Good day everyone. I have isolated an endophyte. From its morphological characters it looks like Geotrichum sp. However, based on its ITS sequence it is a different species. It has 100% match with Tinctoporellus sp. I can't find any morpho-cultrual despcription of Tinctoporellus from which I can compare my isolate. What do you think should I do? Is it common to encounter such problem (mismatch with molecular and morphological based id)?
Depending on the database used, very likely to be missannotated. Very frequent in NCBI nt/nr.
MycoBank allows searching on databases with sequences only from curated culture collections, and it's quite unlikely that anything is missannotated.
Same goes for morphological identification. If your reference material is old, you may easily have a outdated nomenclature and it's another possible source of mismatch.
It's possible. Hence, the interest of always completing the morphological identification by the molecular analyzes. You also have to make sure that you have not confused the strains.
According to the available literature, some taxonomic groups cannot be classified using ITS region. For further identification, you can use other marker genes or polyphasic approach.
Depending on the database used, very likely to be missannotated. Very frequent in NCBI nt/nr.
MycoBank allows searching on databases with sequences only from curated culture collections, and it's quite unlikely that anything is missannotated.
Same goes for morphological identification. If your reference material is old, you may easily have a outdated nomenclature and it's another possible source of mismatch.
Tinctoporellus is a polypore, Getrichum is a mould. Moulds can grow on polypores. Several polypores have asexual (mold) stages. This can be a contamination issue as well. Use curated DNA databases. Check the identity of your fungal source with a traditional taxonomist. You find the macro- and microscopical description of Tinctoporellus in Ryvarden & Johansen 1980. A preliminary polypore flora of East Africa.
Hi
This is possible sometimes, because ITS primers are general. I suggest you, use a specific primer or at least one more primer, also use several data base such as NCBI, EBI, DDBJ, several software for alignment and blast such as Mega, Bioedit. Download some of sequences of Geotrichum and Tinctoporellus and then draw phylogenetic tree, it can be helpful for getting a better decision.
For morphological identification, it’s better use some of identifical keys and some websites such as indexfungorum.org
at last, Geotrichum is a common fungus in lab and it’s not very difficult to identify so if you sure that’s Geotrichum, that’s it!
Good luck 👍🏻
The problem is that your organism is from a taxonomic group that has been morphologically characterized based on its sexual fruiting bodies. It is a member of the subphylum Agaricomycotina, where classification is rarely based on "cultural characteristics" (growth on media). You probably cannot make a proper morphological determination of this organism without having access to its sexual fruiting body (basidiocarp). If the determination of the sequence accession to which you have a 100% match can be verified in some way, then you may be able to make a molecular determination. Otherwise you may have to call this organisms Polyporaceae or Polyporales sp.
I have few suggestions for you regarding your molecular identification.
* make sure you culture is pure before DNA extraction
* When you compare your sequence with available sequences using BLAST, it is better to consider sequences from type strains on the genbank and construct phylogentic tree to confirm your identification.
* You better use one other sequence for confirmation of your finding.
Good Luck
Horizontal gene transfer is observed in fungi, especially in cheese-forming fungi like Geotrichum. Among those genes that were horizontally transfered, there are few mentions of rDNA in fungi. This could explain the discrepancies between molecular and phenotypic data.
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