title: 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.
authors.affiliation: UC Davis Genome Center, University of California Davis, Davis, CA, USA.
authors.forename: Genis
authors.initials: G
authors.lastname: Parra
authors.forename: Keith
authors.initials: K
authors.lastname: Bradnam
authors.forename: Zemin
authors.initials: Z
authors.lastname: Ning
authors.forename: Thomas
authors.initials: T
authors.lastname: Keane
authors.forename: Ian
authors.initials: I
authors.lastname: Korf
mesh_terms: D000818:Animals; D002874:Chromosome Mapping; D005796:Genes; D023281:Genomics; D006801:Humans; D011506:Proteins / Q000235:genetics
chemical_list: D011506:Proteins