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heathobrien
I am a genome scientist based in Bristol, England. I am currently studying the genetic basis of neuropsychiatric disorders, but I have also done research on iridescent plants, plant pathogens and lichens. I have continued my work on lichen-associated algae and cyanobacteria for my blog
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Category Archives: Cyanobacterial photobionts
Photobionts of aquatic Peltigera
After a long hiatus, I’ve decided that it’s time to write some updates on the photobiont sequences that have been released over the last few months. I haven’t been entirely idle during the interim and have made a number of … Continue reading
Posted in Cyanobacterial photobionts, Uncategorized
Tagged Lichen, Nostoc, Peltigera
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Another perspective on diversity of symbiotic cyanobacteria: 16S
Up to this point, I have been focusing on the rbcX locus for all investigations of cyanobacterial photobionts because it is probably the most extensively sampled locus and it is more variable than 16S rDNA. However, it is limited because … Continue reading
Symbiotic Nostoc Revisited
In the three months or so that I’ve been working on this blog there has been some evolution in the methods I’m using. I though it would be worthwhile to revisit the first group I looked at to see if … Continue reading
Posted in Cyanobacterial photobionts
Tagged Cyanobacteria, Degelia, Lichen, reproductive mode
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Gunnera symbionts do not cluster with lichen photobionts
I have been kicking around the idea of setting up an online catalog of lichen photobionts for years before I started doing this. The main impetus to finally start was this paper: Fernández-Martínez, M., de los Ríos, A., Sancho, L., & Pérez-Ortega, … Continue reading
Posted in Cyanobacterial photobionts, Green Algal Photobionts
Tagged gunnera, Nostoc, plant symbiosis
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An In-Depth Look at the Diversity of Symbiotic Nostoc
**Post has been updated with some corrections to the host information in the first phylogeny** Today I am finally going to take a detailed look at the Nostoc phylogeny that I have been working on. But before I can begin, … Continue reading
Adding new sequences (Mistakes were made)
Looking through the tree produced in my last post, I noticed that several interesting sequences were missing from the tree. There are also less sequences in the tree than I get if I search for “Nostoc rbcX” in Entrez. Turns … Continue reading
Adding host information to the Nostoc phylogeny
Having obtained 496 Nostoc rbcX sequences (plus one outgroup) and used them to infer a reasonable phylogeny, all that is left is to assign host association information to the branches. This will require (a) parsing the sequence files to obtain host … Continue reading
Obtaining the sequences
Perhaps not surprisingly given my background, I will be starting with Nostoc photobionts. In my opinion, the most useful marker for this group is rbcX, so I will be starting there. I have decided to use blast to obtain all … Continue reading
