Assessing the gene space in draft genomes

Genis Parra, Keith Bradnam, Zemin Ning, Thomas Keane, Ian F Korf

Research output: Contribution to journalArticle

301 Scopus citations

Abstract

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.

Original languageEnglish (US)
Pages (from-to)289-297
Number of pages9
JournalNucleic Acids Research
Volume37
Issue number1
DOIs
StatePublished - 2009

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ASJC Scopus subject areas

  • Genetics

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