Gene clustering and copy number variation in alkaloid metabolic pathways of opium poppy

Qiushi Li, Sukanya Ramasamy, Pooja Singh, Jillian M. Hagel, Sonja M. Dunemann, Xue Chen, Rongji Chen, Lisa Yu, Joseph E. Tucker, Peter J. Facchini and Sam Yeaman ()
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Qiushi Li: University of Calgary
Sukanya Ramasamy: University of Calgary
Pooja Singh: University of Calgary
Jillian M. Hagel: University of Calgary
Sonja M. Dunemann: University of Calgary
Xue Chen: University of Calgary
Rongji Chen: University of Calgary
Lisa Yu: University of Calgary
Joseph E. Tucker: Willow Biosciences Inc.
Peter J. Facchini: University of Calgary
Sam Yeaman: University of Calgary

Nature Communications, 2020, vol. 11, issue 1, 1-13

Abstract: Abstract Genes in plant secondary metabolic pathways enable biosynthesis of a range of medically and industrially important compounds, and are often clustered on chromosomes. Here, we study genomic clustering in the benzylisoquinoline alkaloid (BIA) pathway in opium poppy (Papaver somniferum), exploring relationships between gene expression, copy number variation, and metabolite production. We use Hi-C to improve the existing draft genome assembly, yielding chromosome-scale scaffolds that include 35 previously unanchored BIA genes. We find that co-expression of BIA genes increases within clusters and identify candidates with unknown function based on clustering and covariation in expression and alkaloid production. Copy number variation in critical BIA genes correlates with stark differences in alkaloid production, linking noscapine production with an 11-gene deletion, and increased thebaine/decreased morphine production with deletion of a T6ODM cluster. Our results show that the opium poppy genome is still dynamically evolving in ways that contribute to medically and industrially important phenotypes.

Date: 2020
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Persistent link: https://EconPapers.repec.org/RePEc:nat:natcom:v:11:y:2020:i:1:d:10.1038_s41467-020-15040-2

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DOI: 10.1038/s41467-020-15040-2

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