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

Nature Communications
Qiushi LiSam Yeaman

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.

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Citations

Oct 1, 2020·The Plant Journal : for Cell and Molecular Biology·Mengmeng JiangM Brian Traw
Jan 8, 2021·Journal of Mass Spectrometry : JMS·Ivette M Menéndez-PerdomoPeter J Facchini
Jul 24, 2020·Chembiochem : a European Journal of Chemical Biology·Jeremy S MorrisPeter J Facchini
Mar 30, 2021·Plant Science : an International Journal of Experimental Plant Biology·Kentaro Fujita, Hideyuki Inui
Jun 19, 2021·Scientific Reports·Jakub VašekJaroslava Ovesná
Nov 16, 2021·Journal of the American Chemical Society·Ryan S Nett, Elizabeth S Sattely

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Methods Mentioned

BETA
RNAseq
Hi-C
proximity ligation
Illumina sequencing
PCR
genotyping
RNA-seq

Software Mentioned

bedtools
Juicebox Assembly Tool
RepeatMasker
Trimmomatic
LACHESIS
CNVnator
BWA
createRepeatLandscape
BioEdit
FastQC

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