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Nucleic Acids Research Advance Access originally published online on November 28, 2008
Nucleic Acids Research 2009 37(1):289-297; doi:10.1093/nar/gkn916
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Nucleic Acids Research, 2009, Vol. 37, No. 1 289-297
© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Genomics

Assessing the gene space in draft genomes

Genis Parra1, Keith Bradnam1, Zemin Ning2, Thomas Keane2 and Ian Korf1,*

1UC Davis Genome Center, University of California Davis, Davis, CA, USA and 2The Wellcome Trust Sanger Institute, Genome Campus, Hinxton, CB10 1SA, UK

*To whom correspondence should be addressed. Tel: +1 530 754 4989; Email: ifkorf{at}ucdavis.edu

Received July 17, 2008. Revised October 28, 2008. Accepted October 30, 2008.

Genome sequencing projects have been initiated for a wide range of eukaryotes. A few projects have reached completion, but most exist as draft assemblies. As one of the main reasons to sequence a genome is to obtain its catalog of genes, an important question is how complete or completable the catalog is in unfinished genomes. To answer this question, we have identified a set of core eukaryotic genes (CEGs), that are extremely highly conserved and which we believe are present in low copy numbers in higher eukaryotes. From an analysis of a phylogenetically diverse set of eukaryotic genome assemblies, we found that the proportion of CEGs mapped in draft genomes provides a useful metric for describing the gene space, and complements the commonly used N50 length and x-fold coverage values.

The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors.


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