After a long haul of 5 years, my group at the University of Colorado School of Medicine finally published the Burmese python genome. This was published in PNAS concurrently with the king cobra genome (on which we are also co-authors), the first two complete and annotated snake genomes published.
Also please see the write-up in Science on "Secrets of Snakes". They do a nice job of covering the genomes as well as some other topics in snake evolution. Especially nice to see them mention our earlier work showing that snake mitochondrial genomes "evolve faster" than other genomes (due to a massive burst of functional redesign). When Todd and I came up with the plan to sequence the python genome, we wanted to see if this was true for snakes' nuclear genomes as well, and it is a major outcome that it seems to be so. The python was a great candidate because of its extreme metabolic changes, (documented by Stephen Secor).
Congratulations to all group members, especially first author Todd Castoe (for the past year an assistant professor at UT Arlington), second author Jason de Koning (for the past year an assistant professor at U Calgary), and third author Kathryn Hall, as well as the rest of the group including Rob Ruggiero, Wanjun Gu, Alex Poole, Jill Castoe, Juan Daza and Daniel Polanco.
Also particular congratulations to Michael Richardson's king cobra group in the Netherlands, including co-first authors Freek Vonk and Nicholas Casewell, and third author Christiaan Henkel. This was a really nice example of two potentially competing groups instead working and cooperating together and sharing data and analyses to create two coordinated contributions that enhance each other. Michael, Freek, Nick, and Christiaan are co-authors on the Burmese python paper, and Todd, Jason, and I are co-authors on the king cobra paper.
I also want to thank the entire group that contributed to the Burmese python paper (this tends to get lost in the news write-ups). In addition to the University of Colorado School of Medicine, contributions cxame from the University of Texas at Arlington (Todd's new lab, as well as independent labs of Matt Fujita and Eric Smith) and the University of Calgary (Jason's new lab), as well as Leiden University, Naturalis Biodiversity Center (Freek's new affiliation in The Netherlands), Bangor University and the Liverpool University of Tropical Medicine (Nick's affiliations in Wales and England), the University of Chicago, Universidad de Antiochia (Columbia, where Juan is now assistant professor), Southeast University (China), Linfield College (Oregon), Amplicon Express (Washington), Mississipi State University, University of Utah, University of Toronto, Washington University, Virginia Commonwealth University, Texas Tech University, ZF Screens (The Netherlands, Christiaan's new home), The University of Northern Colorado, Iowa State University, and the University of Alabama.
That is 6 countries counting USA, Canada (2), The Netherlands (3), United Kingdom (2), China, and Columbia; 8 if you count Wales and Texas as separate countries. Who knew that the US motto was "Government Made Easy"?
In the US, the work includes laboratories from Colorado (2), Texas (4), Illinois, Oregon, Washington, Mississippi, Virginia, Iowa, and Alabama.
Also a major shout-out to co-author Stephen Secor, who discovered the python metabolic and heart and other organ growth story many years ago, and has continued to be a leader in developing this story.
Finally, thanks to Jim McGuire (previously a colleague at LSU, now at UC Berkeley) and Frank Burbrink (my first postdoc, now at SUNY Staten Island; the one with all the tattoos) for getting me to focus on snakes in the first place (the original mitochondrial adaptive redesign and convergence stories), and to Todd Castoe and Steve Mackessy (the rattlesnake venom guy) for keeping me interested in them.
A few cool python or cobralinks (pythons are a problem in Florida): stalking, taxidermy, who would win battle.
News coverage of this all over the place. New Scientist, Science, Huffington Post, NBC, BBC, etc. Original articles by Bob Holmes at New Scientist, Kerry Sheridan at Agence France-Presse and AFP, Tina Saey at Science News, and David Kelly at Denver News, at least. Always entertaining to see what they emphasized and what they got right or wrong (or somewhere in between).
Note: there is a typo in the GenBank number lower down in the paper (swap of last two numbers). However, if you follow the link at the bottom right of the front page, it will lead you correctly to the assembly information.
