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 same script can used to run both analyses. It was modified to use algal species names rather than host names when analysing Trebouxia, to colour the clades in the tree, and to count the number of times each photobiont lineage has been sampled from each lichen genus. All the steps required for this analysis can be see here. All of the files that were generated are available here.
I had previously built a tree from 1840 ITS sequences and identified lineages corresponding to ten named species and five unnamed species. Since then, there have been a number of important papers that have expanded the known diversity of the group and begun to codify the novel lineages. My current ITS tree (PDF version here) has 2335 sequences and includes 12 named species and 12 informally named lineages. Most of the names match those of Muggia et al. 2014, except that T. incrustata is circumscribed more tightly. Also, what they called T. arboricola/T. decolorans is T. decolorans in my tree and what they called Trebouxia sp. 1 is T. arboricola. The informally named lineages include two clades (URa1 and URa3) that were identified by Ruprecht et al. 2012, primarily from Antarctic lecideoid lichens. A third primarily Antarctic group, URa2, formed a paraphyletic assemblage basal to the clade that includes T. gelatinosa, T. impressa, T. incrustata, T. showmanii, T. gigantea, T. assymetrica, T. decolorans, T. arboricola and several informally named lineages. This is a similar arrangement to that of Muggia et al., except that T. impressa and T. gelatinosa were not included in this “crown group” in their phylogeny. This URa2 group was monophyletic in my previous tree (Trebouxia sp. 4), as well as in some of the other analyses that I ran for this post. URa2 was also present in my previous analysis, and named Trebouxia sp. 1. Trebouxia sp. 2 from my previous analysis corresponds to the clade including TR1 and TR9 lineages from Casano et al. 2010. The other two clades that I identified previously are also distinct monophyletic groups in this tree (Trebouxia sp. 3 is basal to T. impressa/ T. gelatinosa and Trebouxia sp. 5 is basal to Trebouxia sp. clade V / URa3). URa1 branches within what I labelled as T. jamesii in my previous analysis, breaking it up into three distinct lineages. One of these has been previously identified by Kroken and Taylor 2001 as T. jamesii ‘letharii’. The other appears to be novel and is called T. jamesii 2 here. Clade BMP1 from Leavitt et al 2013 forms a paraphyletic assemblage at the base of the URa3 lineage in this analysis, while BMP2 clusters with T. gigantea and BMP3 to BMP5 all cluster with T. incrustata. The clade named Trebouxia muralis I from Guzow-Krzeminska 2006 groups with T. asymetrica, as was the case in the Muggia et al. 2014 tree. The final named clade in this analysis corresponds to Antarctic B of Romeike et al. 2002, which also includes photobiobts from Australia and Greece.
I’ve also redone the matrix of counts for each of these 25 photobiont lineages (excluding the minor ones coloured in black in the tree, but including URa2) across all lichen genera for which data are available. This table can be viewed here, and is also available from the “Association Counts” menu in the header. In total, this represents 1968 symbiotic associations (with the remaining 367 photobiont sequences corresponding to minor lineages). This is obviously an extremely rich dataset and a lot of different questions can be asked about it, some of which I plan to explore in future posts.
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 improvements to the workflow that I use to identify and analyze sequences. Metadata is culled from genbank files is now added to a database that’s accessible through the website and this information is then mapped onto the phylogeny automatically. I’ve written a shell script to carry out all steps of the analysis automatically, which is available here. A summary of all the steps is here, and all of the intermediate files are available here. Going forward, the most recent version of these files will be stored here.
A zoomable version of the Nostoc rbcX phylogeny can be viewed within the (modern) browser here, or you can download the pdf version. For each sequence type, name(s) of the host(s) that associate with those photobionts are indicated, along with the number of times that genotype has been sequenced. Names are colour coded according to the family of the lichen mycobionts, with all plant hosts coloured green (free-living strains are well, cyan). Circles on branches indicate aLRT values ≥ 0.9. I’ve highlighted new sequences in yellow.
Most of the sequences that have been added since my last post on Nostoc rbcX are from photobionts of aquatic species of Peltigera, all of which form two clades that are sister to groups of plant symbionts:
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 that very few other people have been bothering to access the github repository where the data are archived. In an effort to improve accessibility, I’ve migrated this blog to a dedicated web server and created a searchable SQL database that can be accessed right from the blog. Below the banner, you’ll find a “Photobiont Sequences” tab, that will allow you to select green algae or cyanobacteria, specific genes, or the entire database. You can search for specific photobiont or host species, or filter the table using the selection boxes below each column.
My hope is that people who are interested in a particular group of lichens can use these tables to find out what photobiont(s) they are associated with. This information is not consistently encoded in Genbank, so until now it has usually required a laborious literature search to obtain it. Please let me know if you find this to be useful and if there are additional enhancements that you would like to see. I will be adding high-resolution trees for each group in the coming weeks, and hope to make them searchable as well if I can overcome the technical challenges of doing so. I’m also hoping to add links to Genbank for all of the sequences in the database.
