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

Citation

Li, Qiushi et al. (2020), Gene clustering and copy number variation in alkaloid metabolic pathways of opium poppy, Dryad, Dataset, https://doi.org/10.5061/dryad.m0cfxpnz9

Abstract

Genes in plant secondary metabolic pathways enable the 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 is increased within clusters and identify novel 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.

Funding

National Research Council of Canada, Award: 86155

Natural Sciences and Engineering Research Council of Canada, Award: 183573