3.12.2007

The Shortest Genome Sequence Paper!

The JGI Los Alamos National Lab has just published one of the shortest (if not the shortest) genome sequence paper. The paper is published online ahead of print in the Journal of Bacteriology and report on the genome sequence of Bacillus thuringiensis Al Hakam, a strain isolated in Iraq by the United Nation Special Commission. The author list is about 1 and 1/2 pages and the text not much longer. This paper was published with the sole intention to announce the release of the sequence in GenBank. There is no science beside the fact that the cry, cyt and vip genes (toxins genes) were not found, did you need the genome for get to that conclusion?
Is this where the future of genome sequence papers is heading? Announcements for GenBank Release. I'm not sure if I like this.

We are now sequencing several strains of the same species and I think it can become somewhat of a problem because some of the sequences turn out to not be very informative. But are we selecting the strain to sequence rationally? A lot of work goes into sequencing, assembling, closing, annotating and analyzing a genome. If nothing novel or interesting comes out of this, that is a lot time and effort wasted without returns for the people involved in terms of papers. I think this work should still be published. I had suggested a while back to convince a journal (PLoS?) to have one issue (or part of) or one section in each issue dedicated to genome sequences, just like NAR does for databases. I think these types of paper would fit better in that context. As a standalone paper in the middle of a new issue of the Journal of Bacteriology might not be the best use of journal pages. What about a community page, just like in PLoS Biology? Wouldn't it be a better format? I think it is important to recognize the work that has gone into sequencing and analysis a genome, but what is the best format? Genome sequences are still very important resources that the scientific community uses. Are we getting to the point where a genome sequence is to be released into GenBank and does not warrant a publication unless its analysis advances scientific knowledge? Just what happened to gene sequences not that long ago!

9 comments:

Jonathan Eisen said...

Actually I have already discussed this issue with multiple journals. PLoS One is VERY interested in being a place to publish such "Marker Papers" and we will be submitting some there. I have also discussed with multiple genome centers the possibility of starting BiomedCentral Genome Sequences or something like that, but PLoS One seemed like a fine option. The advantage of PLoS One over J Bact is you could take the content, since it is all Open Access and make your own mini-journal out of it.

Jonathan Badger said...

With the long author list and short text it reminds me a bit of the Annals of Improbable Research's "The Effect of Peanut Butter on the Rotation of the Earth" -- a long, long, author list and the text "As far as we can determine, there is no effect."

Jacques Ravel said...

We will have many of those coming out, I think this is the way to go. I am interested in the BiomedCentral genome sequences idea. I agree PLoS ONE would also be great. Such a long author list for such a short paper is still a bit over the top for me. What did some of those people do? Most of them are somewhat senior!! I guess sequencing a microbial genome for which many very very close relatives are available at 24X (no kidding read the paper!) required a lot of people!!!!

Steve said...

This is not that different from the original idea behind the journal "DNA Sequence," which was the brainchild of Bart Barrell. I have to say that it was not a great success.

Steve said...

There was something wrong with my linkfor the journal "DNA Sequence." It should have been
http://www.tandf.co.uk/journals/journal.asp?issn=1042-5179&linktype=5

Mark Pallen said...

I am old enough to remember the old days when the sequence of a bacterial gene was enough to justify a paper. Then it slipped down to a section called "For the Record" in Nucleic Acids Research, which worked for a few years before gene sequences became unpublishable. I am sure genome sequences will follow the same trajectory. The problems arise when the rules of the game and expectations of output change within the lifetime of a research project.

We just had a genome paper out in PLoS One. We made several earlier attempts to get the paper published elsewhere, but were hampered by the lack of biological message and uncertainties about what our findings meant (a European isolate of Francisella turned out to be only 8 SNPs different from a US lab strain). PLoS One saved the day for us, particularly, as Jacques points out, completing a genome still depends on a lot of work from a lot of people (although not as much as it used to).

However, I do wonder whether even the PLoS One option will be scalable when next generation sequencing really kicks in. I guess papers will have to describe comparisons between genomes of half a dozen or a dozen strains to be publishable.

Lacy said...

Good post.

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