Publications

Some publications involving BIPAA:

2018

Multi-scale characterization of symbiont diversity in the pea aphid complex through metagenomic approaches.
Guyomar C, Legeai F, Jousselin E, Mougel C, Lemaitre C, Simon JC.
Microbiome. 2018 Oct 10;6(1):181.

hotspots of differentiation and candidate genes involved in the adaptive divergence of pea aphid host races.Nouhaud P, Gautier M, Gouin A, Jaquiéry J, Peccoud J, Legeai F, Mieuzet L, Smadja CM, Lemaitre C, Vitalis R, Simon JC. Identifying genomic
Mol Ecol. 2018 Jul 16.

Fast Evolution and Lineage-Specific Gene Family Expansions of Aphid Salivary Effectors Driven by Interactions with Host-Plants
Boulain H, Legeai F, Guy E, Morlière S, Douglas NE, Oh J, Murugan M, Smith M, Jaquiéry J, Peccoud J, White FF, Carolan JC, Simon JC, Sugio A.
Genome Biol Evol. 2018 Jun 1;10(6):1554-1572.

De novo genome and transcriptome resources of the Adzuki bean borer Ostrinia scapulalis (Lepidoptera: Crambidae)
B.Gschloessl, F.Dorkeld, P.Audiot, A.Bretaudeau, C.Kerdelhué, R.Streiffa
Data in Brief, 2018 Apr;17:781-787. doi: 10.1016/j.dib.2018.01.073

First extensive characterization of the venom gland from an egg parasitoid: structure, transcriptome and functional role.
Cusumano A, Duvic B, Jouan V, Ravallec M, Legeai F, Peri E, Colazza S, Volkoff AN.
J Insect Physiol. 2018 Feb 22;107:68-80. doi: 10.1016/j.jinsphys.2018.02.009.

Disentangling the Causes for Faster-X Evolution in Aphids.
Jaquiéry J, Peccoud J, Ouisse T, Legeai F, Prunier-Leterme N, Gouin A, Nouhaud P, Brisson JA, Bickel R, Purandare S, Poulain J, Battail C, Lemaitre C, Mieuzet L, Le Trionnaire G, Simon JC, Rispe C.
Genome Biol Evol. 2018 Feb 1;10(2):507-520. doi: 10.1093/gbe/evy015.

Draft genome and reference transcriptomic resources for the urticating pine defoliator Thaumetopoea pityocampa (Lepidoptera: Notodontidae).
Gschloessl B, Dorkeld F, Berges H, Beydon G, Bouchez O, Branco M, Bretaudeau A, Burban C, Dubois E, Gauthier P, Lhuillier E, Nichols J, Nidelet S, Rocha S, Sauné L, Streiff R, Gautier M, Kerdelhué C.
Mol Ecol Resour. 2018 Jan 20. doi: 10.1111/1755-0998.12756.

2017

Two genomes of highly polyphagous lepidopteran pests (Spodoptera frugiperda, Noctuidae) with different host-plant ranges.
Gouin A, Bretaudeau A, Nam K, Gimenez S, Aury JM, Duvic B, Hilliou F, Durand N, Montagné N, Darboux I, Kuwar S, Chertemps T, Siaussat D, Bretschneider A, Moné Y, Ahn SJ, Hänniger S, Grenet AG, Neunemann D, Maumus F, Luyten I, Labadie K, Xu W, Koutroumpa F, Escoubas JM, Llopis A, Maïbèche-Coisne M, Salasc F, Tomar A, Anderson AR, Khan SA, Dumas P, Orsucci M, Guy J, Belser C, Alberti A, Noel B, Couloux A, Mercier J, Nidelet S, Dubois E, Liu NY, Boulogne I, Mirabeau O, Le Goff G, Gordon K, Oakeshott J, Consoli FL, Volkoff AN, Fescemyer HW, Marden JH, Luthe DS, Herrero S, Heckel DG, Wincker P, Kergoat GJ, Amselem J, Quesneville H, Groot AT, Jacquin-Joly E, Nègre N, Lemaitre C, Legeai F, d’Alençon E, Fournier P.
Sci Rep. 2017 Sep 25;7(1):11816. doi: 10.1038/s41598-017-10461-4.

Genome scans on experimentally evolved populations reveal candidate regions for adaptation to plant resistance in the potato cyst nematode Globodera pallida.
Eoche-Bosy D, Gautier M, Esquibet M, Legeai F, Bretaudeau A, Bouchez O, Fournet S, Grenier E, Montarry J.
Mol Ecol. 2017 Sep;26(18):4700-4711. doi: 10.1111/mec.14240.

Expression differences in Aphidius ervi (Hymenoptera: Braconidae) females reared on different aphid host species.
Ballesteros GI, Gadau J, Legeai F, Gonzalez-Gonzalez A, Lavandero B, Simon JC, Figueroa CC.
PeerJ. 2017 Aug 21;5:e3640. doi: 10.7717/peerj.3640.

Dosage compensation and sex-specific epigenetic landscape of the X chromosome in the pea aphid.
Richard G, Legeai F, Prunier-Leterme N, Bretaudeau A, Tagu D, Jaquiéry J, Le Trionnaire G.
Epigenetics Chromatin. 2017 Jun 15;10:30. doi: 10.1186/s13072-017-0137-1.

