Testing for dispensable chromosomes and two-speed genome features in the birch pathogenic fungus Taphrina betulina

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Title: Testing for dispensable chromosomes and two-speed genome features in the birch pathogenic fungus Taphrina betulina
Author: Zhang, Panpan
Contributor: University of Helsinki, Faculty of Agriculture and Forestry, Department of Agricultural Sciences
Publisher: Helsingin yliopisto
Date: 2017
Language: eng
URI: http://urn.fi/URN:NBN:fi:hulib-201709225405
Thesis level: master's thesis
Discipline: Kasvintuotantotieteet
Plant Production Science
Abstract: Plant pathogenic fungi parasitize plants and cause invasive infection. With the development of next generation sequencing, a number of plant pathogenic fungi genomes are being sequenced and analyzed. The first completed genome sequence of Taphrina betulina, which is a biotrophic pathogen that causes striking twig clusters, known as witch's broom on birch, has been just finished. Genome sequencing yielded a 13 Mb assembly with 28 chromosomes. However, 10 of 28 chromosomes are considerably small. We hypothesized that these chromosomes may be dispensable chromosomes that are associated with pathogenicity. Essential gene distributions in identified Taphrina, Schizosaccharomyces species, and species identified with known dispensable chromosomes were compared. Evidence is presented that dispensable chromosomes are non-existent in T. betulina and this pipeline could find potential dispensable chromosomes. Furthermore, discontinuous essential gene distribution promotes our second hypothesis that T. betulina has some features of a “two-speed genome”. “Two-speed genome” consists of gene-dense regions and gene- sparse regions. Genes located in gene-sparse regions tend to evolve faster than the rest. Gene ontology (GO) describes the functionality of a gene and its products from three domains: cellular components, molecular functions and biological process. GO enrichment analyses of “slow-speed region” and “fast- speed region” genes were compared, facilitating the finding of candidate virulence effectors.
Subject: comparative genomic study
fungal evolution and bioinformatics

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