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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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Algae Anabaena Asterochloris Azolla Cladonia Cladoniaceae Coccomyxa Cyanobacteria database Degelia Dothideomycetes Eurotiomycetes genbank Green algae gunnera Introduction ITS Lepraria Lichen Methods Nostoc omphalina Paramecium Peltigera Peltigerales Phylogenetics plant symbiosis Pyrenula reproductive mode Rhizonema Scytonema sql Stereocaulaceae Trebouxia Trentepohliales XanthoriaBlogRoll
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Author Archives: heath.obrien
Trebouxia update
After considerable fiddling, I’ve finally managed to update the phylogeny and host-association matrix for the most common lichen photobiont, Trebouxia. The methods are similar to those used in my previous post on Nostoc rbcX sequences, to the extent that the … Continue reading
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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PhotobiontDiversity has moved!
I’ve recently completed migration of this blog from wordpress.com to photobiontdiversity.org This move will allow the creation of a number of new features, the first of which is described in this post. Unfortunately, I’ve not been able to migrate subscriptions … Continue reading
Posted in Uncategorized
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PhotobiontDiversity.org: A searchable database of photobiont sequences
After six months of working on this project, I’ve amassed a collection of over 5,500 sequences from lichen photobionts and their relatives. Storage and retrieval of this data using text files has become increasingly unwieldy for me, and I suspect … Continue reading
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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Green Algal Photobionts: Trentepohlia
While most work has focused on coccoid green algae and/or cyanobacteria, a largely overlooked lineage of lichen photobionts is the Trentepoliales, a group of filamentous, carotenoid producing green algae. Trentepohlian algae are associated with one fifth of lichen species world … Continue reading
Posted in Green Algal Photobionts
Tagged Dothideomycetes, Eurotiomycetes, Lichen, Pyrenula, Trentepohliales
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Green Algal Photobionts: Coccomyxa
After a few weeks of for a vacation, it’s time to get back to green algal photobionts. In addition to Trebouxia and Asterochloris, there are several other genera of Trebouxiophycean algae that act as photobionts for various groups of lichens. … Continue reading
Posted in Green Algal Photobionts
Tagged Coccomyxa, Green algae, omphalina, Paramecium, Peltigerales
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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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Green Algal Photobionts: Asterochloris.
In this post I will be taking a look at the diversity of the junior partner to Trebouxia: Asterochloris. Originally described by Elisabeth Tschermak-Woess in 1980, Asterochloris was subsequently merged with Trebouxia before being split out again on the basis of sequence … Continue reading
Posted in Green Algal Photobionts
Tagged Asterochloris, Cladonia, Cladoniaceae, Lepraria, Lichen, Stereocaulaceae, Xanthoria
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