Extensive Error in the Number of Genes Inferred from Draft Genome Assemblies

Abstract

Current sequencing methods produce large amounts of data, but genome assemblies based on these data are often woefully incomplete. These incomplete and error-filled assemblies result in many annotation errors, especially in the number of genes present in a genome. In this paper we investigate the magnitude of the problem, both in terms of total gene number and the number of copies of genes in specific families. To do this, we compare multiple draft assemblies against higher-quality versions of the same genomes, using several new assemblies of the chicken genome based on both traditional and next-generation sequencing technologies, as well as published draft assemblies of chimpanzee. We find that upwards of 40% of all gene families are inferred to have the wrong number of genes in draft assemblies, and that these incorrect assemblies both add and subtract genes. Using simulated genome assemblies of Drosophila melanogaster, we find that the major cause of increased gene numbers in draft genomes is the fragmentation of genes onto multiple individual contigs. Finally, we demonstrate the usefulness of RNA-Seq in improving the gene annotation of draft assemblies, largely by connecting genes that have been fragmented in the assembly process.

Repeated replacement of an intrabacterial symbiont in the tripartite nested mealybug symbiosis

“…Gene annotation of low-quality draft genome assemblies is known to be problematic (51). We therefore verified that our mealybug assemblies were sufficient for our purpose of establishing gene presence or absence by comparing our gene sets with databases containing core eukaryotic [Core Eukaryotic Genes Mapping Approach (CEGMA)] and Arthropod [Benchmarking Universal Single-Copy Orthologs (BUSCO)] gene sets.…”

Comparative and functional genomics of the Lactococcus lactis taxon; insights into evolution and niche adaptation

“…Briefly, the order and orientation of contigs of such draft assemblies remains unresolved and the differentiation between traits, which are verified to be chromosomally-encoded versus plasmid-encoded, is not possible particularly when one considers plasmid integration events. Most notable, however, is the finite nature of a finished genome which facilitates the comparison of the full genetic content of a strain rather than most of the genetic content, whereas in the case of a draft genome the likelihood of error from missing genes or incorrect copy number is significantly higher [23, 24]. …”

The molecular evolution of spiggin nesting glue in sticklebacks

“…), as draft assemblies are often incorrect in annotating multigene family copy number (Denton et al . ) and whole‐genome shotgun assemblies are typically poor at adequately resolving repeat structures (She et al . ).…”