Abstract
BackgroundThe 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/ResultsWe 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.ConclusionsThe 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.
Highlights
A vast number of insect species are characterized by remarkable and often discontinuous morphological variation in traits related to dispersal capacity [1,2]
While signals of strong divergent natural selection are observed between the ecotypes for the isocitrate dehydrogenase 2 (IDH2) allozymes, dispersal power and body size, no differentiation could be detected for neutral markers, suggesting high levels of gene flow among both ecotypes [6,29,30]
Variant analysis Only reliable properly paired Burrows—Wheeler Aligner (BWA) mapped reads were considered for Single Nucleotide Polymorphism (SNP) calling
Summary
A vast number of insect species are characterized by remarkable and often discontinuous morphological variation in traits related to dispersal capacity [1,2]. While signals of strong divergent natural selection are observed between the ecotypes for the IDH2 allozymes, dispersal power and body size, no differentiation could be detected for neutral markers, suggesting high levels of gene flow among both ecotypes [6,29,30] These findings and the incipient stage of divergence make the salt marsh beetle P. chalceus attractive for genetic studies of selection, adaptation, and gene flow. The resulting assembled and annotated transcriptome sequences constitute comprehensive genomic resources, available for further studies and may provide a fast approach for identifying genes involved in developmental pathways (i.e. wing development, JH, and ECD) relevant to adaptive divergence in this species
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