Date of Graduation

Spring 2017

Degree

Master of Science in Biology

Department

Biology

Committee Chair

Laszlo Kovacs

Abstract

Next-generation sequencing technologies have provided access to vast quantities of nucleic acid sequence data. The resulting wealth of information enables biologists to address complex biological questions in species for which a high-quality well-annotated reference genome sequence has yet to be generated. The cultivated grapevine, Vitis vinifera, has a relatively poorly annotated reference genome. In addition, it is a highly heterozygous species which further hinders the annotation of its genome and the characterization of its transcriptome. Here, I annotated Version 2 of the 12X V. vinifera genome using RNA-seq data derived from the variety ‘Riesling' by employing the most up-to-date computational methods. The results provide the first annotation of ‘Riesling' and the first profile of its transcriptome in relation to the reference transcriptome of the model grape variety ‘Pinot Noir'. In addition, I develop a computational pipeline for the identification of long non-coding RNAs (lncRNAs) in non-model plant species that lack well-sequenced reference genomes. This pipeline was then applied to ‘Riesling' RNA- seq data for the first analysis of lncRNAs in that variety.

Keywords

transcriptome, genome annotation, grapevine, lncRNA, computational biology, gene prediction

Subject Categories

Biology

Copyright

© Zachary Noel Harris

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