README.md

In anabeloff/vic3PCD: Transcriptome analysis of Cryphonectria parasititca allorecognotion

Transcriptome analysis of Cryphonectria parasititca allorecognotion

The package is a supplementary material to: Transcriptome analysis implicates secondary metabolite production, redox reactions and programmed cell death during allorecognition in Cryphonectria parasitica. Belov, A., Witte, T., Overy, D., Smith, M.. G3: GENES, GENOMES, GENETICS. 2020

Installation

library("devtools")

# Install from GitHub
install_github("anabeloff/vic3PCD", build_vignettes = TRUE)

Introduction

When two genetically distinct fungal strains make a hyphal contact (fuse) this triggers a cell death. Multiple fused hyphae along the line of the contact form a separation line made out of the dead hyphae. This separation line is called barrage. Its primary function is to separate genetically distinct strains to prevent the exchange of cellular content.

Here we make an attempt to understand the molecular processes that control allorecognition in C. parasitica, chestnut blight filamentous fungus.

• What triggers cell death in incompatible hyphae?
• What genes play major role?
• What are underlying processes?

Strains

In this work we use three strains of C. parasitica incompatible by vic3 locus. Strains P74-3 and EP155 are of distinct genetic background, but carry identical alleles at all vic loci except for vic3. The EP155 strain carries the vic3-1 haplotype and P74-3 carries the vic3-2 haplotype. Strain DZ-66 is derived from EP155 where genes vic3a-1 and vic3b-1 were knocked out Strains list and original samples codes used for sequencing in FASTQ file names:

• E = EP155 (DK80 - non-homologous-end-joining knockout)
• P = P74-3 (wildtype)
• D = DZ-66 ($\Delta\Delta vic3$ - double vic3 knockout of DK80)
• X = EP155 + P74-3 (mix)
• Z = DZ-66 + P74-3 (mix)

Experiment

We developed a blending technique that allows to maximise the number of contacts formed when two incompatible strains are co-inoculated together.

Three monoculture samples (EP155, P74-3, DZ-66) were used as controls. Two barrage samples were created by mixing equal volumes of monoculture suspensions of incompatible strains (EP155 vs. P74-3 and DZ-66 vs. P74-3). Barrage sample with vic3 knockouts (DZ-66 vs. P74-3) was also used as a control in further analyses.

Vignettes

For further details see vignettes

vignette("Part_1")
vignette("Part_2")
vignette("Part_3")
vignette("Part_4")

anabeloff/vic3PCD documentation built on Dec. 2, 2020, 11:03 a.m.