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Genome Biol. 2007;8(1):R10.

Prediction of effective genome size in metagenomic samples.

Author information

1
European Molecular Biology Laboratory, Meyerhofstrasse 1, D-69117 Heidelberg, Germany. raes@embl.de

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 ecologic complexity as well as species composition (for instance, the presence of eukaryotes). For example, we estimate EGS in a complex, organism-dense farm soil sample at about 6.3 megabases (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.

PMID:
17224063
PMCID:
PMC1839125
DOI:
10.1186/gb-2007-8-1-r10
[Indexed for MEDLINE]
Free PMC Article

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