Cokus et al. have just published a Nature paper on shotgun bisulphite sequencing of the Arabidopsis genome. The analysis was performed by combining bisulphite treatment of genomic DNA with ultra-high-throughput sequencing using the Illumina 1G Genome Analyser and Solexa sequencing technology. The authors named this approach BS-Seq, and state that it enabled them to “describe methylation on previously inaccessible components of the genome and analyse the DNA methylation sequence composition and distribution”
A new publication by Vera et al. describes the sequencing and assembly of a large number of expressed sequence tags from the Glanville fritillary butterfly.
The authors conclude that there is good new for the species that are not in the current genomics limelight , as…
454 sequencing, when performed to provide sufficient coverage depth, allows de novo transcriptome assembly and a fast, cost-effective, and reliable method for development of functional genomic tools for nonmodel species.
A recently published study by Wommack et al. explores the power of using pyrosequencing data to characterize microbial communities. Short reads here refers to pyrosequencing data, as compared to Sanger sequencing data.
In the abstract the authors conclude that:
..more distant homologs of microbial and viral genes are not detected by short read sequences…. ..Noting the current limitation in computational approaches for analysis of short sequences, use of short read length libraries does not appear to be an appropriate tool for metagenomic characterization of microbial communities.
According to GenomeWeb, The National Institute of Dental and Craniofacial Research are releasing generous funding for research into the role of microbes in human oral health and disease using metagenomic approaches.
Research will target the total oral microbial community using metagenomic approaches built upon recent developments in DNA sequencing, gene assembly, and bioinformatics and the goal is to completely characterize all microbes and their genes in the oral environment - including bacteria, archaea, viruses, fungi, and parasites.
Illumina have announced that their scientists have sequenced the genome of an anonymous African male (Yoruba from Ibadan, Nigeria), using the Genome Analyzer.
Apparently this was a sample from the HapMap project. First analysis found a 90% coverage of the genome and claims to have discovered a million new SNP’s and to have confirmed the presence of 2.5 million previously known SNP’s.
It has been an open question how a short read technology like Illumina’s would perform in resolving a complex genome like the human one. Illumina will answer this later in the year, when they have completed some additional analysis work using both long- and short-insert read pairs to characterize known and novel structural variation in this genome.
