Sequence data finally online - includes new genes for TWO genera!

Hello everyone,

So, this current update on the DNA sequences that I sent to GenBank for accession comes a couple of weeks later than I initially anticipated. Of the 12 sequences that were included in this sub-project, 10 did make it online successfully on October 10, which was the date I had set for the release of all of my sequences. However, for some reason, the two non-rRNA sequences (an rbcL sequence for my Spirogyra strain and a tufA sequence for Filamentous 1, a species of Stigeoclonium) were not uploaded at this time. Just a few days ago, after I had communicated with GenBank again, I managed to confirm that these sequences would be made public on October 25 - tomorrow. So I figured I might as well introduce all of the sequences now:

 

This is a screenshot of one of my current entries that is up on GenBank - a portion of the 28S rRNA, the nuclear large ribosomal subunit, sequenced for an isolate of Spirogyra collected in Chico late this July. To my knowledge, this is the first time the 28S rRNA of any member of this genus has been sequenced and made public! Sequences of the large ribosomal subunit from the chloroplast genome (23S rRNA) are available for a number of Spirogyra have been published, but never before from the nuclear genome. One other sequence is fairly new as well: I managed to sequence a small, ~370bp portion of the chloroplast large ribosomal subunit, the 23S rRNA, from Filamentous 2, a species of Cladophora I also collected in Chico. In this genus of algae, there is an appreciable amount of data for the 28S rRNA of Cladophora, but (to my knowledge) none for the chloroplast large ribosomal subunit, sort of the reversed scenario as seen in Spirogyra. This new sequence, however, is a little less impressive in my mind as it is not very informative; perhaps I will eventually work on finding or designing some primers to amplify a longer stretch of the 23S rRNA and apply it here.

My other sequences aren't nearly as novel and many of them are rather short and truncated, but they will still prove to be very useful for my project analyses - and hopefully for those of future scientists as well! In my sequencing of the Spirogyra 28S rRNA, I discovered that very few other algae in the zygnematophyte lineage have had their 28S rRNA sequenced; in fact, the closest-matching DNA available in the GenBank database to this sequence are basically all plants or Coleochaete. Therefore, it is possible I may look more closely at sequencing some other 28S rRNA fragments as I continue my larger project, to help expand the rather small library of zygnematophyte and, to a larger extent, charophyte sequences in general currently available. It's not a particularly commonly-used gene for phylogenetic analysis (unlike the chloroplast rRNA, which has been used heavily), so I certainly think it'd be worth some effort to work on while I'm still studying in this general area.

But I digress. The sequences which are currently available (or will be by tomorrow) are listed as follows, with accession numbers followed by species, strain designation, and the identity of the DNA:

MF998088.1 : Spirogyra sp. "Spiro 1" 28S rRNA (nuclear LSU rRNA)

MG015894-MG015895 : The two non-rRNA sequences; Spirogyra sp. "Spiro 1" rbcL gene and Stigeoclonium sp. "Filamentous 1" tufA gene

MG018619-MG018620 : Cladophora sp. "Filamentous 2" ITS rRNA region and Rhizoclonium sp. "Filamentous 3" ITS rRNA region MG018621-MG018622 : Cladophora sp. "Filamentous 2" 18S rRNA (nuclear SSU rRNA) and Rhizoclonium sp. "Filamentous 3" 18S rRNA MG021094-MG021095 :Cladophora sp. "Filamentous 2" 23S rRNA and Spirogyra sp. "Spiro 1" 23S rRNA (chloroplast LSU rRNA) MG021091-MG021093 : Stigeoclonium sp. "Filamentous 1" 28S rRNA, Cladophora sp. "Filamentous 2" 28S rRNA, and Rhizoclonium sp. "Filamentous 3" 28S rRNA

So that's a wrap for now! I'm currently still working on running some PCR so I can send in a second round of products for new (and repeat) sequencing reactions, which I hope to do by the end of the year. I plan on providing a general update of the project as a whole, and I'll hopefully get an abstract put up of the work I've done so far to help better direct newer experiments and conceptualize new lines of research. Stay tuned.