Six new RNAseq datasets from Chalara fraxinea cultures and detection of mitoviruses infecting Chalara fraxinea

Contributor

Rachel Glover, Ian Adams, Paul Beales. Food and Environment Research Agency, York, UK.

 

Material

Mixed material RNASeq assemblies

AT1, AT2, ATU, Upton Broad, Holt Park

Chalara fraxinea mycelia RNASeq assemblies

Kenninghall Wood, Fera 88, Fera 93, Fera 94, Fera 105, Fera 232, Fera 233

Analysis:

The AT1, AT2, ATU, Upton and Holt mixed-material RNASeq assemblies were searched against the Genbank nr database with blastx in order to investigate the virome of each sample. A number of novel viral sequences were detected. A blastx was then carried out against the Kenninghall wood (KW) mycelia assembly to determine whether any of these viral sequences were likely to be infecting Chalara fraxinea. While none of the novel viruses originally discovered in the other datasets were present in the KW assembly, a 2.4kb mitovirus was detected. A tblastx search of this mitovirus sequence against the mixed-material samples discovered shorter contigs in the Holt and Upton assemblies which had homology to the KW mitovirus but which had not been detected in the original blastx against Genbank.
Fera has been testing large numbers of samples as part of the response to the presence of Ash Dieback in the UK and so we sequenced six cultured isolates of Chalara fraxinea (RNASeq with MiSeq) to investigate the prevalence of mitoviruses in a small number of our cultures. Mitoviruses were detected in the Fera 88, 93 and 94 samples but not Fera 105, 232 and 233.

 

fera1

Figure: Mitovirus positive samples are shown with red pins, negative with white pins.

Interpretation:

The presence or absence of mitovirus does not appear to be geographically correlated but the Fera samples were not comprehensively sequenced so mitoviruses may be present in these samples but not sequenced. Further work is required to investigate whether these mitoviruses confer hypovirulence to Chalara fraxinea.