Jason Myers

Abstract

The objectives of this study were to develop a transcriptomic reference resource and to characterize polymorphism between isolates of Erysiphe necator (syn. Uncinula necator), grape powdery mildew. The wine and fresh fruit markets are economically vital to many countries worldwide, and E. necator infection can cause severe crop damage and subsequent financial loss. Most of the publicly available sequence data for Erysiphales are from research done on Blumeria graminis f. sp. hordei, barley powdery mildew, which occupies a distinct clade within the Erysiphales. We obtained 641,601 sequencing reads from a Roche 454–FLX next–generation sequencer (RNA–Seq) and performed multiple assemblies using the Mira assembly software. The best assembly was de novo and yielded 39,686 contiguous sequences. The reference was then ordered based on similarity to B. graminis genes and annotated based on sequence similarity to known proteins. 11,605 SNPs and 5,248 INDELs were called against the reference using RNA–Seq data from 55 additional geographically and phenotypically distinct isolates of E. necator. The reference transcriptome, annotations, and polymorphic characterization collections from this project represent a vast resource for E. necator and should allow for future research of this organism and other Erysiphales. Our results illustrate that RNA–Seq is a valid alternative to whole–genome sequencing for genetic characterization of non-model organisms.

Library of Congress Subject Headings

Nucleotide sequence; RNA splicing; Grape powdery mildew disease--Genetics

Publication Date

8-10-2012

Document Type

Thesis

Department, Program, or Center

Thomas H. Gosnell School of Life Sciences (COS)

Advisor

Newman, Dina

Advisor/Committee Member

Cadle-Davidson, Lance

Advisor/Committee Member

Baldo, Angela

Comments

Note: imported from RIT’s Digital Media Library running on DSpace to RIT Scholar Works. Physical copy available through RIT's The Wallace Library at: QP625.N89 M94 2012

Campus

RIT – Main Campus

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