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Sequence and annotation of 42 cannabis genomes reveals extensive copy number variation in cannabinoid synthesis and pathogen resistance genes

View ORCID ProfileKevin J. McKernan, Yvonne Helbert, Liam T. Kane, Heather Ebling, Lei Zhang, Biao Liu, Zachary Eaton, Stephen McLaughlin, View ORCID ProfileSarah Kingan, Primo Baybayan, View ORCID ProfileGregory Concepcion, Mark Jordan, Alberto Riva, William Barbazuk, View ORCID ProfileTimothy Harkins
doi: https://doi.org/10.1101/2020.01.03.894428
Kevin J. McKernan
1Medicinal Genomics, 100 Cummings Center, suite 406-L, Beverly, MA 01915
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  • ORCID record for Kevin J. McKernan
  • For correspondence: kevin@medicinalgenomics.com
Yvonne Helbert
1Medicinal Genomics, 100 Cummings Center, suite 406-L, Beverly, MA 01915
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Liam T. Kane
1Medicinal Genomics, 100 Cummings Center, suite 406-L, Beverly, MA 01915
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Heather Ebling
1Medicinal Genomics, 100 Cummings Center, suite 406-L, Beverly, MA 01915
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Lei Zhang
1Medicinal Genomics, 100 Cummings Center, suite 406-L, Beverly, MA 01915
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Biao Liu
1Medicinal Genomics, 100 Cummings Center, suite 406-L, Beverly, MA 01915
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Zachary Eaton
1Medicinal Genomics, 100 Cummings Center, suite 406-L, Beverly, MA 01915
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Stephen McLaughlin
1Medicinal Genomics, 100 Cummings Center, suite 406-L, Beverly, MA 01915
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Sarah Kingan
3Pacific Biosciences, 1305 O’Brien Dr, Menlo Park, CA 93025
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  • ORCID record for Sarah Kingan
Primo Baybayan
3Pacific Biosciences, 1305 O’Brien Dr, Menlo Park, CA 93025
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Gregory Concepcion
3Pacific Biosciences, 1305 O’Brien Dr, Menlo Park, CA 93025
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  • ORCID record for Gregory Concepcion
Mark Jordan
4Minnibis, 1708 17th Ave, Longmont, CO 80501
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Alberto Riva
2The University of Florida Interdisciplinary Center for Biotechnology Research, Gainesville, Florida 32611
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William Barbazuk
2The University of Florida Interdisciplinary Center for Biotechnology Research, Gainesville, Florida 32611
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Timothy Harkins
1Medicinal Genomics, 100 Cummings Center, suite 406-L, Beverly, MA 01915
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  • ORCID record for Timothy Harkins
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Abstract

Cannabis is a diverse and polymorphic species. To better understand cannabinoid synthesis inheritance and its impact on pathogen resistance, we shotgun sequenced and assembled a Cannabis trio (sibling pair and their offspring) utilizing long read single molecule sequencing. This resulted in the most contiguous Cannabis sativa assemblies to date. These reference assemblies were further annotated with full-length male and female mRNA sequencing (Iso-Seq) to help inform isoform complexity, gene model predictions and identification of the Y chromosome. To further annotate the genetic diversity in the species, 40 male, female, and monoecious cannabis and hemp varietals were evaluated for copy number variation (CNV) and RNA expression. This identified multiple CNVs governing cannabinoid expression and 82 genes associated with resistance to Golovinomyces chicoracearum, the causal agent of powdery mildew in cannabis. Results indicated that breeding for plants with low tetrahydrocannabinolic acid (THCA) concentrations may result in deletion of pathogen resistance genes. Low THCA cultivars also have a polymorphism every 51 bases while dispensary grade high THCA cannabis exhibited a variant every 73 bases. A refined genetic map of the variation in cannabis can guide more stable and directed breeding efforts for desired chemotypes and pathogen-resistant cultivars.

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Sequence and annotation of 42 cannabis genomes reveals extensive copy number variation in cannabinoid synthesis and pathogen resistance genes

Footnotes

  • http://www.medicinalgenomics.com

  • https://genomevolution.org/coge/GenomeView.pl?gid=55184&tracks=sequence%2Cfeatures

  • https://www.ncbi.nlm.nih.gov/sra/?term=PRJNA575581

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 January 05, 2020.
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Sequence and annotation of 42 cannabis genomes reveals extensive copy number variation in cannabinoid synthesis and pathogen resistance genes
Kevin J. McKernan, Yvonne Helbert, Liam T. Kane, Heather Ebling, Lei Zhang, Biao Liu, Zachary Eaton, Stephen McLaughlin, Sarah Kingan, Primo Baybayan, Gregory Concepcion, Mark Jordan, Alberto Riva, William Barbazuk, Timothy Harkins
bioRxiv 2020.01.03.894428; doi: https://doi.org/10.1101/2020.01.03.894428
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Sequence and annotation of 42 cannabis genomes reveals extensive copy number variation in cannabinoid synthesis and pathogen resistance genes
Kevin J. McKernan, Yvonne Helbert, Liam T. Kane, Heather Ebling, Lei Zhang, Biao Liu, Zachary Eaton, Stephen McLaughlin, Sarah Kingan, Primo Baybayan, Gregory Concepcion, Mark Jordan, Alberto Riva, William Barbazuk, Timothy Harkins
bioRxiv 2020.01.03.894428; doi: https://doi.org/10.1101/2020.01.03.894428

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