GO Explorations

Figure 1 Breakdown of GO_slim terms in the reference sea star transcriptome.

Figure 1 Breakdown of GO_slim terms in the reference sea star transcriptome.

This morning was one of great gene ontology adventures.  We picked up where we’d left off on Monday, working on our list of annotations for the sea star reference transcriptome.  We then used the UniProt accession numbers in this file to join GO and GO_slim terms onto the file.  Once we had this we were able to explore breakdowns of the major terms in the transcriptome (Fig. 1 and my notebook).  There were tons of interesting annotations, including ones that might have implications for sea star immunity.  Hopefully they’ll pop up again tomorrow when we start to look at deferentially expressed genes and the actual experiment that was done.  We then ventured over to Galaxy to examine taxonomic breakdowns of our annotations.  A large portion of our annotations is in fact derived from Phylum Echinodermata (YAY!).  A more detailed version of what we did, plus some graphs, can be found in my iPython notebook from today:

This afternoon was a wonderful discussion of viral diseases of various marine organisms, including WSSV and PaV1, which infect commercial crustaceans and wild lobsters respectively.  According to CABI, P. monodon (which is the primary host of WSSV) is invasive to the Mediterranean, Hawaii, the Atlantic and Gulf Coasts of the US, and various South American/Caribbean areas.  All of these introductions have likely come from aquaculture and pose serious threats as while WSSV is primarily found in P. monodon, it has been shown to be capable of infecting many species of crustaceans.  This could cause problems for native species of shrimp in all of these areas.  You can read more from the CABI report: here.

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