1. Cox1 Barcoding of Penicillium and Fusarium Keith A. Seifert, Scott Gilmore and Karol Rivera Biodiversity, Agriculture & Agri-Food Canada, Ottawa, Ontario, Canada. Agriculture and Agri-Food Canada Agriculture et Agroalimentaire Canada Canada

2. Gene 1 tree

3. T 474 Outgroup 1 24432 T T 478 Outgroup 1 45782 T 483 Outgroup 1 45672 T 475 Outgroup 1 45872 T 485 Outgroup 2 46272 T 486 Outgroup 2 43993 T 488 Outgroup 2 50873 T 487 Outgroup 2 18472 T 354 Taxon 3 13567 T 352 Taxon 3 47984 T L Taxon 3 22130 T 357 Taxon 3 23438 T 066 Taxon 2 44978 T 068 Taxon 2 46695 T T 071 Taxon 2 T 342 Taxon 1 101032 T 347 Taxon 1 46595 T 348 Taxon 1 46495 1 change 100 98 99 Taxon 3 complex Gene 2 Taxon 3 Taxon 2 Taxon 1 Cox1 Taxon 1 Taxon 2 Taxon 3 Gene 1

4. beta-tubulin Cox1 Taxon 1 Taxon 2 Taxon 3 Taxon 4 Taxon 5 Taxon 6 Taxon 7 Taxon 8 Gene 1 tree Gene 2 tree

5. Comparison of Three Potential Barcoding Loci Gene 1Gene 2Gene 3 Mean bp545446555 Infraspecific0.060.830.51 range0-0.6 0-4.90-5.3 Interspecificx5.614.45.1 range0-15.40.5-67.20-26.8 Species 67.181.224.5 resolution Or 9210033 PCR success rate95%75%95% Introns030 Gaps0258150

6. Comparison of Three Potential Barcoding Loci in Penicillium subgenus Penicillium Cox1BenAITS Mean bp545446555 Infraspecific0.060.830.51 range0-0.6 0-4.90-5.3 Interspecificx5.614.45.1 range0-15.40.5-67.20-26.8 Species 67.181.224.5 resolution Or 9210033 PCR success rate95%75%95% Introns030 Gaps0258150

8. Neighbour joining analysis of Cox1 exon region between Fusarium intron 4b and end of barcode (439bp).

9. Hypocreales – Primer Design 1234567891011 AHyFu-F FI3-F FI3-R AHyFu-R FI4b-F

10. Acknowledgements This work was funded by grants to the Canadian Barcode of Life Network by –The Natural Sciences and Engineering Research Council of Canada (NSERC) –Genome Canada