Category Archives: genome sequencing

Next next-gen sequencing technology

I’m not at AGBT, but Jonathan and Anthony both have coverage of Pacific Biosciences’s new sequencing technology that uses detection of DNA polymerase activity to determine sequence.  I believe some of the details are in the paper “Selective aluminum passivation for targeted immobilization of single DNA polymerase molecules in zero-mode waveguide nanostructures“, but I’ve not had a chance to read it.

More updates on Saccharomyces resequencing project at Sanger

I’ve paraphrased an email sent by David Carter to folks interested in Saccharomyces resequencing project.

The latest version of the SGRP data is on the web site and ftp site. This release is somewhat provisional, and motivated more by the fact that we have a paper deadline coming up than by any claim to finality. It should be quite a bit better than what was there before, but doesn’t have a correct treatment of transposons.

You can get the data by starting here:
http://www.sanger.ac.uk/Teams/Team71/durbin/sgrp/datadoc.shtml

There is also a new version of the browser:
http://www.sanger.ac.uk/Teams/Team71/durbin/sgrp/browser.shtml

There are a few new features in the browser which [David] is going to document over the next couple of days.

Major new features of the data are that there should be much better consistency between alignments; Solexa/Illumina data has been incorporated for the strains that had it; and the S. paradoxus alignments are based on a new assembly that created a few weeks ago and which covers about 95% of the genome; a description is at
http://www.sanger.ac.uk/Teams/Team71/durbin/sgrp/spara_assembly.shtml

Saccharomyces strain sequencing

Blogging on Peer-Reviewed ResearchWhile many strains of S. cerevisiae are being sequenced, a single strain, YJM789, isolated from the lung of an AIDS patient was sequenced a few years ago at Stanford and published this summer. The genome was described in a paper entitled “Genome sequencing and comparative analysis of Saccharomyces cerevisiae strain YJM789”.

Continue reading Saccharomyces strain sequencing

Mucor circinelloides genome update

I recently heard through the grapevine that the Mucor ircinelloides genome 4X assembly was completed by JGI and a BLAST server is available if you contact the authors. Mucorales (previously Zygomycota which is not monophyletic) includes previously sequenced Rhizopus oryzae and Phycomyces blakesleeanus which we’ve blogged about before.

Continue reading Mucor circinelloides genome update

Yeast resequencing update

Ed Louis at Nottingham sent out an email today outlining plans for publishing analyses of the Saccharomyces Genome Resequencing Project.  They are in process of analyzing the data and ask that people respect their use of the data, but also invite collaborations and companion papers.

“If anyone has done or plans on doing a global analysis with a tight clean result which you think should be included in the overview paper, please contact us [Richard Durbin and Ed Louis; emails available through above links]. The analysis would have to be complete by 14 December and you would have to be willing to have the details transparently displayed on the web pages associated with the project.”

Yes, Ecology can improve Genomics

Blogging on Peer-Reviewed ResearchFew organisms are as well understood at the genetic level as Saccharomyces cerevisiae. Given that there are more yeast geneticists than yeast genes and exemplary resources for the community (largely a result of their size), this comes as no surprise. What is curious is the large number of yeast genes for which we’ve been unable to characterize. Of the ~6000 genes currently identified in the yeast genome, 1253 have no verified function (for the uninclined, this is roughly 21% of the yeast proteome). Egads! If we can’t figure this out in yeast, what hope do we have in non-model organisms?Lourdes Peña-Castillo and Timothy R. Hughes discuss this curious observation and its cause in their report in Genetics.

Continue reading Yes, Ecology can improve Genomics

Next gen sequencing technology

Nature has an overview of what goes in and out of next generation sequencers with an interview with a smiling Chad Nusbaum from the Broad Institute. Most of these have been out and about for a while, but it seems that the hayride/bandwagon is starting to pick up more steam as GT‘s Genome Scan has several posts about sequencing referencing J. Craig V, George Church, and the Nature news article (not free).

Note that Solexa is no longer the cool name – “Genome analyzer” being the name for the machine that was previously called Solexa 1G. I’m holding out hope for funnier names in the future. I do feel that ABI’s choice of SOLiD is more exciting than 310/3700/3730 that is as inspiring as HAL9000.

But I mean if your technology is called pyrosequencing, I am hoping Roche will come up with a firey or at least smoldering play on words if they rename 454 again (GS FLX for now).

Fusarium graminearum genome published

The genome of the wheat and cereal pathogen Fusarium graminearum was published in Science this week in an article entitled “The Fusarium graminearum Genome Reveals a Link Between Localized Polymorphism and Pathogen Specializationtion”. The project was a collaboration of many different Fusarium research groups. The genome sequencing was spearheaded by the Broad Institute at Harvard and MIT and is part of a larger project to sequence several different species of Fusarium. The group sequenced a second strain in order to identify polymorphisms.

Some of the key findings

  • The presence of Repeat Induced point-mutation (RIP) has likely limited the amount of repetitive and duplicated sequences in the genome
  • Most of the genes unique to F. graminearum (and thus not present in 4 other Fusarium spp genomes) are found in the telomeres
  • Between the sequenced strains SNP density ranged from 0 to 17.5 polymorphisms per kb.
  • Some of the genes expressed uniquely during plant infection (408 total) include known virulence factors and many plant cell-wall degrading enzymes.
  • The genes showing some of the highest SNP diversity tended to be unique to Fusarium and often unique to F. graminearum