Abstract
The complexity of eukaryote genomes makes assembly errors inevitable in the process of constructing reference genomes. Next-generation sequencing (NGS) could provide an efficient way to validate previously assembled genomes. Here, we exploited NGS data to interrogate the chicken reference genome and identified 35 pairs of nearly identical regions with >99.5 % sequence similarity and a median size of 109 kb. Several lines of evidence, including read depth, the composition of junction sequences, and sequence similarity, suggest that these regions present genome assembly errors and should be excluded from forthcoming genomic studies.
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Acknowledgments
QZ was supported by the Department of Human Evolutionary Biology, Harvard University. NB acknowledges postdoctoral research funding from the Swedish Research Council (VR grant 2009-693). We thank the anonymous reviewers for the helpful comments on an earlier version of this manuscript.
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Zhang, Q., Backström, N. Assembly errors cause false tandem duplicate regions in the chicken (Gallus gallus) genome sequence. Chromosoma 123, 165–168 (2014). https://doi.org/10.1007/s00412-013-0443-8
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DOI: https://doi.org/10.1007/s00412-013-0443-8