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Identification of a novel interspecific hybrid yeast from a metagenomic open fermentation sample using Hi-C

Caiti Smukowski Heil, Joshua N. Burton, Ivan Liachko, Anne Friedrich, Noah A. Hanson, Cody L. Morris, Joseph Schacherer, View ORCID ProfileJay Shendure, James H. Thomas, View ORCID ProfileMaitreya J. Dunham
doi: https://doi.org/10.1101/150722
Caiti Smukowski Heil
a Department of Genome Sciences, University of Washington, Seattle, WA
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Joshua N. Burton
a Department of Genome Sciences, University of Washington, Seattle, WA
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Ivan Liachko
a Department of Genome Sciences, University of Washington, Seattle, WA
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Anne Friedrich
d Genetics, Genomics, and Microbiology, University of Strasbourg, Strasbourg, France
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Noah A. Hanson
a Department of Genome Sciences, University of Washington, Seattle, WA
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Cody L. Morris
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Joseph Schacherer
d Genetics, Genomics, and Microbiology, University of Strasbourg, Strasbourg, France
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Jay Shendure
a Department of Genome Sciences, University of Washington, Seattle, WA
f Howard Hughes Medical Institute
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James H. Thomas
a Department of Genome Sciences, University of Washington, Seattle, WA
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Maitreya J. Dunham
a Department of Genome Sciences, University of Washington, Seattle, WA
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  • ORCID record for Maitreya J. Dunham
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Abstract

Interspecific hybridization is a common mechanism enabling genetic diversification and adaptation; however, the detection of hybrid species has been quite difficult. The identification of microbial hybrids is made even more complicated, as most environmental microbes are resistant to culturing and must be studied in their native mixed communities. We have previously adapted the chromosome conformation capture method Hi-C to the assembly of genomes from mixed populations. Here, we show the method’s application in assembling a hybrid genome directly from an uncultured, mixed population from an open-fermentation beer sample. Our assembly method has enabled us to de-convolute 4 bacterial and 4 yeast genomes from this sample, including a putative yeast hybrid. Downstream isolation and analysis of this hybrid confirmed its genome to consist of Pichia membranifaciens and that of another related, but undescribed yeast. Our work shows that Hi-C-based metagenomic methods can overcome the limitation of traditional sequencing methods in studying complex mixtures of genomes.

Nucleic Acid Sequences Sequences are deposited in NCBI Assembly under the Project ID PRJNA390460.

Footnotes

  • ↵* co-first authors

  • COI: JNB, IL, J. Shendure, and MJD have financial interests in Phase Genomics, a company that has commercialized the Hi-C genome assembly technique. IL is a current employee of Phase Genomics.

Copyright 
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 4.0 International license.
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Posted June 15, 2017.
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Identification of a novel interspecific hybrid yeast from a metagenomic open fermentation sample using Hi-C
Caiti Smukowski Heil, Joshua N. Burton, Ivan Liachko, Anne Friedrich, Noah A. Hanson, Cody L. Morris, Joseph Schacherer, Jay Shendure, James H. Thomas, Maitreya J. Dunham
bioRxiv 150722; doi: https://doi.org/10.1101/150722
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Identification of a novel interspecific hybrid yeast from a metagenomic open fermentation sample using Hi-C
Caiti Smukowski Heil, Joshua N. Burton, Ivan Liachko, Anne Friedrich, Noah A. Hanson, Cody L. Morris, Joseph Schacherer, Jay Shendure, James H. Thomas, Maitreya J. Dunham
bioRxiv 150722; doi: https://doi.org/10.1101/150722

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