I am trying to detect the active eukaryotic microbes / protists from marine sponge transcripts. I think 18S rRNA can be detected as long as the cell is well preserved during sampling. Thus, only functional genes found in transcripts are true indicators for the active members. Before posting the question,I screened the current eIF4E database but not many sequences available which made it hard to design degenerate primers for PCR. Besides eIF4E, what else I can choose? Thanks.
Fang Liu--you might try the new genes recently evaluated by a student of mine, Donald Walker. The paper is attached. One marker is MS204--a subunit of a guanine nucleotide binding protein. The other marker may not be as useful for you--FG1093--a 60S ribosomal protein. Good luck. Jim White, Rutgers University
Hi James, I searched the MS204&FG1093 in FUNYBASE single-copy families but it seemed they didn't exist in the database any more. Here's the link:http://genome.jouy.inra.fr/funybase/FUNYCG/WEB/CGI-BIN/funycg_results.cgi I couldn't find any info of those two genes on the list.
Then I searched the complete genome database using key word "guanine nucleotide-binding protein" and found a long list of results. There were 76 alpha-subunit sequences and 33 beta-subunit （MS204）sequences. Seems like the MS204 is not well represented in the database. For more extensive understanding of sponge symbiotic fungal diversity, I may need to try other genes. Do you think so? I am still a rookie. Looking forward to more advices from you.
Among non-RNA markers tested for fungi, RPB1 performed quite well. It showed less problems than RPB2 and MCM7:
https://www.researchgate.net/publication/229087468_Nuclear_ribosomal_internal_transcribed_spacer_%28ITS%29_region_as_a_universal_DNA_barcode_marker_for_Fungi
Article Nuclear ribosomal internal transcribed spacer (ITS) region a...
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