%0 Journal Article %J eLife %D 2021 %T The rise and fall of the ancient northern pike master sex-determining gene %A Pan, Qiaowei %A Feron, Romain %A Jouanno, Elodie %A Darras, Hugo %A Herpin, Amaury %A Koop, Ben %A Rondeau, Eric %A Goetz, Frederick W %A Larson, Wesley A %A Bernatchez, Louis %A Tringali, Mike %A Curran, Stephen S %A Saillant, Eric %A Denys, Gaël %A von Hippel, Frank A %A Chen, Songlin %A López, J Andrés %A Verreycken, Hugo %A Ocalewicz, Konrad %A Guyomard, Rene %A Eche, Camille %A Lluch, Jerome %A Roques, Celine %A Hu, Hongxia %A Tabor, Roger %A DeHaan, Patrick %A Nichols, Krista M %A Journot, Laurent %A Parrinello, Hugues %A Klopp, Christophe %A Interesova, Elena A %A Trifonov, Vladimir %A Schartl, Manfred %A Postlethwait, John %A Guiguen, Yann %B eLife %V 10 %8 Apr-01-2023 %G eng %U https://elifesciences.org/articles/62858 %R 10.7554/eLife.62858 %0 Journal Article %J Marine Drugs %D 2021 %T Transcriptome Profiling of the Pacific Oyster Crassostrea gigas Visceral Ganglia over a Reproduction Cycle Identifies Novel Regulatory Peptides %A Réalis-Doyelle, Emilie %A Schwartz, Julie %A Cabau, Cédric %A Le Franc, Lorane %A Bernay, Benoît %A Guillaume Rivière %A Klopp, Christophe %A Favrel, Pascal %B Marine Drugs %V 19 %P 452 %8 Jan-08-2021 %G eng %U https://www.mdpi.com/1660-3397/19/8/452 %N 8 %! Marine Drugs %R 10.3390/md19080452 %0 Journal Article %J Mar Drugs %D 2021 %T Transcriptome Profiling of the Pacific Oyster Visceral Ganglia over a Reproduction Cycle Identifies Novel Regulatory Peptides. %A Réalis-Doyelle, Emilie %A Schwartz, Julie %A Cabau, Cédric %A Le Franc, Lorane %A Bernay, Benoît %A Riviere, Guillaume %A Klopp, Christophe %A Favrel, Pascal %X

The neuropeptides involved in the regulation of reproduction in the Pacific oyster () are quite diverse. To investigate this diversity, a transcriptomic survey of the visceral ganglia (VG) was carried out over an annual reproductive cycle. RNA-seq data from 26 samples corresponding to VG at different stages of reproduction were de novo assembled to generate a specific reference transcriptome of the oyster nervous system and used to identify differentially expressed transcripts. Transcriptome mining led to the identification of novel neuropeptide precursors (NPPs) related to the bilaterian Eclosion Hormone (EH), crustacean female sex hormone/Interleukin 17, Nesfatin, neuroparsin/IGFBP, prokineticins, and urotensin I; to the protostome GNQQN, pleurin, prohormones 3 and 4, prothoracotropic hormones (PTTH), and QSamide/PXXXamide; to the lophotrochozoan CCWamide, CLCCY, HFAamide, and LXRX; and to the mollusk-specific NPPs CCCGS, clionin, FYFY, GNamide, GRWRN, GSWN, GWE, IWMPxxGYxx, LXRYamide, RTLFamide, SLRFamide, and WGAGamide. Among the complete repertoire of NPPs, no sex-biased expression was observed. However, 25 NPPs displayed reproduction stage-specific expression, supporting their involvement in the control of gametogenesis or associated metabolisms.

%B Mar Drugs %V 19 %8 2021 Aug 07 %G eng %N 8 %R 10.3390/md19080452 %0 Journal Article %J BMC Bioinformatics %D 2015 %T GigaTON: an extensive publicly searchable database providing a new reference transcriptome in the pacific oyster Crassostrea gigas. %A Guillaume Rivière %A Klopp, Christophe %A Ibouniyamine, Nabihoudine %A Huvet, Arnaud %A Boudry, Pierre %A Pascal Favrel %K Animals %K Base Sequence %K Computational Biology %K Crassostrea %K Databases, Genetic %K Gene Library %K Gene Ontology %K Genome %K High-Throughput Nucleotide Sequencing %K Molecular Sequence Data %K Sequence Analysis, RNA %K Software %K Transcriptome %X

BACKGROUND: The Pacific oyster, Crassostrea gigas, is one of the most important aquaculture shellfish resources worldwide. Important efforts have been undertaken towards a better knowledge of its genome and transcriptome, which makes now C. gigas becoming a model organism among lophotrochozoans, the under-described sister clade of ecdysozoans within protostomes. These massive sequencing efforts offer the opportunity to assemble gene expression data and make such resource accessible and exploitable for the scientific community. Therefore, we undertook this assembly into an up-to-date publicly available transcriptome database: the GigaTON (Gigas TranscriptOme pipeliNe) database.

DESCRIPTION: We assembled 2204 million sequences obtained from 114 publicly available RNA-seq libraries that were realized using all embryo-larval development stages, adult organs, different environmental stressors including heavy metals, temperature, salinity and exposure to air, which were mostly performed as part of the Crassostrea gigas genome project. This data was analyzed in silico and resulted into 56621 newly assembled contigs that were deposited into a publicly available database, the GigaTON database. This database also provides powerful and user-friendly request tools to browse and retrieve information about annotation, expression level, UTRs, splice and polymorphism, and gene ontology associated to all the contigs into each, and between all libraries.

CONCLUSIONS: The GigaTON database provides a convenient, potent and versatile interface to browse, retrieve, confront and compare massive transcriptomic information in an extensive range of conditions, tissues and developmental stages in Crassostrea gigas. To our knowledge, the GigaTON database constitutes the most extensive transcriptomic database to date in marine invertebrates, thereby a new reference transcriptome in the oyster, a highly valuable resource to physiologists and evolutionary biologists.

%B BMC Bioinformatics %V 16 %P 401 %8 2015 %G eng %R 10.1186/s12859-015-0833-4