5/16/13Green Algal Photobionts: Trebouxia | PhotobiontDiversity
Green Algal Photobionts: Trebouxia
Posted on May 16, 2013
Having beaten the phylogeny of symbiotic cyanobacteria into submission in my previous post, I am now
tackling the green algae. My plan was to start with a big-picture analysis of 18S ribosomal RNA sequences, but
my initial blast search returned over 10,00o 454 reads from metagenomic projects which was a lot more
“environmental isolate XXX” than I felt like dealing with. Besides, I don’t know that I could add much to this
recent overview. Therefore, I am going to focus on the most important lineage of lichenized algae: Trebouxia.
There have been a large number of studies that have obtained photobiont ITS sequences from a variety of
Trebouxia associated lichens, so these are the data that I looked at.
The methods are the same as the ones that I described in detail previously for Nostoc ITS sequences. Briefly, I
used two ITS sequences (T. impressa JN204819 and T. arboricola JQ993781) as queries to identify all
homologous (E-value <= 1e-100) sequences in the nt database. Sequences were aligned with MAFFT, duplicate
sequences were removed with MetaPIGA, alignment positions corresponding to gaps in the references
sequence (T. arboricola JQ993758) were removed with trimal, and phylogenetic relationships were inferred
This procedure produced a tree with 794 taxa representing 1840 Trebouxia ITS sequences. The actual number
of Trebouxia associated lichens that have been sequenced is much higher than this because many authors only
deposit representative sequences of each haplotype that they obtained. At some point I will dig into the papers
where this has been done to extract the real numbers, but I have not done so yet.
For now, I am going to focus on the taxonomy of the algae. I will leave a discussion of the host-association
patterns for a future post. Here is the Trebouxia ITS phylogeny color-coded by species (tree file can be found
Genetic diversity of lichen photobionts
and related organisms
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Trebouxia ITS phylogeny color-coded by species (dark green: T. jamesii, yellow: T. corticola, light green: T. incrustata,
brown: T. asymmetrica, ornage: T. gigantea, purple: T. gelatinosa, dark blue: T. impressa, light red: T. arboricola, light
blue: T. decolorans, dark red: other, grey: T. sp.). Sequences recovered from multiple named species are in black. Black
circles indicate aLRT support > 0.9
With a few exceptions, sequences from named algae tend to cluster very well. T. gelatinosa (purple) is nested
within T. impressa (dark blue), though given the long branch separating these two species from all of the
others, I don’t entirely trust the rooting of this clade. T. jamesii (dark green) is a very heterogeneous group as
has been recognised previously. A number of photobionts that group with T. decolorans (light blue) have been
identified as T. arboricola (light red). Three major lineages have no named members (except for some
presumably misidentified T. decolorans sequences).
In addition to the differentially coloured species, there are several additional species names that are
represented by a small number of sequences, all of which are colored dark red in the tree. T. australis, T.
brindabellae, T. showmanii and T. usneae are each found in distinct clusters and are likely to represent
additional good species. T. australis and T. brindabellae are both in clusters near the base of one of the T.
jamesii clades (dark green). Two T. showmanii sequences form the sister group to T. incrustata (light
green). T. usneae forms a distint lineage with a misidentified T. corticola sequence sister to the T. corticola
lineage (yellow). All other rare species are deeply nested within other common species and appear not to be
distinct. These include T. potteri which is nested within T. impressa (dark blue), T. aggregata and T.
crenulata which are nested within T. arboricola (light red) and T. simplex, which includes six sequences that
are identical to T. jamesii (black) and two other sequences that are nested within one of the T. jamesii clades
(dark green). T. flava is identical to a T. impressa sequence and is coloured black in the tree.
In conclusion, >1840 Trebouxia ITS sequences that have been obtained from lichens cluster into about 24
distinct species, 13 of which appear to have suitable named representatives in the database. Two of the T.
jamesii clusters have been given the provisional names T. “vulpinea” and T. “letharii” but it looks like at least
three additional names are needed for this group.
That’s it for now. In my next post I will map host information onto this tree.
This entry was posted in Green Algal Photobionts and tagged Algae, Lichen, Phylogenetics, Trebouxia. Bookmark the permalink.
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