Widespread false gene gains caused by duplication errors in genome assemblies

Abstract

False duplications in genome assemblies lead to false biological conclusions. We quantified false duplications in previous genome assemblies and their new counterparts of the same species (platypus, zebra finch, Anna's hummingbird) generated by the Vertebrate Genomes Project (VGP). Whole genome alignments revealed that 4 to 16% of the sequences were falsely duplicated in the previous assemblies, impacting hundreds to thousands of genes. These led to overestimated gene family expansions. The main source of the false duplications was heterotype duplications, where the haplotype sequences were more divergent than other parts of the genome leading the assembly algorithms to classify them as separate genes or genomic regions. A minor source was sequencing errors. Although present in a smaller proportion, we observed false duplications remaining in the VGP assemblies that can be identified and purged. This study highlights the need for more advanced assembly methods that better separates haplotypes and sequence errors, and the need for cautious analyses on gene gains.

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Automated assembly of high-quality diploid human reference genomes

“…The sequencing enzymes used often have difficulty reading through regions with complex structures, such as GC-rich regions often found in promoters that regulate gene expression 9, 10 . It is also now clear that mixing diverse haplotypes in a single assembly, even from the same individual, can introduce many errors with standard assembly tools 8, 10, 11 . These errors include: switch errors where variants from each haplotype are assembled into the same pseudo- haplotype; false duplications and associated gaps where more divergent haplotype homologs are assembled as separate false paralogs; and consensus errors due to collapses between haplotypes.…”