Prediction of effective genome size in metagenomic samples 英文参考文献.docVIP

Open Access M d 2007RaesetVoal.lumeetho8, Issue 1, Article R10 Prediction of effective genome size in metagenomic samples ¤ ¤ Jeroen Raes *, Jan O Korbel *?, Martin J Lercher*, Christian von Mering*? and Peer Bork* Addresses: *European Molecular Biology Laboratory, Meyerhofstrasse 1, D-69117 Heidelberg, Germany. ?Molecular Biophysics Biochemistry Department, Yale University, Whitney Avenue, New Haven, Connecticut, USA. ?Institute of Molecular Biology, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland. ¤ These authors contributed equally to this work. Correspondence: Peer Bork. Email: bork@embl.de Published: 15 January 2007 Received: 29 August 2006 Revised: 31 October 2006 Accepted: 15 January 2007 Genome Biology 2007, 8:R10 (doi:10.1186/gb-2007-8-1-r10) The electronic version of this article is the complete one and can be found online at /2007/8/1/R10 ? 2006 Raes et al.; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. PredictingrepadAs.n/opveeffectivel computgenomeational asizepproach shows a link between genome size and habitat from analysis of environmental metagenomic DNA 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.