A computational framework for transcriptome assembly and annotation in non-model organisms: the case of venturia inaequalis

dc.contributor.advisorChristoffels, Alan
dc.contributor.advisorJasper, D
dc.contributor.advisorRees, G
dc.contributor.authorKimbung, Stanley Mbandi
dc.date.accessioned2015-03-10T12:47:13Z
dc.date.accessioned2024-05-09T08:19:22Z
dc.date.available2015-03-10T12:47:13Z
dc.date.available2024-05-09T08:19:22Z
dc.date.issued2014
dc.descriptionPhilosophiae Doctor - PhDen_US
dc.description.abstractIn this dissertation three computational approaches are presented that enable optimization of reference-free transcriptome reconstruction. The first addresses the selection of bona fide reconstructed transcribed fragments (transfrags) from de novo transcriptome assemblies and annotation with a multiple domain co-occurrence framework. We showed that selected transfrags are functionally relevant and represented over 94% of the information derived from annotation by transference. The second approach relates to quality score based RNA-seq sub-sampling and the description of a novel sequence similarity-derived metric for quality assessment of de novo transcriptome assemblies. A detail systematic analysis of the side effects induced by quality score based trimming and or filtering on artefact removal and transcriptome quality is describe. Aggressive trimming produced incomplete reconstructed and missing transfrags. This approach was applied in generating an optimal transcriptome assembly for a South African isolate of V. inaequalis. The third approach deals with the computational partitioning of transfrags assembled from RNA-Seq of mixed host and pathogen reads. We used this strategy to correct a publicly available transcriptome assembly for V. inaequalis (Indian isolate). We binned 50% of the latter to Apple transfrags and identified putative immunity transcript models. Comparative transcriptomic analysis between fungi transfrags from the Indian and South African isolates reveal effectors or transcripts that may be expressed in planta upon morphogenic differentiation. These studies have successfully identified V. inaequalis specific transfrags that can facilitate gene discovery. The unique access to an in-house draft genome assembly allowed us to provide preliminary description of genes that are implicated in pathogenesis. Gene prediction with bona fide transfrags produced 11,692 protein-coding genes. We identified two hydrophobin-like genes and six accessory genes of the melanin biosynthetic pathway that are implicated in the invasive action of the appressorium. The cazyome reveals an impressive repertoire of carbohydrate degrading enzymes and carbohydrate-binding modules amongst which are six polysaccharide lyases, and the largest number of carbohydrate esterases (twenty-eight) known in any fungus sequenced to dateen_US
dc.identifier.urihttps://hdl.handle.net/10566/13533
dc.language.isoenen_US
dc.publisherUniversity of the Western Capeen_US
dc.rights.holderUniversity of the Western Capeen_US
dc.subjectRNA-Seqen_US
dc.subjectQuality filteringen_US
dc.subjectTranscriptome reconstructionen_US
dc.subjectTransfragsen_US
dc.subjectCoding potentialen_US
dc.subjectComparative transcriptomicsen_US
dc.subjectOpen reading frameen_US
dc.subjectHost-pathogen interactionen_US
dc.subjectVenturia inaequalisen_US
dc.subjectOrthologen_US
dc.titleA computational framework for transcriptome assembly and annotation in non-model organisms: the case of venturia inaequalisen_US
dc.typeThesisen_US

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