Assessing the gene space in draft genomes

Nucleic Acids Res. 2009 Jan;37(1):289-97. doi: 10.1093/nar/gkn916. Epub 2008 Nov 28.


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.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Animals
  • Chromosome Mapping
  • Genes*
  • Genomics*
  • Humans
  • Proteins / genetics


  • Proteins