In a new paper out in PNAS, Michael Lynch and colleagues report their findings from a comparative whole-genome pyrosequencing of yeast genomes. A total of four haploid genomes were sequenced in the study using the 454 platform. Surprisingly, the researchers found that the number of large scale genome events (insertions, deletions, duplications etc) was comparable to the number of point mutations that occurred.
Sequencing was done with highly variable coverage along the genomes and this have caused the authors to hypothesize that the yeast clones are actually not truly haploid but seem to be entering a partly diploid stage where some chromosomes are diploid and some haploid.
GenomeWeb has an interview with the first author where he elaborates on this
Today, a U.S. Department of Agriculture team, funded with more than $10 million from Mars Inc., announced that they will start sequencing the cocoa genome. The results are likely to help in the battle against cocoa plant diseases and, much more importantly, they could also lead to better-tasting chocolate.
A lot of people would probably also be thankful if the results could guide us towards a diet version with the same taste 
Update: IMB has posted a video promotion of this research project at YouTube.
Helicos Biosciences have announced a partnership with the Children’s Oncology Group (COG) where Helicos will use their NGS platform to experimentally characterize different tissue types from patients with Ewing’s sarcoma, a rare cancer.
In their press release they state that:
These samples include a normal bone marrow sample and tumor cell lines derived from a Ewing’s sarcoma primary tumor biopsy and the metastasis from the same patient obtained after two cycles of chemotherapy. It is hoped that an in-depth comparison of genomic DNA sequence and RNA expression between the normal tissue, primary tumor, and treatment resistant metastasis will reveal structural and functional genomic changes associated with clinical aggressiveness and treatment resistance.
The study will include an ambitious range of applications for NGS technology as it will aim to identify rare mutations, polymorphisms, copy number variants, true whole-genome RNA transcriptional activity, and global methylation patterns.
The press release does not mention anything about the tissue sample sizes that will be collected as starting material, so I guess I will have to read the papers at some point . However, the ability to characterize very small tissue samples is one of the most interesting features of the single molecule sequencing technologies, so it will be interesting to see how the technology performs for this type of problems.
I once had the pleasure of visiting David Lambert, an expert and pioneer in ancient DNA studies. With Dave I had some of the most interesting and thought provoking discussion about biology, that I have ever had.
Now Dave and his colleagues have a new review out in TREE on New developments in ancient genomics that I can’t wait to read when I get back to work next week.
Here is the abstract:
Ancient DNA research is on the crest of a ‘third wave’ of progress due to the introduction of a new generation of DNA sequencing technologies. Here we review the advantages and disadvantages of the four new DNA sequencers that are becoming available to researchers. These machines now allow the recovery of orders of magnitude more DNA sequence data, albeit as short sequence reads. Hence, the potential reassembly of complete ancient genomes seems imminent, and when used to screen libraries of ancient sequences, these methods are cost effective. This new wealth of data is also likely to herald investigations into the functional properties of extinct genes and gene complexes and will improve our understanding of the biological basis of extinct phenotypes.
PolITiGenomics have posted some details about the upcoming update to the 454 system.
According to the blog, the next upgrade will be called Titanium and will have twice the number of cycles increasing the average read length from 250 to around 400 bases. Furthermore, the new version will have smaller, more densely packed wells on the picotiter plate which will increases the number of DNA fragments sequenced per run. All together, 454 FLX Titanium runs will quintuple their data output from 100 Mb to about 500 Mb.
Obviously, the increased data amount will put even more strain on the downstream image- and sequence analyses pipelines.
