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Prediction of effective genome size in metagenomic samples

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Item Type:Article
Title:Prediction of effective genome size in metagenomic samples
Creators Name:Raes, J. and Korbel, J.O. and Lercher, M.J. and von Mering, C. and Bork, P.
Abstract:We introduce a novel computational approach to predict effective genome size (EGS - a measure that includes multiple plasmid copies, inserted sequences and associated phages and viruses) from short sequencing reads of environmental genomics (or metagenomics) projects. We observe considerable EGS differences between environments and link this with ecological complexity as well as species composition (i.e. eukaryotes). For example, we estimate EGS in a complex, organism-dense farm soil sample at about 6.3 Mb whereas that of the bacteria therein is only 4.7 Mb; for bacteria in a nutrient-poor, organism-sparse ocean surface water sample, EGS is as low as 1.6 Mb. The method also permits evaluation of completion status and assembly bias in single-genome sequencing projects.
Keywords:Artifacts, Bacterial Genome, DNA Sequence Analysis, Environment, Genetic Markers, Genetic Models, Genomics, Prokaryotic Cells, Reproducibility of Results
Source:Genome Biology
ISSN:1465-6906
Publisher:BioMed Central (U.K.)
Volume:8
Number:1
Page Range:R10
Date:15 January 2007
Official Publication:https://doi.org/10.1186/gb-2007-8-1-r10
PubMed:View item in PubMed

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