Much ado about plants and blogs in PLoS Biology

Some good new articles in PLoS Biology in the last few weeks worth checking out.  There is definitely a theme there if you want to look for it.  So here are some of the papers connected to that theme and even one that covers both.

Paramecium whining

I just got an announcement from Linda Sperling, announcing the publication of a paper on the Paramecium genome

Dear ciliate researcher,

We are pleased to announce that the Paramecium genome article is now available as an advanced online publication at the following address:

http://www.nature.com/nature/journal/vaop/ncurrent/abs/nature05230.html

We thank all of you for your interest and support.

Jean Cohen and Linda Sperling

Linda Sperling
Centre de Génétique Moléculaire
CNRS
Avenue de la Terrasse
91198 Gif-sur-Yvette CEDEX
FRANCE

sperling@cgm.cnrs-gif.fr
+33 (0)1 69 82 32 09 (telephone)
+33 (0)1 69 82 31 50 (fax)
http://paramecium.cgm.cnrs-gif.fr/

She sent this to an email list for ciliate researchers. I am writing about this in my blog because a blog is where you are supposed to write things these days when you are pissed off. Why am I pissed off about this? Well, the Paramecium paper makes no mention whatsoever of our paper on the genome of a close relative of Paramecium (Tetrahymena thermohila for those interested) which was published in August. And they do not even explicitly mention the Tetrahymena genome project (even though they say they took our data and used it). I guess I am not too surprised since their paper is published in Nature, which recently seems to be taking many liberties with referencing things in Open Access journals (ours was in PLoS Biology).

What is most annoying about this whole thing is that Linda Sperling is on the Scientific Advisory Board of our project, and has been privy to all of our work from the inside and was I am sure fully aware of our paper being accepted long before theirs was. Common courtesy in science would have been for them to have made a reference to our paper in press or at least our project. But for whatever reason, they carefulyl crafter their words to make no mention of our work. Interestingly, here is the email I sent to the same ciliate list on August 29, 2006

For those interested, our paper on the Tetrahymena MAC genome has been published online at PLoS Biology

http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pbio.0040286

Jonathan Eisen

Strikingly, their paper was then accepted August 31, 2006. I hate to believe in conspiracies, but it seems just a little too coincidental that their was accepted just after ours was published. And yet still no mention of our work in their paper. Hmmm …

Fortunately, since our paper was in PLoS Biology, they cannot say “sorry – we did not have access to it.” Whatever they say, I can say clearly that Linda Sperling will not be invited to our next SAB meeting.

Open Access Biology highlights – The Intriguing Life of Endosymbionts

Two new articles published in the last issue of PLoS Biology bring forth some wildly interesting details about the lives of endosymbiotic bacteria.

One of the articles is about the role Wolbachia may play in speciation in Drosophila species. Wolbachia are a type of bacteira that are found to infect a wide diversity of invertebrate species. These bacteria are transmitted directly from mother to offspring much like mitochondria. Interestingly, many have evolved specialized means of negatively impacting male offspring. In the PLoS Biology study, the researchers were working on a type of Wolbachia known to cause cytoplasmic incompatability in which infected male offspring cannot produce offspring with uninfected females. Since these males can produce offspring with infected females, this helps contribute to the spread of the Wolbachia in the population. To make a long story short, the current paper proposes that not only can Wolbachia apparently lead to speciation through behavioral affects on the host, but that these affects can be stimulated even in species not infected by Wolbachia, if another similar species in the same area is infected. To learn more about the study read the synopsis here. I am personally interested in this story because we published the first Wolbachia genome a few years ago in PLoS Biology.

The second story to me is even more interesting. This relates to a bacterial symbiont that is found in the gut of a stinkbug species. The paper is important because the symbiont in this case does not live inside the cells of its host as do many other gut symbionts of insects. Instead, the symbiont lives in an extracellular capsule. Interestingly, the symbiont is transmitted to offspring not directly in eggs as in many other symbionts, but indirectly. The mother deposits a mass of the bacteria near the eggs and these are then consumed by the young just after hatching (the video of this is amazing).

