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J Proteomics. 2016 Mar 1;135:51-61. doi: 10.1016/j.jprot.2015.06.017. Epub 2015 Jul 11.

Proteogenomic insights into the core-proteome of female reproductive tissues from crustacean amphipods.

Author information

1
Irstea, Unité de Recherche MALY, Laboratoire d'écotoxicologie, CS70077, F-69626 Villeurbanne, France; CEA-Marcoule, DSV/IBICTEC-S/SPI/Li2D, Laboratory "Innovative Technologies for Detection and Diagnostic", BP 17171, F-30200 Bagnols-sur-Cèze, France.
2
CEA-Marcoule, DSV/IBICTEC-S/SPI/Li2D, Laboratory "Innovative Technologies for Detection and Diagnostic", BP 17171, F-30200 Bagnols-sur-Cèze, France.
3
Irstea, Unité de Recherche MALY, Laboratoire d'écotoxicologie, CS70077, F-69626 Villeurbanne, France.
4
Irstea, Unité de Recherche MALY, Laboratoire d'écotoxicologie, CS70077, F-69626 Villeurbanne, France. Electronic address: olivier.geffard@irstea.fr.
5
CEA-Marcoule, DSV/IBICTEC-S/SPI/Li2D, Laboratory "Innovative Technologies for Detection and Diagnostic", BP 17171, F-30200 Bagnols-sur-Cèze, France. Electronic address: jean.armengaud@cea.fr.

Abstract

As a result of the poor genome sequence coverage of crustacean amphipods, characterization of their evolutionary biology relies mostly on phenotypic traits. Here, we analyzed the proteome of ovaries from five amphipods, all from the Senticaudata suborder, with the objective to obtain insights into the core-proteome of female reproductive systems. These amphipods were from either the Gammarida infraorder: Gammarus fossarum, Gammarus pulex, Gammarus roeseli, or the Talitrida infraorder: Parhyale hawaiensis and Hyalella azteca. Ovaries from animals sampled at the end of their reproductive cycle were dissected. Their whole protein contents were extracted and their proteomes were recorded by high-throughput nanoLC-MS/MS with a high-resolution mass spectrometer. We interpreted tandem mass spectrometry data with the protein sequence resource from G. fossarum and P. hawaiensis, both recently established by RNA sequencing. The large molecular biodiversity within amphipods was assessed by the ratio of MS/MS spectra assigned for each sample, which tends to diverge rapidly along the taxonomic level considered. The core-proteome was defined as the proteins conserved along all samples, thus detectable by the homology-based proteomic assignment procedure. This specific subproteome may be further enriched in the future with the analysis of new species and update of the protein sequence resource.

KEYWORDS:

Amphipods; Comparative proteomics; Crustaceans; Non-model organisms; Ovaries; Polymorphism; Proteogenomics; RNA-seq; Reproduction

PMID:
26170043
DOI:
10.1016/j.jprot.2015.06.017
[Indexed for MEDLINE]

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