Assessing the gene space in draft genomes.
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.
Parra
Genis
G
UC Davis Genome Center, University of California Davis, Davis, CA, USA.
Bradnam
Keith
K
Ning
Zemin
Z
Keane
Thomas
T
Korf
Ian
I
D000818:Animals; D002874:Chromosome Mapping; D005796:Genes; D023281:Genomics; D006801:Humans; D011506:Proteins / Q000235:genetics
D011506:Proteins