# Gene and genome duplications have contrasting impacts on biosynthetic and flower developmental pathways in California poppy

## TL;DR

The California poppy's genome reveals how gene duplication affects biosynthesis and flower development differently.

## Contribution

A haplotype-resolved genome assembly and expression atlas for California poppy, revealing contrasting duplication impacts on biosynthetic and developmental genes.

## Key findings

- BIA biosynthesis genes diversified through localized duplications, with expression similarity linked to phylogenetic relatedness.
- Carotenoid biosynthesis genes lack phylogenetic clustering, while floral regulators retained duplicates from ancient polyploidy.
- California poppy's genomic resources provide a valuable model for comparative studies in flowering plants.

## Abstract

Benzylisoquinoline alkaloids (BIAs) represent a vast group of specialized plant metabolites with diverse pharmaceutical applications, synthesized by a variety of gene families. Among the multiple plant lineages that produce BIAs, the most notable is the poppy family (Papaveraceae), with California poppy (Eschscholzia californica) emerging as a model organism. Here, we report a haplotype-resolved genome assembly, in combination with a high-density expression atlas, for California poppy. Genome analyses reveal recent diversification of BIA biosynthesis genes in poppy through localized duplications. Furthermore, we demonstrate that the degree of phylogenetic relatedness among paralogs within BIA biosynthesis-associated gene families correlates with similarities in gene expression. In contrast, gene families involved in carotenoid biosynthesis, which contributes to the intense orange petal pigmentation, are not phylogenetically clustered, and floral developmental regulators exhibit a high degree of retention of gene duplicates associated with ancient polyploidy events. These findings illustrate alternative roles for gene and genome duplications as drivers of trait evolution. Given the position of California poppy in the angiosperm phylogeny, the high-quality genomic resources generated for this work constitute a valuable resource for comparative genomic and transcriptomic analyses for poppies and flowering plants more generally.

The analysis of the California poppy genome sequence and expression atlas reveals contrasting histories of duplication and loss for metabolic pathway and floral development genes.