title: Proteogenomics of Gammarus fossarum to document the reproductive system of amphipods.
abstract: Because of their ecological importance, amphipod crustacea are employed worldwide as test species in environmental risk assessment. Although proteomics allows new insights into the molecular mechanisms related to the stress response, such investigations are rare for these organisms because of the lack of comprehensive protein sequence databases. Here, we propose a proteogenomic approach for identifying specific proteins of the freshwater amphipod Gammarus fossarum, a keystone species in European freshwater ecosystems. After deep RNA sequencing, we created a comprehensive ORF database. We identified and annotated the most relevant proteins detected through a shotgun tandem mass spectrometry analysis carried out on the proteomes from three major tissues involved in the organism's reproductive function: the male and female reproductive systems, and the cephalon, where different neuroendocrine glands are present. The 1,873 mass-spectrometry-certified proteins represent the largest crustacean proteomic resource to date, with 218 proteins being lineage specific. Comparative proteomics between the male and female reproductive systems indicated key proteins with strong sexual dimorphism. Protein expression profiles during spermatogenesis at seven different stages highlighted the major gammarid proteins involved in the different facets of reproduction.
authors.affiliation: From the ‡Irstea, Unité de Recherche MALY, Laboratoire d'écotoxicologie, CS70077, F-69626 Villeurbanne, France; §CEA, DSV, IBEB, Lab Biochim System Perturb, Bagnols-sur-Cèze, F-30207, France.
authors.forename: Judith
authors.initials: J
authors.lastname: Trapp
authors.affiliation: From the ‡Irstea, Unité de Recherche MALY, Laboratoire d'écotoxicologie, CS70077, F-69626 Villeurbanne, France; jean.armengaud@cea.fr olivier.geffard@irstea.fr.
authors.forename: Olivier
authors.initials: O
authors.lastname: Geffard
authors.affiliation: §CEA, DSV, IBEB, Lab Biochim System Perturb, Bagnols-sur-Cèze, F-30207, France.
authors.forename: Gilles
authors.initials: G
authors.lastname: Imbert
authors.affiliation: §CEA, DSV, IBEB, Lab Biochim System Perturb, Bagnols-sur-Cèze, F-30207, France.
authors.forename: Jean-Charles
authors.initials: JC
authors.lastname: Gaillard
authors.affiliation: §CEA, DSV, IBEB, Lab Biochim System Perturb, Bagnols-sur-Cèze, F-30207, France.
authors.forename: Anne-Hélène
authors.initials: AH
authors.lastname: Davin
authors.affiliation: From the ‡Irstea, Unité de Recherche MALY, Laboratoire d'écotoxicologie, CS70077, F-69626 Villeurbanne, France;
authors.forename: Arnaud
authors.initials: A
authors.lastname: Chaumot
authors.affiliation: §CEA, DSV, IBEB, Lab Biochim System Perturb, Bagnols-sur-Cèze, F-30207, France jean.armengaud@cea.fr olivier.geffard@irstea.fr.
authors.forename: Jean
authors.initials: J
authors.lastname: Armengaud
mesh_terms: D033304:Amphipoda / Q000235:genetics*; D000818:Animals; D003307:Copulation / Q000502:physiology; D030562:Databases, Protein; D005260:Female; D005618:Fresh Water; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D016678:Genome; D008297:Male; D058977:Molecular Sequence Annotation; D020543:Proteome / Q000235:genetics*; D012098:Reproduction / Q000235:genetics; D012727:Sex Characteristics; D013091:Spermatogenesis / Q000235:genetics*
chemical_list: D020543:Proteome