The nematode Panagrolaimus superbus can survive for extended peri-
ods of time in a desiccated state (anhydrobiosis) and is also freezing tol-
erant (cryobiotic). These adaptations make it an interesting candidate for
genome and transcriptome sequencing using second generation high through-
put methods. In this project the transcriptome of P. superbus was sequenced
using the 454 (Roche) platform. To enrich for stress-related genes, nema-
todes were exposed to one of the following stresses (desiccation, cold, heat
or oxidation). Equal numbers of nematodes from each stress treatment were
combined with unstressed control nematodes prior to RNA extraction. Nor-
malised and unnormalised cDNA libraries were prepared from this mixed
population. A de novo assembly of the transcriptome was generated using a
variety of assembly programs and strategies. A Sanger sequenced expressed
sequence dataset comprising 3,982 unigenes was fully annotated and inte-
grated into the de novo transcriptome assembly. The de novo assembly has
also been annotated and putative stress response genes were identified. The
haploid karyotype of P. superbus was determined to be n=4. P. superbus
genomic DNA was sequenced using 454 (Roche) methods along with 50 bp
and 100 bp paired end Illumina reads. Eight different gDNA assemblies were
prepared, generating predicted genome sizes ranging from 87.9 kilobases to
159.7 kilobases. The longest contigs were obtained from the 454 genomic
DNA assembly and the assemblies of the Illumina reads generated shorter
contigs. The gene order of the P. superbus mitochondrial DNA genome was
obtained and a draft assembly of the mitochondrial genome is presented.
The current transcriptome assembly is a resource suitable for use as a refer-
ence for aligning high throughput RNA Seq reads. Both the transcriptome
and genome assemblies can be used to generate a protein reference database
for the mass spectrometry based identification of the proteome of control
and desiccated P. superbus for future studies
