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

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 researchers from Indiana University quantify the extent of such errors, by comparing several draft genomes against completed versions of the same sequences. Surprisingly, they 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. This 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.

rna-seq

Denton JF, Lugo-Martinez J, Tucker AE, Schrider DR, Warren WC, et al. (2014) Extensive Error in the Number of Genes Inferred from Draft Genome Assemblies. PLoS Comput Biol 10(12): e1003998. [article]

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