Posts Tagged ‘RIP’

Next-Generation Sequencing of Sordaria Genome

May 1st, 2010

sordariaAs I reported earlier, the genome of the filamentous pathogenic fungus Grosmannia clavigera has been assembled from a combination of Sanger, 454, and Solexa sequence data.  The genome of the giant panda (Ailuropoda melanoleura) — specifically of the female Beijing Olympics mascot Jingjing — has also been determined using short-read Illumina sequencing technology, “un tour de force” for such a complex genome. This was the first reported de novo assembly of a large mammalian genome achieved using next-generation sequencing methods. These two studies demonstrated the feasibility for using next-generation sequencing technologies (454 & Illumina) for accurate, cost-effective and rapid de novo assembly of eukaryotic genomes. In a recent issue of PLoS Genetics, Nowrousian et al. published the de novo assembly of the 40 Mb genome of Sordaria macrospora from short sequence reads. They generated 3.4 Gb of sequence data from four lanes from a 300 bp library and three lanes from a 500 bp library using the Illumina GA. In addition, 415 Mb of sequence data were produced by 454 sequencing. Assembly of the Solexa reads only as well as the combined Solexa and 454 reads was carried out with the Velvet assembler.

Diego Martinez and Mary Anne Nelson discuss the technical merits of this work in their Perspective paper in PLoS Genetics.

The natural habitat of the saprobic S. macrospora is herbivore dung. With 10,789 predicted genes, the gene repertoire in S. macrospora is similar to that of N. crassaS. macrospora harbors duplications of several genes involved in self/nonself-recognition and contains more polyketide biosynthesis genes than N. crassa. One putative polyketide biosynthesis (PKS) cluster might have been acquired through horizontal gene transfer (HGT) from a distantly related ascomycete group. This finding supports recent suggestions that HGT is widespread in fungi both for the transfer of single genes, clustered genes like PKS genes, or even larger stretches of DNA up to whole chromosomes as was found in the phytopathogenic fungus Nectria haematococca. The S. macrospora genome contains even fewer transposable elements than its closest relative, Neurospora crassa, despite the absence of active RIP.

Nowrousian M, Stajich JE, Chu M, Engh I, Espagne E, et al. (2010) De novo Assembly of a 40 Mb Eukaryotic Genome from Short Sequence Reads: Sordaria macrospora, a Model Organism for Fungal Morphogenesis. PLoS Genet 6(4): e1000891. doi:10.1371/journal.pgen.1000891.

Li et al. (2010) The sequence and de novo assembly of the giant panda genome. Nature 463, 311-317.

Martinez DA, Nelson MA (2010) The Next Generation Becomes the Now Generation. PLoS Genet 6(4): e1000906.

Photo: S. macrocarpa protoperithecium (Nowrousian et al. 2010. PLoS Genetics).).