Sunday, December 26, 2010

Marine genomes

Craig Venter's team hits again with another large-scale sequence survey. This time they report on 197 complete prokaryotic genomes from the surface ocean's plankton. Note this means roughly a 15% increase in the total number of fully-sequenced species that was available this far. What is perhaps most notable, however, is that these species belong to a largely unexplored part of earth's microbial diversity: that living in the open ocean.

They divided the sequenced genomes into two sets: 34 that seem to be ubiquitous and abundant (present in most ocean samples), and 163 that appeared only at few locations, and compared their genome contents. Widespread planktonic species seem to have reduced genomes, with several functional classes such as gene regulation, cell motility, and membrane transport highly reduced or nearly absent. 

"cryptic escape"
In light of such differences, they propose that these ubiquitous species with reduced metabolic flexibility has adapted to survive in the open ocean by "becoming invisible", that is, reducing their size and metabolism to scape from predators and survive in a poor environment.

Altenative forces driving genome reduction
It is unclear whether reduced cell density can actually serve to scape predation from viruses or plankton-grazing organisms, and this hypothesis needs further testing. This first survey only looks at big numbers, and it is for certain that future more in-depth analyses may reveal more clues on what adaptative strategies are represented by these genomes. One interesting aspect is that forces driving genome reduction here should be different from those experienced by pathogens and endosymbionts, which constitute the best studied cases of genome reduction. In contrast to pathogens and endosymbionts, which live in rich and protected environments, marine prokaryotes thrive in one of the poorest environments with respect to nutrients. Therefore it would be very enlightening to look for differences and parallelisms in these two different adaptations that resulted in streamlined genomes.

Wednesday, December 22, 2010

Useful tool:phylowidget

Hi, I wanted to share this finding (phylowidget) that is making my life easier with respect to collaborations with experimentalists that are not used to handle newick files.

 I used to send .pdf or .png figures in order to share the results on my phylogenetic analyses, but having the possibility to interactively work with the figure is much better.

 Now I can send a simple link in this way (a very simple example):'(A:0.1,B:0.2,(C:0.3,D:0.4):0.5);'

and your colleague will be able to explore it. You can play around with the layout and really generate cool images. If the tree is huge you will have to place the file somewhere and provide the URL to phylowidget. This project was developed by a student within the google's summer of code program, which highlights the interest of this initiative.

In the future we plan to have something similar implemented in ETE.

Tuesday, December 21, 2010

Hello world

This is my first appearance in the so-called blogosfere and, to be honest, I don't know how long will it take before I get extinct.