See our guest blog post on "Adaptation and Convergence in Regulatory Systems" at phylogenomics blog "This Tree of Life"
We invite you to attend our third (now SMBE Satellite) meeting/workshop on Mechanisms of Protein Evolution (Thermodynamics, Phylogenetics, and Structure) in Denver, 2014. This will probably be in early February, so mark your calendars. Organizers: David Pollock, Richard Goldstein, and Belinda Chang.
We are always looking for multiple talented evolutionary biologists with a mixture of training in mathematical, computational, and molecular laboratory techniques. We are especially interested in candidates at the postdoctoral level; please contact us well in advance to arrange funding. Contact David Pollock.
Postdocs Todd Castoe and Jason de Koning both started new assistant professor positions Fall 2012, and Jill Castoe has a new genomics core job. Todd and Jill went to the University of Texas Arlington, and Jason went to the University of Calgary. Vijetha Vemulapalli got her PhD and has started a new job at Berg Biosystems in Boston, and Ken Daigaro Yokoyama is doing a second postdoc in Illinois.
New lab members are Seena Shah (postdoc), Jonathan Shortt (HMGGP), Aaron Wacholder (IQ Bio), and Stephen Pollard (Structure and Biochem). Kara Schmitz, Aviva Getschel, Dillon Riebel, and Monica Narona completed rotations or internships this summer and Fall. Corey Cox, Jaime Merlano, and Robert Ruggiero count as the old guard now.
A new version of PLEX (0.95) is up, along with a new extended user manual.
I uploaded Saturate code, but use at your own risk. Please let me know if you get it to work.
We've aborted the laboratory blog. May try again when we move to a better web service.
SP transcription factor paralogs and DNA binding sites coevolve and adaptively converge in mammals and birds, Yokoyama and Pollock, Genome Biology and Evolution (in press; abstract). 2012
Phylogenetics, Likelihood, Evolution and Complexity (PLEX), de Koning et al, Bioinformatics (Advance Access). 2012
Amino acid coevolution induces an evolutionary Stokes shift, Pollock et al, PNAS. 2012
Rapid microsatellite identification from Illumina paired-end genomic sequencing in two birds and a snake, Castoe et al, PLoS One. 2012
Modeling Protein Evolution, Pollock and Goldstein, in Dokholyan, Computational Modeling of Biological Systems. 2012
Germline TRAV5D-4 T Cell Receptor Sequence Targets a Primary Insulin Peptide of NOD Mice, Nakayama et al, Diabetes 2012
Repetitive elements may comprise over two-thirds of the human genome, de Koning et al, PLoS Genet. 2011
Bayesian analysis of high-throughput quantitative measurement of protein-DNA interactions, Pollock, et al. PLoS One. 2011
The genome of the green anole lizard and a comparative analysis with birds and mammals, Alföldi, et al. Nature. 2011
Sequencing the genome of the Burmese python (Python molurus bivittatus) as a model for studying extreme adaptations in snakes, Castoe, et al, Genome Biol. 2011
Discovery of highly divergent repeat landscapes in snake genomes using high-throughput sequencing, Castoe, et al, Genome Biol Evol. 2011
The Genomics course is planned again for Spring 2014. This will be taught as an intensive 3-week session. We are also developing a course in Advanced Scientific Programming for Spring 2014. Please contact David Pollock if interested.
Updating programs: PLEX, PCLOUDS, CodeMLAncestral, TFCoEvolve, SULDEX
"I would describe...how passionately, how incandescently, how incestuously...art and science meet in an insect" Nabokov (now vindicated)
The Genome 10K project is moving forward, a project to assemble a collection of DNA sequences representing the genomes of 10,000 vertebrate species. Working towards integrating our work on snake and mammalian genomics.
NLM Training Grant postdoctoral fellowships are available yearly on a competitive basis. See Computational Bioscience Program for more information.