The paper shows that these symbionts possess many of the genomic features found in other transmissable symbionts – including small genomes, high AT contents, and high rates of evolution (you can read more about this in my recent paper on symbionts of the glassy winged sharpshooter here or in my earlier blog). Many previously thought that these genomic features were related to the intracellular lifestyle of symbionts. But given that the same features are found in these extracellular symbionts, this suggests that the shared genome features are probably related to experiencing population bottlenecks in transmission from mother to offspring. See the synopsis of the paper here.

Tackling the hairy beast – Tetrahymena genome

ResearchBlogging.org

Just thought I would put out a little self-promotional posting here on a paper we have published today on the genome of a very interesting organism called Tetrahymena thermophila. This organism is a single-celled eukaryote that lives in fresh water ponds.

This species has served as a powerful model organism for studies of the workings of eukaryotic cells. Studies of this species have led to some fundamental discoveries about how life works. For example, telomerase, the enzyme that helps keep the ends of linear chromsomes from degrading, was discovered in this species. This may not seem too important, but many folks think that degradation of chromosome ends in humans is involved in aging. Perhaps even more importantly, (to me at least) studies of this species were fundamental to the discovery that RNA can be an enzyme. This discovery of catalytic RNA revolutionized our understanding of how cells work and how life evolved. Tom Cech and Sidney Altman were given the Nobel Prize in 1989 for this discovery.

Many (including myself) believe that having the genome sequence of this species will further spur research and its use as a model organism. In addition, we believe that some of the findings we report in our paper will further cement the importace of this species. For example, this species, though single celed, encodes nearly as many proteins as humans and possesses many processes and pathways shared with animals but missing from other model single celled species.

The project that led to this publication was undertaken while I was at TIGR (The Institute for Genomic Research) and involved a collaboration among people at dozens of research institutions around the world. It all started in 2001 when Ed Orias and his colleagues sought to see if anyone at TIGR would be interested in putting in a grant to sequence this species’ genome. I responded to the email saying I was interested, especially since I had interacted with multiple people who used this species as a model system (e.g., Laura Landweber at Princeton and Laura Katz at Smith). So I went to a FASEB meeting where the Tetrahymena Genome Steering Committee was meeting and discussed with them how TIGR might help sequence the genome. And after talking to other genome centers, they selected TIGR to put in a grant proposal with them.

We ended up getting funding from two grant proposals – one from NIGMS and the other from the NSF Microbial Genome Sequencing Program. The sequencing was done in a rapid burst at the new Joint Technology Center which TIGR shares with the Venter Institute. And then we spent ~1.5 years analyzing the sequence data (and assemblies) that came out and in the end we fortunately were able to get our paper into PLoS Biology, in my opinion the best place available to publish biology research.

Importantly PLoS Biology is Open Access which allows anyone anywhere to read about our work. This goes well with the free and open release we made of the genome sequence data. In fact, many people published papers on the genome before we did (sometimes scooping us). In the end, I accepted the risks of releasing the genome data with no restrictions inexchange for advancing research on this organisms. I think this risk was well worth it as we still got our big paper published and the field has advanced more rapidly than if we had not released the data.

Other links that may be of interest to people:

Eisen, J., Coyne, R., Wu, M., Wu, D., Thiagarajan, M., Wortman, J., Badger, J., Ren, Q., Amedeo, P., Jones, K., Tallon, L., Delcher, A., Salzberg, S., Silva, J., Haas, B., Majoros, W., Farzad, M., Carlton, J., Smith, R., Garg, J., Pearlman, R., Karrer, K., Sun, L., Manning, G., Elde, N., Turkewitz, A., Asai, D., Wilkes, D., Wang, Y., Cai, H., Collins, K., Stewart, B., Lee, S., Wilamowska, K., Weinberg, Z., Ruzzo, W., Wloga, D., Gaertig, J., Frankel, J., Tsao, C., Gorovsky, M., Keeling, P., Waller, R., Patron, N., Cherry, J., Stover, N., Krieger, C., del Toro, C., Ryder, H., Williamson, S., Barbeau, R., Hamilton, E., & Orias, E. (2006). Macronuclear Genome Sequence of the Ciliate Tetrahymena thermophila, a Model Eukaryote PLoS Biology, 4 (9) DOI: 10.1371/journal.pbio.0040286