"right, thanks for pointing out my taxonomic bias! looks like there is no universally constant region within the 28S that could serve as a handle without needing exceptions.
but rather than trimming sequences to within these motifs, what would be…"
"we have been routinely trimming our ITS sequences to beginning and ending with the CATTA- and -GACCT motifs. The -GACCT motif can vary a bit depending on which groups you work in (highly variable in Hygrocybe, for instance), but in my experience…"
We have not used these new primers in lichens and very few ascos. Since they were designed with basidios in mind (Agaricomycetes, in fact) I cannot recommend them over the standard ITS4 and ITS5 pair that is typically used for ascos.
I’m involved in, or am interested in the following barcoding initiatives
DNA Barcoding Initiative for Conservation
I’m involved in or interested in the following iBOL Working Groups
I’m involved in the following aspects of barcoding:
Fieldwork/specimen collecting, Museum work/specimen curation, Labwork/generating barcode sequences, Management of barcode data, Analysis of barcode data, Using barcode data in taxonomy/systematic biology, Organizing/managing barcoding projects
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