., Rispe C. (2010) Comparative analysis of the Acyrthosiphon pisum genome and expressed sequence tag-based gene sets from other aphid species. Ins. Mol. Biol. Vol19,0,33-45


Legeai F., Rizk G., Walsh T., Edwards O., Gordon K., Lavenier D., Leterme N., Méreau A., Nicolas J., Tagu D., Jaubert-Possamai S. (2010) Bioinformatic prediction, deep sequencing of microRNAs and expression analysis during phenotypic plasticity in the pea aphid, Acyrthosiphon pisum. BMC Genomics  2010 May 5;11(1):281


Legeai F., Malpel S., Montagné N., Monsempes C., Cousseran F., Merlin C., François MC., Maïbèche-Coisné M., Gavory F., Poulain J., Jacquin-Joly E. (2010) An Expressed Sequence Tag collection from the male antennae of the Noctuid moth Spodoptera littoralis: a resource for olfactory and pheromone detection research (Submitted to BMC Genomics)

Le Trionnaire G, Francis F, Jaubert-Possamai S, Bonhomme J, De Pauw E, Gauthier JP, Haubruge E, Legeai F, Prunier-Leterme N, Simon JC, Tanguy S, Tagu D. (2009) Transcriptomic and proteomic analyses of  seasonal photoperiodism in the pea aphid BMC Genomics. 2009 Sep 29;10:456.

Foucher, F, Chevalier, M, Corre, C, Soufflet-Freslon V, Legeai, F, and Hibrand-Saint Oyant L. (2008) New resources for studying the rose flowering process. Genome 51(10): 827–837

Moroldo, M, Paillard, S, Marconi, R, Legeai, F, Canaguier, A, Cruaud, C, De Berardinis, V, Guichard, C, Brunaud, V, Le Clainche, I, Scalabrin, S, Testolin, R, Di Gaspero, G, Morgante, M, Adam-Blondon, AF (2008). A physical map of the heterozygous grapevine 'Cabernet Sauvignon' allows mapping candidate genes for disease resistance. BMC Plant Biol., 8:66.

Legeai, F, Paux, E, Guilhot, N, Adam-Blondon, AF, Alaux, M, Salse, J, Sourdille, P, Leroy, P, Feuillet, C (2008). Physical mapping in large genomes: accelerating anchoring of BAC contigs to genetic maps through in silico analysis. Funct. Integr. Genomics, 8, 1:29-32.

 

Rispe, C, Kutsukake, M, Doublet, V, Hudaverdian, S, Legeai, F, Simon, JC, Tagu, D, Fukatsu, T (2008). Large gene family expansion and variable selective pressures for cathepsin B in aphids. Mol. Biol. Evol., 25, 1:5-17.

 

Rispe, C, Legeai, F, Gauthier, JP, Tagu, D (2007). Strong heterogeneity in nucleotidic composition and codon bias in the pea aphid (Acyrthosiphon pisum) shown by EST-based coding genome reconstruction. J. Mol. Evol., 65, 4:413-24.

 

Jaillon, O, Aury, JM, Noel, B, Policriti, A, Clepet, C, Casagrande, A, Choisne, N, Aubourg, S, Vitulo, N, Jubin, C, Vezzi, A, Legeai, F, Hugueney, P, Dasilva, C, Horner, D, Mica, E, Jublot, D, Poulain, J, Bruyère, C, Billault, A, Segurens, B, Gouyvenoux, M, Ugarte, E, Cattonaro, F, Anthouard, V, Vico, V, Del Fabbro, C, Alaux, M, Di Gaspero, G, Dumas, V, Felice, N, Paillard, S, Juman, I, Moroldo, M, Scalabrin, S, Canaguier, A, Le Clainche, I, Malacrida, G, Durand, E, Pesole, G, Laucou, V, Chatelet, P, Merdinoglu, D, Delledonne, M, Pezzotti, M, Lecharny, A, Scarpelli, C, Artiguenave, F, Pè, ME, Valle, G, Morgante, M, Caboche, M, Adam-Blondon, AF, Weissenbach, J, Quétier, F, Wincker, P (2007). The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature, 449, 7161:463-7.

Gauthier, JP, Legeai, F, Zasadzinski, A, Rispe, C, Tagu, D (2007). AphidBase: a database for aphid genomic resources. Bioinformatics, 23, 6:783-4.

Lamoureux, D, Bernole, A, Le Clainche, I, Tual, S, Thareau, V, Paillard, S, Legeai, F, Dossat, C, Wincker, P, Oswald, M, Merdinoglu, D, Vignault, C, Delrot, S, Caboche, M, Chalhoub, B, Adam-Blondon, AF (2006). Anchoring of a large set of markers onto a BAC library for the development of a draft physical map of the grapevine genome. Theor. Appl. Genet., 113, 2:344-56.

Sabater-Muñoz, B, Legeai, F, Rispe, C, Bonhomme, J, Dearden, P, Dossat, C, Duclert, A, Gauthier, JP, Ducray, DG, Hunter, W, Dang, P, Kambhampati, S, Martinez-Torres, D, Cortes, T, Moya, A, Nakabachi, A, Philippe, C, Prunier-Leterme, N, Rahbé, Y, Simon, JC, Stern, DL, Wincker, P, Tagu, D (2006). Large-scale gene discovery in the pea aphid Acyrthosiphon pisum (Hemiptera). Genome Biol., 7, 3:R21.

Tagu, D, Prunier-Leterme, N, Legeai, F, Gauthier, JP, Duclert, A, Sabater-Muñoz, B, Bonhomme, J, Simon, JC (2004). Annotated expressed sequence tags for studies of the regulation of reproductive modes in aphids. Insect Biochem. Mol. Biol., 34, 8:809-22.

Small, I, Peeters, N, Legeai, F, Lurin, C (2004). Predotar: A tool for rapidly screening proteomes for N-terminal targeting sequences. Proteomics, 4, 6:1581-90.

Nicot, N, Chiquet, V, Gandon, B, Amilhat, L, Legeai, F, Leroy, P, Bernard, M, Sourdille, P (2004). Study of simple sequence repeat (SSR) markers from wheat expressed sequence tags (ESTs). Theor. Appl. Genet., 109, 4:800-5.

Samson, D, Legeai, F, Karsenty, E, Reboux, S, Veyrieras, JB, Just, J, Barillot, E (2003). GénoPlante-Info (GPI): a collection of databases and bioinformatics resources for plant genomics. Nucleic Acids Res., 31, 1:179-82.

 


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