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.
The initial publication of the genome sequence of many plants, animals, and microbes is often accompanied with great fanfare. However, these genomes are almost always first-drafts, with a lot of missing data, many gaps, and many errors in the published sequences. Compounding this problem, the genes identified in draft genome sequences are also affected by incomplete genome assemblies: the number and exact structure of predicted genes may be incorrect. Here we quantify the extent of such errors, by comparing several draft genomes against completed versions of the same sequences. Surprisingly, we find huge numbers of errors in the number of genes predicted from draft assemblies, with more than half of all genes having the wrong number of copies in the draft genomes examined. Our investigation also reveals the major causes of these errors, and further analyses using additional functional data demonstrate that many of the gene predictions can be corrected. The results presented here suggest that many inferences based on published draft genomes may be erroneous, but offer a way forward for future analyses.
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