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Assessing the gene space in draft genomes.

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.

SUBMITTER: Parra G

PROVIDER: S-EPMC2615622 | biostudies-literature | 2009 Jan

REPOSITORIES: biostudies-literature

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Assessing the gene space in draft genomes.

Parra Genis G Bradnam Keith K Ning Zemin Z Keane Thomas T Korf Ian I

Nucleic acids research 20081128 1

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 ...[more]

PMID: 19042974

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