Heath OBrien (2013). PhotobiontDiversity.org: a searchable database of photobiont sequences PhotobiontDiversity.org : http://dx.doi.org/10.6084/m9.figshare.841758
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 some groups of symbiotic cyanobacteria do not have rbcX sequences in the database. These include symbionts of the water fern Azolla which has traditionally been called Anabaena azolae and the photobionts of a variety of primarily tropical lichens that have traditionally been classified within the genus Scytonema. 16S sequences are available for both of these groups, as are sequences from a variety of other related genera of cyanobacteria. Furthermore, it is useful to compare the patterns revealed from analyses of rbcX to those based on an independent locus, often sampled from independent specimens. Continue reading
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 these changes in the methods affect my results. There have also been some additional sequences released since I started…
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 wide and are particularly common as a photobiont of eipiphytic lichens in the tropics. Trenepohlian algae are also very commonly found as free-living colonies on tree bark, leaves and rocks. Like most of the groups discussed here, the taxonomy of the Trentepholiales has not held up to scrutiny with molecular phylogenetic methods and the various genus names do not appear to be meaningful.
The only published study that I am aware of on the diversity of Trenetpohlian photobionts is Nelsen et al. 2011 (J. Phycol. 47, 282–290). They found that lichenized strain are mixed with free-living ones throughout the phylogeny and that lichen fungi from different classes can associate with very similar photobionts. Since the publication of this study, a large number of additional sequences from Trentepohlian photobionts have been deposited in the databases. These includes sequences of both ITS, which is the marker that has been used the most widely in studies of Trebouxiophycean photobionts and rbcL, a chloroplast gene that is probably the most extensively used phyologenetic marker in plants. Since rbcL was used in the study mentioned above, that is what I used for the analysis presented here. Continue reading
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. The most significant of these is probably Coccomyxa, which is the photobiont of many mushroom-forming basidiolichens and is also the green algal component of tripartite lichens in the Peltigerales.
There hasn’t been much work on Coccomyxa, but there were two papers in 2003 that each sequenced ITS from 20-25 specimens. One study found that photobionts of basidiolichens, photobionts of Peltigeralian lichens and free-living strains each formed a distinct lineage (Zoller et al. 2003), while the other found that photobionts of two species each of Nephroma and Peltigera were nearly identical (variable at a single position), which a single Peltigera britannica photobiont was found to be significantly different (Lohtander et al. 2003). Coccomyxa and Pseudococcomyxa have also been reported as symbionts of protists including Paramecium and Stentor. Continue reading
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, S. (2013). Diversity of Endosymbiotic Nostoc in Gunnera magellanica (L) from Tierra del Fuego, Chile Microbial Ecology DOI: 10.1007/s00248-013-0223-2
I have been interested in the relationships between lichenized Nostoc and those that form symbioses with ferns, cycads, liverworts and the flowering plant Gunnera for a long time, but my efforts to address the issue were hampered by inadequate sampling and others who had better sampling used a genetic marker with a complex history that made such comparisons difficult. Finally, here was a paper with extensive sampling across the range of a plant host of Nostoc who used the same genetic marker that has been widely adopted in work on lichen photobionts. Unfortunately, while the paper has a lot of interesting things to say about the Nostoc-Gunnera symbiosis (genetically monomorphic within individuals, lots of variability among individuals, reduced symbiont diversity in recently deglaciated areas, etc), they included very few lichen photobionts in their analyses, so I wasn’t able to get the answers to the questions I’m interested in from the paper.
Now that I’ve developed a decent phylogentic framework for symbiotic Nostoc, it should now be possible to address these questions. Here is how the G. magellanica symbionts fit in: Continue reading
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 data in the late 1990s. For the most part, Asterochloris is thought to be restricted to associations with lichens in two closely related families, Cladoniaceae and Stereocaulaceae. However, this includes Cladonia, one of the more charismatic (and ecologically important) lichen groups, so Asterochloris has been extensively sampled. Continue reading
Having gone through the steps to build a phylogeny of the most common lichen photobiont, Trebouxia in my last post, I will now go on to discussing the host association patterns that it reveals. Here is the Trebouxia ITS tree generated previously:
Trebouxia ITS phylogeny. Major clades are differentilly coloured and named according to authentic strains
I’ve coloured all of the taxa within clades according to the colours of the named strains and I’ve assigned unique colours to each clade that does not contain named strains. I have not attempted to break up T. jamesii or T. impressa into sub-clades, though doing so would probably be justified. This will be a topic for a future post. I should also point out that T. jamesii is referred to as T. simplex is some papers.
In contrast to Nostoc photobionts where the fasta headers were consistently labeled with the host information, these sequences are …not. I used a bioperl wrapper to NCBI’s Eutils interface to download genbank format sequences and parsed them to extract host association information from the “host”, “note” and “isolation source” annotions. I also extracted information about the author of each sequence and where it was published while I was at it: Continue reading