Abstract
BackgroundThe club-legged grasshopper Gomphocerus sibiricus is a Gomphocerinae grasshopper with a promising future as model species for studying the maintenance of colour-polymorphism, the genetics of sexual ornamentation and genome size evolution. However, limited molecular resources are available for this species. Here, we present a de novo transcriptome assembly as reference resource for gene expression studies. We used high-throughput Illumina sequencing to generate 5,070,036 paired-end reads after quality filtering. We then combined the best-assembled contigs from three different de novo transcriptome assemblers (Trinity, SOAPdenovo-trans and Oases/Velvet) into a single assembly.ResultsThis resulted in 82,251 contigs with a N50 of 1357 and a TransRate assembly score of 0.325, which compares favourably with other orthopteran transcriptome assemblies. Around 87% of the transcripts could be annotated using InterProScan 5, BLASTx and the dammit! annotation pipeline. We identified a number of genes involved in pigmentation and green pigment metabolism pathways. Furthermore, we identified 76,221 putative single nucleotide polymorphisms residing in 8400 contigs. We also assembled the mitochondrial genome and investigated levels of sequence divergence with other species from the genus Gomphocerus. Finally, we detected and assembled Wolbachia sequences, which revealed close sequence similarity to the strain pel wPip.ConclusionsOur study has generated a significant resource for uncovering genotype-phenotype associations in a species with an extraordinarily large genome, while also providing mitochondrial and Wolbachia sequences that will be useful for comparative studies.
Highlights
The club-legged grasshopper Gomphocerus sibiricus is a Gomphocerinae grasshopper with a promising future as model species for studying the maintenance of colour-polymorphism, the genetics of sexual ornamentation and genome size evolution
We present a de novo transcriptome assembly for the club-legged grasshopper Gomphocerus sibiricus, an alpine-dwelling species that is unusual for its striking sexual dimorphism in front leg morphology [18] and is characterized by the widespread occurrence of a balanced green-brown polymorphism [17]
We here present a high quality transcriptome assembly for G. sibiricus, a species of grasshopper with a large genome that is of particular evolutionary interest
Summary
The club-legged grasshopper Gomphocerus sibiricus is a Gomphocerinae grasshopper with a promising future as model species for studying the maintenance of colour-polymorphism, the genetics of sexual ornamentation and genome size evolution. There are still major challenges inherent to genomic approaches for genotype-phenotype associations in non-model organisms [2] One of these challenges is imposed by species with large genomes, as genome assemblies are difficult to construct for highly repetitive regions [3]. To some degree, this issue will be mitigated by the Transcriptomics offers an alternative to genomic approaches, as the size of the transcriptome does not scale linearly with genome size and most functional differences with phenotypic effects should be reflected in the transcriptome [5]. One prerequisite for an analysis of transcript abundance is a high quality transcriptome assembly, as this acts as a reference against which short read RNA sequencing data can be mapped [8]
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