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    De novo sequencing, assembly and analysis of the genome and transcriptome of the nematode Panagrolaimus superbus


    O'Mahony Zamora, Georgina (2013) De novo sequencing, assembly and analysis of the genome and transcriptome of the nematode Panagrolaimus superbus. PhD thesis, National University of Ireland Maynooth.

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    Abstract

    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.

    Item Type: Thesis (PhD)
    Keywords: De novo sequencing; genome; transcriptome; nematode; Panagrolaimus superbus;
    Academic Unit: Faculty of Science and Engineering > Biology
    Item ID: 6746
    Depositing User: IR eTheses
    Date Deposited: 07 Jan 2016 17:01
    URI:

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