# Phylogenomic synteny reveals paleohexaploid-derived genomic blocks across Asteraceae

## TL;DR

This study uses genome comparisons to trace the evolutionary history of Asteraceae plants, revealing how ancient genome duplications shaped their genetic makeup and contributed to their diversity.

## Contribution

The study reconstructs the paleohexaploid ancestor genome of Asteraceae and identifies 157 triplicated genes linked to evolutionary innovations like floral capitula.

## Key findings

- Modern Asteraceae genomes are mosaics of three progenitor genomes shaped by rearrangements and gene loss.
- 157 genes retained three syntenic paralogs, with overrepresentation of transcription factors and auxin-related genes.
- The syntenic framework provides a tool for understanding genome evolution and innovation in Asteraceae.

## Abstract

Comparative genomics is a powerful approach for studying the evolution of organisms and their traits. However, deep evolutionary comparisons in plants remain challenging due to the highly dynamic nature of plant genome evolution. In this study, we investigated genome evolution in Asteraceae, the largest family of flowering plants, by reconstructing 16 linkage groups of the paleohexaploid ancestor of all Asteraceae species, dating to ~80 Mya. Our analysis revealed that most modern Asteraceae genomes are mosaics of three progenitor genomes and have undergone extensive reshaping through genome rearrangements and gene fractionation. This phylogenomic synteny framework provides valuable insights into the complex evolutionary history of Asteraceae and provides a window into exploring genome evolution at deep timescales.

The Asteraceae (Compositae) is the largest flowering plant family, ubiquitous in most terrestrial communities, and morphologically diverse. A two-step, ancient whole genome triplication (paleohexaploidization) occurred at approximately the same time as the evolutionary innovation and adaptive radiation of the family during the middle Eocene. Despite its importance, the consequences of this triplication have yet to be tracked in context of the Asteraceae genome evolution. To do so, we applied a synteny oriented phylogenomic analysis of 23 Asterales genomes. We identified 16 genomic groups that date back to the common diploid ancestor of all Asteraceae. Each group underwent triplication, resulting in 48 genomic blocks (16 × 3) that collectively represent the ancestral Asteraceae genome, excluding the early-diverging lineages which do not share the second step. We then analyzed the evolutionary dynamics of the 48 genomic blocks across the Asteraceae phylogeny. We found that modern Asteraceae genomes are genetic mosaics of three progenitor genomes, shaped by genomic exchanges, chromosomal rearrangements, and gene fractionation. One hundred fifty-seven genes retained three paleohexaploid-derived syntenic paralogs across most Asteraceae species. Transcription factors and auxin-related genes are significantly overrepresented in these triplets, and expression of the paleohexaploidy paralogs is spatiotemporally differentiated. These genes are involved in the development of floral capitula, a remarkable morphological innovation of the family. The discovery of the 157 triplicated genes can direct further study to understand the evolutionary innovation, and the synteny-phylogenomic framework provides a comparative framework to characterize newly sequenced Asteraceae genomes.