Vaillancourt, Lisa

Vaillancourt Lab Introduction

In our laboratory we study the genetics and genomics of plant pathogenic fungi. Specifically, our goal is to understand the basic mechanisms that fungi use to invade their host plants and cause symptoms. In support of that research, we generate whole genome sequences of multiple strains of Colletotrichum and Fusarium. We need to assemble and annotate these genomes, map genes/transcripts and amplification products, and map and compare genetic markers, especially single nucleotide polymorphisms (SNPS). We need to store all this information and use it to generate summary reports and graphical representations of the data. We will also conduct genetic crosses among various strains and examine the segregation patterns of SNP markers among individual progeny and progeny pools. By analyzing these SNPs, we aim to identify regions of the genome associated with important traits like aggressiveness, toxigenicity, and competitiveness under different management conditions. We will look for genetic markers that deviate significantly from the expected 1:1 ratio and are linked to these traits. To support this work we need to use various genomic and statistical tools that are available on the HPC platform (described below).

Role of toxin chemotypes in the aggressiveness and toxicity of Fusarium graminearum on wheat.

Students:

Simran Goyal (Graduate RA).

Role of fungal signal peptidase in pathogenicity of Colletotrichum graminicola to maize.

Students:

Caleb Mathias (Graduate RA)

Renata Belisario (Graduate RA)

Comparative functional effectoromics of Colletotrichum graminicola and Colletotrichum sublineola.

Students:

Renata Belisario (Graduate RA)

Computational Methods:

Genome assembly, genome annotation, variant calling, differential gene expression analysis, phylogenetics. Most, if not all, of the software is already installed on systems in the HPC cluster.

Software:

edgeR, DESeq2, SNAP, Augustus, MAKER, BLAST, samtools, bedtools, velvet, canu, vcftools, bcftools, trinity, fastqc, cutadapt, tophat, BWA, bowtie2, hisat2, minimap2, raxml

UK and non-UK collaborators:

Mark Farman

Grants:

Publications: