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Shyam Rallapalli edited this page Feb 18, 2015 · 44 revisions

Welcome to the ash dieback crowdsource wiki! In this wiki we aim to crowdsource information and genomic resources for Ash Dieback.

So far, the transcriptomes of four infected Ash samples have been sequenced and the transcriptome of unifected Ash:

  • 2 samples of infected Ash from Ashwellthorpe lower wood (The Sainsbury Laboratory)
  • 1 sample of infected Ash from Holt Country Park (The Sainsbury Laboratory)
  • 1 sample of infected Ash from Upton Broad and Marshes (The Sainsbury Laboratory)
  • 1 sample of uninfected Ash from Ashwellthorpe lower wood (The Sainsbury Laboratory)

The genome of a purified culture of Chalara fraxinea isolated from infected Ash collected at Kenninghall Wood has also been sequenced.

Contributors List of all contributors .. to date!

Sequence reads

Assemblies

Analysis

June 2014

12 June 2014 - Genome sequencing of 23 strains of H. pseudoalbidus from Europe

09 June 2014 - 20 UK isolates sequenced and submitted by The Genome Analysis Centre

May 2014

19 May 2014 - Analysis of UK Ash diversity set- morphological traits and disease susceptibility

02 May 2014 - Year 1 Report available on BiorXiv

April 2014

22 Apr 2014 - FIR analysis: genes encoding predicted secreted proteins occur in both gene sparse and gene dense regions of the H. pseudoalbidus genome

07 Apr 2014 - Identification of protein coding genes putatively involved in infection by combining metagenomics analysis and protein orthologue clustering

March 2014

11 March 2014 - Regression analysis of gene expression values against disease symptoms

January 2014

27 Jan 2014 - Potential inhibition of a putative alternative oxidase identified in C. fraxinea reduces fungal growth in culture

November 2013

28 Nov 2013 - Repeated mRNA-Seq analysis of Tree 35

September 2013

24 Sept 2013 - Variant analysis of different isolates and fruiting bodies of Chalara fraxinea

24 Sept 2013 - Metagenomic analysis to identify species composition of Fraxinus excelsior, Chalara fraxinea and infected material samples

24 Sept 2013 - SNP patterns in various isolates of Chalara fraxinea

24 Sept 2013 - Analysis of the Chalara genome suggests that it is AT repeat rich

24 Sept 2013 - Lignin degrading enzymes in the Chalara genome assembly

16 Sept 2013 - Assessing the origin of the UK Ash dieback pathogen

10 Sept 2013 - The top 100 ranked C. fraxinea candidate effector tribes

10 Sept 2013 - Mining for putative effectors in the Chalara fraxinea KW1 genome

August 2013

29 Aug 2013 - Six new RNAseq datasets from Chalara fraxinea cultures and detection of mitoviruses infecting Chalara fraxinea

19 Aug 2013 - mRNA-Seq analysis of Tree 35

July 2013

05 July 2013 - RNAseq analysis of primordial and mature fruiting bodies of H. pseudoalbidus

June 2013

12 June 2013 - Both mating types of Hymenoscyphus pseudoalbidus (Chalara fraxinea) are present in Ashwellthorpe lower wood

12 June 2013 - Chalara-induced Ash dieback fungal fruiting bodies identified in Norfolk woodland

04 June 2013 - Putative alternative oxidase identified in Chalara fraxinea

May 2013

26 May 2013 - Compositionally Non Homogenous Domains identified

26 May 2013 - Carbohydrate Active Enzyme Domains in Proteins

16 May 2013 - Tree 35 Assembly Stats

10 May 2013 - Preliminary analysis of expression profiles of Ash genes during infection

03 May 2013 - Putative alternative oxidase identified in Chalara fraxinea

03 May 2013 - Hymenoscyphus pseudoalbidus primordial fruiting bodies imaged by cryo-scanning electron microscopy

April 2013

26 Apr 2013 - Primordial fruiting bodies of H. pseudoalbidus identified on material collected from Ashwellthorpe lower wood

02 Apr 2013 - Both mating types of Hymenoscyphus pseudoalbidus (Chalara fraxinea) are present at nursery, recent planting and natural spread sites

March 2013

18 Mar 2013 - Forest Research Strain mating type info for H.pseudoalbidus and H.albidus

01 March 2013 - Sequence analysis of fruiting bodies isolated from Ash trees at Ashwellthorpe lower wood

Feb 2013

17 Feb 2013 - Chalara fraxinea gene predictions

January 2013

28 Jan 2013 - AT1 and AT2 are of a different mating type to KW1

25 Jan 2013 - Analysis of the MAT1 locus of C. fraxinea KW1 isolate

14 Jan 2013 - Is the high representation of fungal transcripts in the infected ash material unusual or alarming?

December 2012

21 Dec 2012 - AT1 Transcript assemblies - which one?!

21 Dec 2012 - Phylogenetic tree of Chalaria fraxinea based on ITS / 5.8S rRNA sequences

20 Dec 2012 - brief comment on pfam for Avr of plant origin

19 Dec 2012 - AT2 RNA-seq transcripts blastx-ed against eukaryotic protein database also show high fungal enrichment

17 Dec 2012 - Comments on predicted proteins Pfam domains and map to GO, KOG, PRK and EC numbers

16 Dec 2012 - How useful is the AT1 assembly?

13 Dec 2012 - Nep1-like proteins (NLPs) identified in AT1 assembled transcripts using tblastn

13 Dec 2012 - AT1 RNA-seq transcripts blastx-ed against eukaryotic protein database show high proportion of fungal enrichment

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