title: Analysis of the black-chinned tilapia Sarotherodon melanotheron heudelotii reproducing under a wide range of salinities: from RNA-seq to candidate genes.
abstract: The black-chinned tilapia Sarotherodon melanotheron heudelotii is an ecologically appealing model as it shows exceptional adaptive capacities, especially with regard to salinity. In spite of this, this species is devoid of genomic resources, which impedes the understanding of such remarkable features. De novo assembly of transcript sequences produced by next-generation sequencing technologies offers a rapid approach to obtain expressed gene sequences for non-model organisms. It also facilitates the development of quantitative real-time PCR (qPCR) assays for analysing gene expression under different environmental conditions. Nevertheless, obtaining accurate and reliable qPCR results from such data requires a number of validations prior to interpretation. The transcriptome of S. melanotheron was sequenced to discover transcripts potentially involved in the plasticity of male reproduction in response to salinity variations. A set of 54 candidate and reference genes was selected through a digital gene expression (DGE) approach, and a de novo qPCR assay using these genes was validated for further detailed expression analyses. A user-friendly web interface was created for easy handling of the sequence data. This sequence collection represents a major transcriptomic resource for S. melanotheron and will provide a useful tool for functional genomics and genetics studies.
authors.affiliation: Institut des Sciences de l'Evolution de Montpellier, UMR 226 IRD-CNRS-UM2, BP5095, Montpellier Cedex 05, 34196, France.
authors.forename: J-C
authors.initials: JC
authors.lastname: Avarre
authors.forename: R
authors.initials: R
authors.lastname: Dugué
authors.forename: P
authors.initials: P
authors.lastname: Alonso
authors.forename: A
authors.initials: A
authors.lastname: Diombokho
authors.forename: C
authors.initials: C
authors.lastname: Joffrois
authors.forename: N
authors.initials: N
authors.lastname: Faivre
authors.forename: C
authors.initials: C
authors.lastname: Cochet
authors.forename: J-D
authors.initials: JD
authors.lastname: Durand
mesh_terms: D000818:Animals; D023681:Cichlids / Q000235:genetics* / Q000502:physiology*; D019295:Computational Biology; D059014:High-Throughput Nucleotide Sequencing; D008969:Molecular Sequence Data; D009997:Osmotic Pressure; D054712:Salinity; D017421:Sequence Analysis; D059467:Transcriptome
keywords: gene expression; non-model organism; reference gene; salinity; spermatogenesis; tilapia