Scutopus ventrolineatus mitochondrial genome published

A couple weeks ago the first aplacophoran mitochondrial genome was published by Davide Osca et al.! Way to go Zardoya lab!

Scutopus is considerate enough to have a pretty typical molluscan mitochondrial genome organization and it is not an especially long branch. I was very impressed by the mitochondrial gene trees, which largely agree with the 2011 duelling Nature mollusc phylogenomics papers. When I've tried to make mollusc mt genome trees before they've turned out pretty wacky (but it seems the authors wisely avoided some of the more long-branched taxa). They also conducted analyses including nuclear ribosomal proteins from a diverse sampling of molluscs both with and without the mitochondrial data and found support for Aculifera and Aplacophora (albeit with weak support in some analyses).

Scutopus is actually the second aplacophoran mitochondrial genome that is publicly available. The mitochondrial genome of Chaetoderma nitidulum is also available on NCBI but it was never published.

Link to the paper:
http://www.biomedcentral.com/1471-2148/14/197/

Scutopus ventrolineatus
(photo by Christiane Todt)

2014 Frontiers in Phylogenetics Symposium

Last week I presented a talk entitled "Deep metazoan phylogeny and the utility of taxon-specific ortholog sets" at the Smithsonian Frontiers in Phylogenetics symposium. This year's theme was Genome Scale Phylogenetics: Analyzing the Data. My talk was on my research using custom, taxon-specific core ortholog sets in the program HaMStR as a computationally tractable alternative to more computationally intensive all-versus-all BLAST-based approaches (e.g., OrthoMCL) or similar approaches (e.g., OMA).

Here's a link to a video of the talk for anyone interested in checking it out (Guillermo's introduction for my talk starts around 1:28 in)
http://www.ustream.tv/recorded/52713111

Here's the abstract:
Orthology determination based on a set of pre-defined orthologs is a powerful and computationally tractable approach to identify molecular data suitable for genome-scale phylogenetics. However, genes that are single copy among the taxa used to prepare such a set may have undergone lineage-specific duplications in other clades, suggesting taxon-specific core ortholog sets are advantageous. I will present studies of deep metazoan phylogeny based on custom sets of core orthologs that are specific to the taxon sampling of a given project. By selecting a small but representative subset of around 5-10 taxa with high quality transcriptomes (and ideally at least one taxon with a high quality genome) and using all-versus-all BLAST, OrthoMCL, and our PhyloTreePruner software, HaMStR core ortholog sets that are specific to a group of interest can easily be generated. Importantly, these core ortholog sets tend to contain many more genes than the sets based on broader taxon sampling. Starting from a larger pool of orthologous sequences allows for stricter gene selection criteria, enabling the investigator to exclude genes with e.g., large amounts of missing data, few unambiguously aligned positions, a high rate of evolution, different rates of evolution among taxa, etc.

International Congress on Invertebrate Morphology 3

Last month I attended the International Congress on Invertebrate Morphology in Berlin, Germany. This has quickly become my favorite meeting. A lot of really strong research was presented here and it was really nice to catch up with a lot of old friends. This ICIM had a very strong molluscan showing with a pleasantly surprising majority of the mollusc talks / posters dealing, at least in part, with aculiferans!

Link to the program:
http://www.icim3.org/program.htm

Talks dealing with aculiferans
Evolution and development of photoreceptors in Polyplacophora
Ollie Vöcking

Hox gene expression in polyplacophoran molluscs
Martin Fritsch

It's only a model: seeking an osphradium in more obscure molluscs
Julia Sigwart

Development of the metanephridial and coelomic system in molluscs – more variability than allowed? 
Gerhard Haszprunar

EvoDevo and its bearing on molluscan phylogeny. 
Andi Wanninger

Posters dealing with aculiferans
New insights into molluscan biomineralization through studies of aculiferans
Kevin Kocot

Chitons that live in the dark can see light (Mollusca, Polyplacophora, Lepidopleurida)
Julia Sigwart and Lauren Sumner-Rooney 

A new class of aplacophoran mollusk – or “just” a footless solenogaster?
Christiane Todt  
 
 

Successful Friday Harbor Labs trip

Last week I visited Friday Harbor Labs to collect aplacophorans and chiton's for biomineralization studies. I managed to get about 10 specimens of a soon-to-be described species of Hypomenia and 3 specimens of a new Macellomenia we're working on describing (see pic below).

Macellomenia sp. "schanderi"

The Marine Invertebrate Zoology course shared an unusual mutant Tonicella line at a lacking the normal shell pigment pattern.

Tonicella lineata "blue albino"

Kevin Kocot 2014 Northern Hemisphere Tour

I'm still waiting on official approval from UQ's powers that be, but I will be visiting the U.S. and Germany this July-August.

July 9-15: Auburn (with a trip to NC for friends' wedding)
July 15-21: Friday Harbor Labs
July 21-31: Auburn
August 1-10: Berlin (for the International Conference of Invertebrate Morphology)
August 10-24: Auburn, St. Louis, and Destin, FL (for my sissie's wedding!). Details forthcoming...

My cup overflowith

One challenge I've faced in my project studying aculiferan biomineralization has been getting samples of aplacophorans suitable for RNA-based work. Often times, aplacs can be rare and I really need multiple specimens to have biological replicates for some of the experiments I plan to do. I had hoped to collect Epimenia here in Australia but so far that hasn't panned out. Fortunately, my wonderful collaborator and friend Dr. Christiane Todt was just on a cruise and collected tons of specimens of Stylomenia sulcodoryata and Chaetoderma nitidulum as well as one specimen each of Neomenia carinata and Scutopus ventrolineatus. Now I'm armed with plenty of material for traditional transcriptomes of mantle tissue a well as laser capture microdsisection and CEL-seq and in situ hybridization to look at gene expression in the cells secreting sclerites in these beasts as well as proteomic work looking at the protein component of the sclerites.

Stylomenia sulcodoryata
(source: http://www.artsdatabanken.no/Article/Article/398)

Chaetoderma
(source: http://www.whoi.edu/science/B/aplacophora/defchaetneo.html)

Pleurobrachia bachei (Ctenophora) genome published in Nature this week

No, it's not an aculiferan mollusc but I just had to post about this...

Our paper on the genome of the ctenophore Pleurobrachia bachei was published this week in Nature! I'm really proud to have had a part in this exciting work and I'm eager to see what the future holds for some of the unanswered questions and surprising findings made here and by the Mnemiopsis leidyi genome study.

 

Link to the paper itself at Nature

Link to News & Views write-up by Andy Hejnol