To compare our samples with those in the databases, our ITS genotypes were used as queries to retrieve closely related sequences (≥90% sequence identities) with comparable lengths from GenBank.
To retrieve closely related SDR sequences from other species, T. reesei candidate SDRs were used in a BLASTP search against the NCBI database.
The conserved region of RT was translated and the region representing peptide domains 2 though 7 [ 29] was used in a BLASTp search to retrieve closely related accessions from Genbank.
Our initial search for putative orthologs retrieved two closely related proteins, ArtI and ArtJ, in a subset of the genomes as explained above.
These results are compatible with our initial search for putative orthologs which retrieved two closely related proteins, ArtI and ArtJ, in a subset of the genomes, suggesting that the artJ gene is absent from most genomes.
In cases in which EMC components could not be identified in this manner, transcriptomes and genomes were searched using bioinformatically validated sequences from the previous step that were retrieved from closely related species.
It should be noted that for one open reading frame (ORF) we retrieved two closely related proteins, ArtI and ArtJ, in a subset of the genomes and that the corresponding artI/ artJ gene is located on the opposite strand immediately upstream of the lkt operon.
The genome clusters are calculated at different thresholds and the taxonomic ids are mapped to NCBI bioproject ids every month thereby enabling users to retrieve the closely related genomes.
In oomycetes, Ectocarpus, Monosiga and Chlorella, we also retrieved proteins sequences of closely related kinases found using a Blastp search.
Articles meeting initial inclusion criteria (Table 1) were retrieved and examined more closely in collaboration with a second researcher (CKR) until consensus was reached.
