Abstract
Finished genome sequences and assemblies are available for only a few vertebrates. Thus, investigators studying many species must rely on draft genomes. Using the rhesus macaque as an example, we document the effects of sequencing errors, gaps in sequence and misassemblies on one automated gene model pipeline, Gnomon. The combination of draft genome with automated gene finding software can result in spurious sequences. We estimate that approximately 50% of the rhesus gene models are missing, incomplete or incorrect. The problems identified in this work likely apply to all draft vertebrate genomes annotated with any automated gene model pipeline and thus represent a pervasive challenge to the analysis of draft genomes.
Highlights
Genomic sequences and assemblies have been provided for many vertebrate species
Draft genomes are known to be less complete than finished genomes, the implications of working with resources derived from draft genomes is not always appreciated by investigators not involved in their production
We examined the draft genome sequence and assembly of the rhesus macaque (Macaca mulatta) [1], an important biomedical research model [2,3,4,5,6,7,8]
Summary
Genomic sequences and assemblies have been provided for many vertebrate species. Only a few have reached "finished" status. Draft genomes are known to be less complete than finished genomes, the implications of working with resources derived from draft genomes is not always appreciated by investigators not involved in their production. Independent assessments of possible misassemblies and sequencing errors are rarely done. The quality metrics reported when a new genome is published provide a global assessment of completeness but provide little information on the quality of the gene models derived from the sequence and assemblies
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