CEGMA - a pipeline to accurately annotate core genes in eukaryotic genomes

Instead of relying solely on N50 or other simple measures, Assemblathon-2 paper came up with many novel ways to judge qualities of genome assembly and one of them is CEGMA. CEG here stands for ‘core eukaryotic genes’ and represents a set of 458 highly conserved genes present in all eukaryotes.

The original CEGMA paper was published in 2007, but its importance has only gone up in recent years given that so many highly complex genomes are being assembled from NGS libraries.

In this article, we introduce a computational method to obtain a set of reliable gene structures in any eukaryotic genome. Our goal is not to provide the complete catalog of genes in a genome, but to generate a highly accurate set of genes for those genomes without experimental data. The strategy relies on a simple fact: some highly conserved proteins are encoded in essentially all eukaryotic genomes. We use the KOGs database to build a set of these highly conserved, ubiquitous proteins. We call these protein families core proteins and the genes that encode them core genes. We define a set of 458 core proteins and present an accurate mapping protocol that maps the likely ortholog of each gene in a genomic sequence and then predicts the exonintron structure. We show that our procedure does not need any previous knowledge of the target genome, that it is highly accurate, and that it can be used even for those genomes in draft stages.