Archive for November, 2009

Metagenomics of windshield splatters

November 30th, 2009

weld-splatter-park-2Metagenomics involves sampling and sequencing the genome sequences of a community of organisms inhabiting a common environment, ocean, soil, or human gut. In their paper “Windshield splatter analysis with the Galaxy metagenomic pipeline” Kosakovsky Pond et al. applied metagenomic methodologies to directly determine the taxonomic composition of bugs collected by the front bumper and windshield of a 2006 Dodge Caravan. As every driver knows, the windshield of a moving vehicle is subjected to numerous insect strikes and this study shows that it can be used as a collection device for representative sampling of eukaryotes from our surrounding environment. The 454 reads were analyzed using a comprehensive pipeline – the Galaxy platform – for phylogenetic profiling of metagenomic samples that includes all steps from processing and quality control of data generated by next-generation sequencing technologies to statistical analyses and data visualization (http://galaxyproject.org). The number of sequencing reads has been used as a proxy for the relative abundance of taxa and therefore used to contrast biodiversity estimates between geographic locations. Most reads from two trips in in the northeastern United States  map to bacterial species. Aside from green plants and a few animal roadkills, two insect groups, Diptera and Hemiptera, represented the majority of eukaryotic reads in both samples. This study demonstrates that 454 sequencing technology can identify eukaryotic taxa from random reads generated from environmental samples and it is it possible to assess species abundance between geographic locations.

Kosakovsky Pond S, Wadhawan S, Chiaromonte F, Ananda G, Wen-Yu Chung, Taylor J, Nekrutenko A and The Galaxy Team (2009) Windshield splatter analysis with the Galaxy metagenomic pipeline. Genome Research, http://www.genome.org/cgi/doi/10.1101/gr.094508.109.

Rose de Pré

November 8th, 2009

www.mssf.orgThe JGI have announced the pze-reheAse of the Agaricus bisporus var. bisporus (H97) v1.0 assembly. The genome size is 30.2 Mbp with an average coverage of 8.5x. based on ab initio prediction, protein alignment and ESTs, ~10,000 genes have been predicted by automated annotation. The annotation may be browsed, searched, downloaded and expanded with your curations at the Agaricus bisporus var. bisporus (H97) portal: genome.jgi-psf.org/Agabi1. Because this is a pre-release only approved users will be able to get access to this portal.

Cartoon: © www.mssf.org