I am analysing my sponge meta-transcripts data obtained from GeoChip. According to my data, at least over 1000 fungal genes showed transcriptional activity, most of them are assigned to filamentous fungi. However, I couldn't find any mycelium in my TEM/SEM pictures. Also there's no convincing picture that shows the fungal mycelium in sponge tissue. Yet, people can isolate filamentous fungi from marine sponges and amplify fungal 18S rRNA/ITS genes from sponge metagenome. I am thinking the paradox is due to the genes related to mycelium development are somehow transcriptionally inactive. But I don't know much about fungal genomics. Can someone give me some guidance? Thanks.
Maybe dimorphic fungi with yeast-like stages? Try amplified FISH if you have the possibility in order to check where they may be located.
Or your sponge transcripts resemble high similarities with fungal transcripts? They are evolutionary not so far away after all. That's a long shot of course...
You are right Chris. According to my RNA-seq data, sponge transcripts resembled way higher similarities with fungal transcripts than I expected. In the end I used GhostKOALA instead of blast to distinguish if it's fungal transcript or sponge transcript. But I did recover ~20,000 fungal transcripts, including several house-keeping genes like actin.
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