title: Identification of Mytilus edulis genetic regulators during early development.
abstract: Understanding the mechanisms that enable growth and survival of an organism while driving it to the full range of its adaptation is fundamental to the issues of biodiversity and evolution, particularly regarding global climatic changes. Here we report the Illumina RNA-sequencing (RNA-seq) and de novo assembly of the blue mussel Mytilus edulis transcriptome during early development. This study is based on high-throughput data, which associates genome-wide differentially expressed transcript (DET) patterns with early activation of developmental processes. Approximately 50,383 high-quality contigs were assembled. Over 8000 transcripts were associated with functional proteins from public databases. Coding and non-coding genes served to design customized microarrays targeting every developmental stage, which encompass major transitions in tissue organization. Consequently, multi-processing pattern exploration protocols applied to 3633 DETs helped discover 12 unique coordinated eigengenes supposedly implicated in various physiological and morphological changes that larvae undergo during early development. Moreover, dynamic Bayesian networks (DBNs) provided key insights to understand stage-specific molecular mechanisms activated throughout ontogeny. In addition, delayed and contemporaneous interactions between DETs were coerced with 16 relevant regulators that interrelated in non-random genetic regulatory networks (GRNs). Genes associated with mechanisms of neural and muscular development have been characterized and further included in dynamic networks necessary in growth and functional morphology. This is the first large-scale study being dedicated to M. edulis throughout early ontogeny. Integration between RNA-seq and microarray data enabled a high-throughput exploration of hidden processes essential in growth and survival of microscopic mussel larvae. Our integrative approach will support a holistic understanding of systems biology and will help establish new links between environmental assessment and functional development of marine bivalves.
authors.affiliation: Institut des Sciences de la Mer de Rimouski, Université du Québec à Rimouski, 310 allée des Ursulines, Rimouski, Québec G5L3A1, Canada; Laboratoire des Sciences de l'Environnement Marin, Institut Universitaire Européen de la Mer, Université de Bretagne Occidentale, Rue Dumont d'Urville, 29280 Plouzané, France.
authors.forename: Sleiman
authors.initials: S
authors.lastname: Bassim
authors.affiliation: UPMC Université Paris 6, UMR 7144, Génétique et adaptation en milieu extrême, Station biologique de Roscoff, France.
authors.forename: Arnaud
authors.initials: A
authors.lastname: Tanguy
authors.affiliation: Institut des Sciences de la Mer de Rimouski, Université du Québec à Rimouski, 310 allée des Ursulines, Rimouski, Québec G5L3A1, Canada.
authors.forename: Bertrand
authors.initials: B
authors.lastname: Genard
authors.affiliation: Laboratoire des Sciences de l'Environnement Marin, Institut Universitaire Européen de la Mer, Université de Bretagne Occidentale, Rue Dumont d'Urville, 29280 Plouzané, France.
authors.forename: Dario
authors.initials: D
authors.lastname: Moraga
authors.affiliation: Institut des Sciences de la Mer de Rimouski, Université du Québec à Rimouski, 310 allée des Ursulines, Rimouski, Québec G5L3A1, Canada. Electronic address: rejean_tremblay@uqar.ca.
authors.forename: Rejean
authors.initials: R
authors.lastname: Tremblay
mesh_terms: D000818:Animals; D001499:Bayes Theorem; D042002:Chromatin Assembly and Disassembly; D017143:Fuzzy Logic; D018507:Gene Expression Regulation, Developmental; D053263:Gene Regulatory Networks; D059014:High-Throughput Nucleotide Sequencing; D007814:Larva / Q000235:genetics; D008675:Metamorphosis, Biological / Q000235:genetics; D049880:Mytilus edulis / Q000235:genetics* / Q000254:growth & development*; D025341:Principal Component Analysis; D059467:Transcriptome
keywords: Bivalve; Development; Gene regulatory networks; Next-generation sequencing; Transcriptome