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De novo transcriptome assembly and SNP discovery in the wing polymorphic salt marsh beetle Pogonus chalceus (Coleoptera, Carabidae)
Van Belleghem, S.M.; Roelofs, D.; Van Houdt, J.; Hendrickx, F. (2012). De novo transcriptome assembly and SNP discovery in the wing polymorphic salt marsh beetle Pogonus chalceus (Coleoptera, Carabidae). PLoS One 7(8): 1-13. dx.doi.org/10.1371/journal.pone.0042605
In: PLoS One. Public Library of Science: San Francisco. ISSN 1932-6203; e-ISSN 1932-6203, more
Peer reviewed article  
Available in  Authors 
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  • Van Belleghem, S.M., more
  • Roelofs, D.
  • Van Houdt, J., more
  • Hendrickx, F., more
Abstract

    Background

    The salt marsh beetle Pogonus chalceus represents a unique opportunity to understand and study the origin and evolution of dispersal polymorphisms as remarkable inter-population divergence in dispersal related traits (e.g. wing development, body size and metabolism) has been shown to persist in face of strong homogenizing gene flow. Sequencing and assembling the transcriptome of P. chalceus is a first step in developing large scale genetic information that will allow us to further study the recurrent phenotypic evolution in dispersal traits in these natural populations.

    Methodology/Results

    We used the Illumina HiSeq2000 to sequence 37 Gbases of the transcriptome and performed de novo transcriptome assembly with the Trinity short read assembler. This resulted in 65,766 contigs, clustering into 39,393 unique transcripts (unigenes). A subset of 12,987 show similarity (BLAST) to known proteins in the NCBI database and 7,589 are assigned Gene Ontology (GO). Using homology searches we identified all reported genes involved in wing development, juvenile- and ecdysteroid hormone pathways in Tribolium castaneum. About half (56.7%) of the unique assembled genes are shared among three life stages (third-instar larva, pupa, and imago). We identified 38,141 single nucleotide polymorphisms (SNPs) in these unigenes. Of these SNPs, 26,823 (70.3%) were found in a predicted open reading frame (ORF) and 6,998 (18.3%) were nonsynonymous.

    Conclusions

    The assembled transcriptome and SNP data are essential genomic resources for further study of the developmental pathways, genetic mechanisms and metabolic consequences of adaptive divergence in dispersal power in natural populations.

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