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Data from: The transcriptomics of sympatric dwarf and normal lake whitefish (Coregonus clupeaformis spp., Salmonidae) divergence as revealed by next-generation sequencing

When using this data, please cite the original article:

Jeukens J, Renaut S, St-Cyr J, Nolte AW, Bernatchez L (2010) The transcriptomics of sympatric dwarf and normal lake whitefish (Coregonus clupeaformis spp., Salmonidae) divergence as revealed by next-generation sequencing. Molecular Ecology 19(24): 5389-5403. doi:10.1111/j.1365-294X.2010.04934.x

Additionally, please cite the Dryad data package:

Jeukens J, Renaut S, St-Cyr J, Nolte AW, Bernatchez L (2010) Data from: The transcriptomics of sympatric dwarf and normal lake whitefish (Coregonus clupeaformis spp., Salmonidae) divergence as revealed by next-generation sequencing. Dryad Digital Repository. doi:10.5061/dryad.1924
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Dryad Package Identifier doi:10.5061/dryad.1924    318 views  
Abstract Gene expression divergence is one of the mechanisms thought to be involved in the emergence of incipient species. Next-generation sequencing has become an extremely valuable tool for the study of this process by allowing whole transcriptome sequencing, or RNA-Seq. We have conducted a 454 GS-FLX pyrosequencing experiment in order to refine our understanding of adaptive divergence between dwarf and normal lake whitefish species (Coregonus clupeaformis spp.). The objectives were to: (1) investigate transcriptomic divergence as measured by liver RNA-Seq; (2) test the correlation between divergence in expression and sequence polymorphism and (3) investigate the extent of allelic imbalance. We also compared the results of RNA-seq with those of a previous microarray study performed on the same fish. Following de novo assembly, results showed that normal whitefish over-expressed more contigs associated with protein synthesis while dwarf fish over-expressed more contigs related to energy metabolism, immunity and DNA replication and repair. Moreover, 63 SNPs showed significant allelic imbalance, and this phenomenon prevailed in the recently diverged dwarf whitefish. Results also showed an absence of correlation between gene expression divergence as measured by RNA-Seq and either polymorphism rate or sequence divergence between normal and dwarf whitefish. This study reiterates an important role for gene expression divergence, and provides evidence for allele-specific expression divergence as well as evolutionary decoupling of regulatory and coding sequences in the adaptive divergence of normal and dwarf whitefish. It also demonstrates how next-generation sequencing can lead to a more comprehensive understanding of transcriptomic divergence in a young species pair.
Keywords Fish, Molecular Evolution, Natural Selection and Contemporary Evolution, Speciation, Transcriptomics,
Date Deposited 2010-08-30T20:18:02Z
Scientific Names Coregonus clupeaformis
Spatial Coverage Cliff Lake
Maine (USA)
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De novo contigs from RNA-Seq of the whitefish liver transcriptome    122 views   46 downloads View File Details
Excel spreadsheet with de novo contigs from RNA-Seq of the whitefish liver transcriptome. Contig consensus sequences and gene expression values (RPKM) for dwarf and normal whitefish are presented.
Download: Supporting Information for online publication only_TS2.xls ( 1.345Mb )
To the extent possible under law, the authors have waived all copyright and related or neighboring rights to this data.  


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