Monthly Archives: June 2014

Genome sequencing of 23 strains of H. pseudoalbidus from Europe

The Contributors

Georgios Koutsovoulos, Mark Blaxter
The University of Edinburgh

Adam Vivian-Smith & Ari Hietala
Skog og Landskap – Norwegian Forest and Landscape Institute
Bioforsk – Norwegian Institute for Agricultural and Environmental Research

Renaud Ioos & colleagues
Unité de Mycologie, Laboratoire de la Santé des Végétaux, Domaine de Pixérécourt, Malzéville, France

Summary

Genome assembly summary of 23 Strains of H. pseudoalbidus sequenced at The University of Edinburgh

Table 1: 23 strains of H. pseudoalbidus from Europe

Strain Year Country
2008-81-6      2008      NORWAY
2008-125/2      2008      NORWAY
2008-139/1      2008      NORWAY
2008-142/5      2008      NORWAY
2008-148/4      2008      NORWAY
2008-152/4      2008      NORWAY
2009-86/3      2009      NORWAY
2010-189/4      2010      NORWAY
2010-189/5      2010      NORWAY
2011-11/1      2011      NORWAY
2012-24/1      2012      NORWAY
2012-38/2/2      2012      NORWAY
2012-42/1/1      2012      NORWAY
CBS122191      ?      AUSTRIA
CBS122503      2011      POLAND
CBS122504      2005      POLAND
CBS122505      2000      POLAND
CBS122507      2000      POLAND
FON-M-1      2009      FRANCE
GIR-M-2      2009      FRANCE
LAN-M-1      2009      FRANCE
MIG-M-1      2009      FRANCE
LSVM82      2008      FRANCE

Table 2: Summary of assembly stats

Strain contigs (>500) span of contigs (MB) N50 GC% diff. from K1 indels from K1 span of indels
2008-125/2 6267 53.5 24303 42.67 193829 37014 75714
2008-139/1 6041 53.5 24414 42.69 174930 32599 68413
2008-142/5 6138 53.5 25254 42.72 180469 32502 69266
2008-148/4 7560 51.8 18776 43.18 175814 32875 68400
2008-152/4 6736 52.8 22327 42.9 176916 34024 70682
2008-81/6 7387 51.6 19538 43.19 187222 36522 72017
2009-86/3 6160 53.5 25295 42.72 164775 32603 64923
2010-189/4 6348 53.3 23729 42.78 179776 33438 70108
2010-189/5 6331 53.4 24880 42.77 179106 33429 69312
2011-11/1 6118 53.4 25094 42.73 188201 37279 75145
2012-24/1 6317 53.3 24080 42.77 177522 33805 69614
2012-38/2/2 6094 53.5 24711 42.67 174888 33466 67026
2012-42/1/1 6516 53.1 23078 42.83 173764 32218 67008
CBS122191 6252 53.5 24172 42.71 181217 32820 69030
CBS122503 6700 53.2 22119 42.77 195226 35872 74082
CBS122504 6365 56.7 30182 41.76 191934 33400 68770
CBS122505 6422 53.5 23708 42.67 172436 32440 66584
CBS122507 6387 53.1 23038 42.79 180121 34599 70054
FON-M-1 6436 53.3 23037 42.73 179944 35230 70160
GIR-M-2 4770 51.9 34647 43.59 196420 37771 95254
LAN-M-1 6534 52.5 23965 43.15 168898 31707 64028
LSVM82 35509 77.3 19479 38.33 171274 34758 92767
MIG-M-1 6498 52.8 23204 42.91 200012 36898 78521

Reports and Raw data

Reports and presentations of complete assemblies are available at OADB github Assembly reports of European strains

And raw data was submitted to The European Nucleotide Archive (ENA) ERP006093
Further information of raw data and assembled genomes are available at Genome assemblies of European strains
and at http://www.ebi.ac.uk/ena/data/view/ERS480843-ERS480865

20 UK isolates sequenced and submitted by The Genome Analysis Centre

The Contributors

Mark McMullan, Matt Clark, Louisa Williamson, James Lipscombe, Rachel Piddock, Fiore Cugliandolo, Fiona Fraser, Tom Barker, Mario Caccamo
The Genome Analysis Centre, Norwich

Summary

Hymenoscyphus pseudoalbidus (Chalara fraxinea) were isolated from across Great Britain and sent to TGAC by the The Food and Environment Research Agency (FERA). FERA purified DNA from each isolate which was sent to TGAC, where it was QC’d, libraries constructed and finally sequenced on a HiSeq2500 (150bp) paired end run. The 20 isolates were sequenced over two lanes (20 isolates per lane) to an average of ~50x depth per isolate.
Following are the 20 isolates
FERA_cc086
FERA_cc087
FERA_cc088
FERA_cc095
FERA_cc096
FERA_cc097
FERA_cc099
FERA_cc101
FERA_cc105
FERA_cc106
FERA_cc107
FERA_cc108
FERA_cc111
FERA_cc113
FERA_cc118
FERA_cc119
FERA_cc121
FERA_cc133
FERA_cc134
FERA_cc139

and their sequence information is available at OADB github

Downstream analyses (genome assembly, phylogenies and selection analyses) have been done at TGAC (MM).
These analyses await data from European isolates sequenced in Edinburgh.