In PLoS Genetics this week, an international research team reports that de novo assembly of genomes from short sequence reads alone is feasible for filamentous fungi — a finding they demonstrate with their draft sequence of the Sordaria macrospora genome. The team shows that filamentous fungi, which contain few repetitive regions within their 30 to 90 Mb genomes, are amenable to de novo genomic assembly from short sequence reads alone, though a combination of Illumina/Solexa and Roche/454 sequencing "substantially improves the assembly." For their study, the team used paired-end Solexa sequencing of S. macrospora genomic DNA to 85-fold coverage and added an extra 10-fold coverage using single-end 454 sequencing. When compared with its closed sequenced relative, Neurospora crassa, the S. macrospora genome contains fewer repeat regions and more polyketide biosynthesis genes.
In a PLoS Genetics commentary, Diego Martinez and Mary Anne Nelson at the University of New Mexico write that, in genomics, "the next generation becomes the now generation." In demonstrating what the authors call the "shortcomings of next-generation technology" and post-Sanger sequencing methods, they refer to the de novo assembly of the S. macrospora genome by Nowrousian et al. "The technical merits of this publication make it an excellent starting point for future genome sequencing using post-Sanger platforms. The assembly phase has been a particular sticking point for de novo genome sequencing in eukaryotes, as the complexity of the genomes makes it difficult to correctly place short reads," the authors write, adding that "given this demonstrated success in resolving a difficult region containing duplicate genes, researchers and physicians can consider the previously unfeasible next-gen sequencing technologies when deciding whether to sequence an entire genome."
In the same journal, researchers at Stanford University report their reverse population genomic analysis of transposable elements in populations of Drosophila from contrasting climates. By integrating information from the populations based on potential environmental selective agents, population behavior, and molecular and functional information for known transposable elements and their nearby genes in the Drosophila genome, the team was able to "infer the plausible phenotypics consequences" of such insertions. The authors suggest that "adaptation to temperate environments in widespread in Drosophila and that transposable elements play a significant role in this adaptation."
A paper published in PLoS One this week reports the work of investigators at the MD Anderson Cancer Center in Houston. The authors interrogated SOX9 interaction sites in the genome of chondrocytes using ChIP-on-chip experiments with SOX9 antibodies. In hybridizing the ChIP DNA to a microarray covering 80 genes, the team deciphered hybridization peaks at several cartilage extra-cellular matrix genes. "Our results provide a broad understanding of the strategies used by a 'master' transcription factor of differentiation in control of the genetic program of chrondrocytes," the team concludes.