FEELnc: a tool for long non-coding RNA annotation and its application to the dog transcriptome.
Wucher V, Legeai F, Hédan B, Rizk G, Lagoutte L, Leeb T, Jagannathan V, Cadieu E, David A, Lohi H, Cirera S, Fredholm M, Botherel N, Leegwater PA, Le Béguec C, Fieten H, Johnson J, Alföldi J, André C, Lindblad-Toh K, Hitte C, Derrien T.
Nucleic Acids Res. 2017 Jan 3. pii: gkw1306. doi: 10.1093/nar/gkw1306.

2016

De novo transcriptome assembly of the grapevine phylloxera allows identification of genes differentially expressed between leaf- and root-feeding forms.
Rispe C, Legeai F, Papura D, Bretaudeau A, Hudaverdian S, Le Trionnaire G, Tagu D, Jaquiéry J, Delmotte F.
BMC Genomics. 2016 Mar 11;17:219. doi: 10.1186/s12864-016-2530-8.

Rapid transcriptional plasticity of duplicated gene clusters enables a clonally reproducing aphid to colonise diverse plant species.
Mathers TC, Chen Y, Kaithakottil G, Legeai F, Mugford ST, Baa-Puyoulet P, Bretaudeau A, Clavijo B, Colella S, Collin O, Dalmay T, Derrien T, Feng H, Gabaldón T, Jordan A, Julca I, Kettles GJ, Kowitwanich K, Lavenier D, Lenzi P, Lopez-Gomollon S, Loska D, Mapleson D, Maumus F, Moxon S, Price DR, Sugio A, van Munster M, Uzest M, Waite D, Jander G, Tagu D, Wilson AC, van Oosterhout C, Swarbreck D, Hogenhout SA.
Genome Biol. 2017 Feb 13;18(1):27. doi: 10.1186/s13059-016-1145-3.

Whole genome sequence of the soybean aphid, Aphis glycines.
Wenger JA, Cassone BJ, Legeai F, Johnston JS, Bansal R, Yates AD, Coates BS, Pavinato VA, Michel A.
Insect Biochem Mol Biol. 2017 Jan 22. pii: S0965-1748(17)30005-X. doi: 10.1016/j.ibmb.2017.01.005.

Long noncoding RNA repertoire in chicken liver and adipose tissue.
Muret K, Klopp C, Wucher V, Esquerré D, Legeai F, Lecerf F, Désert C, Boutin M, Jehl F, Acloque H, Giuffra E, Djebali S, Foissac S, Derrien T, Lagarrigue S.
Genet Sel Evol. 2017 Jan 10;49(1):6. doi: 10.1186/s12711-016-0275-0.

Differential gene expression according to race and host plant in the pea aphid.
Eyres I, Jaquiéry J, Sugio A, Duvaux L, Gharbi K, Zhou JJ, Legeai F, Nelson M, Simon JC, Smadja CM, Butlin R, Ferrari J.
Mol Ecol. 2016 Sep;25(17):4197-215. doi: 10.1111/mec.13771. Epub 2016 Aug 26.

2015

Bretaudeau A, Monjeaud C, Le Bras Y, Legeai F, Collin O, BioMAJ2Galaxy: automatic update of reference data in Galaxy using BioMAJ. GigaScience 015 May 9;4:22.

Legeai F, Derrien T. Identification of long non-coding RNAs in insects genomes Current Opinion in Insect Science (in press)

Dumas P, Legeai F, Lemaitre C, Scaon E, Orsucci M, Labadie K, Gimenez S, Clamens AL, Henri H, Vavre F, Aury JM, Fournier P, Kergoat GJ, d’Alençon E. Spodoptera frugiperda (Lepidoptera: Noctuidae) host-plant variants: two host strains or two distinct species? Genetica. 2015 Feb 19.

Gouin A, Legeai F, Nouhaud P, Whibley A, Simon JC, Lemaitre C. Whole-genome re-sequencing of non-model organisms: lessons from unmapped reads. Heredity 2015 May;114(5):494-501.

2014

Legeai F, Gimenez S, Duvic B, Escoubas JM, Gosselin Grenet AS, Blanc F, Cousserans F, Séninet I, Bretaudeau A, Mutuel D, Girard PA, Monsempes C, Magdelenat G, Hilliou F, Feyereisen R, Ogliastro M, Volkoff AN, Jacquin-Joly E, d’Alençon E, Nègre N, Fournier P. Establishment and analysis of a reference transcriptome for Spodoptera frugiperda. BMC Genomics. 2014 Aug 23;15:704.

Jaquiéry J, Stoeckel S, Larose C, Nouhaud P, Rispe C, Mieuzet L, Bonhomme J, Mahéo F, Legeai F, Gauthier JP, Prunier-Leterme N, Tagu D, Simon JC. Genetic control of contagious asexuality in the pea aphid. PLoS Genet. 2014 Dec 4;10(12)

2013

Glaser N, Gallot A, Legeai F, Montagné N, Poivet E, Harry M, Calatayud PA, Jacquin-Joly E. Candidate chemosensory genes in the Stemborer Sesamia nonagrioides. Int J Biol Sci. 2013 May 21;9(5):481-95.

Poivet E, Gallot A, Montagné N, Glaser N, Legeai F, Jacquin-Joly E. A comparison of the olfactory gene repertoires of adults and larvae in the noctuid moth Spodoptera littoralis. PLoS One. 2013;8(4)

2012

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.

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.

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.

2011

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.

2010

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.

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)

2009

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.

2008

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.