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Widespread false gene gains caused by duplication errors in genome assemblies

View ORCID ProfileByung June Ko, View ORCID ProfileChul Lee, View ORCID ProfileJuwan Kim, View ORCID ProfileArang Rhie, View ORCID ProfileDongAhn Yoo, View ORCID ProfileKerstin Howe, View ORCID ProfileJonathan Wood, Seoae Cho, Samara Brown, View ORCID ProfileGiulio Formenti, Erich D. Jarvis, View ORCID ProfileHeebal Kim
doi: https://doi.org/10.1101/2021.04.09.438957
Byung June Ko
1Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
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Chul Lee
2Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea
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Juwan Kim
2Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea
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Arang Rhie
3Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, USA
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DongAhn Yoo
2Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea
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Kerstin Howe
4Wellcome Sanger Institute, Cambridge, UK
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Jonathan Wood
4Wellcome Sanger Institute, Cambridge, UK
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Seoae Cho
5eGnome, Inc, Seoul, Republic of Korea
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Samara Brown
6Laboratory of the Neurogenetics of Language, The Rockefeller University, New York, NY, USA
7Howard Hughes Medical Institute, Chevy Chase, MD, USA
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Giulio Formenti
6Laboratory of the Neurogenetics of Language, The Rockefeller University, New York, NY, USA
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Erich D. Jarvis
6Laboratory of the Neurogenetics of Language, The Rockefeller University, New York, NY, USA
7Howard Hughes Medical Institute, Chevy Chase, MD, USA
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  • For correspondence: ejarvis@mail.rockefeller.edu heebal@snu.ac.kr
Heebal Kim
1Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
2Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea
5eGnome, Inc, Seoul, Republic of Korea
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  • For correspondence: ejarvis@mail.rockefeller.edu heebal@snu.ac.kr
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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.

Competing Interest Statement

The authors have declared no competing interest.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted April 09, 2021.
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Widespread false gene gains caused by duplication errors in genome assemblies
Byung June Ko, Chul Lee, Juwan Kim, Arang Rhie, DongAhn Yoo, Kerstin Howe, Jonathan Wood, Seoae Cho, Samara Brown, Giulio Formenti, Erich D. Jarvis, Heebal Kim
bioRxiv 2021.04.09.438957; doi: https://doi.org/10.1101/2021.04.09.438957
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Widespread false gene gains caused by duplication errors in genome assemblies
Byung June Ko, Chul Lee, Juwan Kim, Arang Rhie, DongAhn Yoo, Kerstin Howe, Jonathan Wood, Seoae Cho, Samara Brown, Giulio Formenti, Erich D. Jarvis, Heebal Kim
bioRxiv 2021.04.09.438957; doi: https://doi.org/10.1101/2021.04.09.438957

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