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De novo transcriptome assembly and SNP discovery in the wing polymorphic salt marsh beetle Pogonus chalceus (Coleoptera, Carabidae)

(2012) PLOS ONE. 7(8).
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HPC-UGent: the central High Performance Computing infrastructure of Ghent University
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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Citation

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Chicago
Van Belleghem, Steven, Dick Roelofs, Jeroen Van Houdt, and Frederik Hendrickx. 2012. “De Novo Transcriptome Assembly and SNP Discovery in the Wing Polymorphic Salt Marsh Beetle Pogonus Chalceus (Coleoptera, Carabidae).” Plos One 7 (8).
APA
Van Belleghem, S., 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).
Vancouver
1.
Van Belleghem S, Roelofs D, Van Houdt J, Hendrickx F. De novo transcriptome assembly and SNP discovery in the wing polymorphic salt marsh beetle Pogonus chalceus (Coleoptera, Carabidae). PLOS ONE. 2012;7(8).
MLA
Van Belleghem, Steven et al. “De Novo Transcriptome Assembly and SNP Discovery in the Wing Polymorphic Salt Marsh Beetle Pogonus Chalceus (Coleoptera, Carabidae).” PLOS ONE 7.8 (2012): n. pag. Print.
@article{2966955,
  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.},
  articleno    = {e42605},
  author       = {Van Belleghem, Steven and Roelofs, Dick and Van Houdt, Jeroen and Hendrickx, Frederik},
  issn         = {1932-6203},
  journal      = {PLOS ONE},
  language     = {eng},
  number       = {8},
  pages        = {13},
  title        = {De novo transcriptome assembly and SNP discovery in the wing polymorphic salt marsh beetle Pogonus chalceus (Coleoptera, Carabidae)},
  url          = {http://dx.doi.org/10.1371/journal.pone.0042605},
  volume       = {7},
  year         = {2012},
}

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