Gene duplication dynamics and regulatory evolution shape the diversification of Asteraceae

Area of Science:

• Genomics
• Evolutionary Biology
• Plant Science

Background:

• The order Asterales shows a significant disparity in species richness between the family Asteraceae (>30,000 species) and its sister family Calyceraceae (<50 species).
• Understanding the genomic underpinnings of this diversification imbalance is crucial for evolutionary studies.

Purpose of the Study:

• To investigate the genomic basis for the extreme species richness disparity within the Asterales order.
• To compare the genomes of Asteraceae and Calyceraceae to identify factors contributing to diversification.

Main Methods:

• Assembly of three new chromosome-level genomes, including the first for Calyceraceae.
• Re-annotation of five existing genomes.
• Comparative genomic analyses focusing on repeat content, chromosomal rearrangements, and whole-genome duplications (WGDs).

Main Results:

• Both Asteraceae and Calyceraceae exhibit high repeat content and frequent chromosomal rearrangements.
• Evidence for both shared and lineage-specific whole-genome duplications (WGDs) was found.
• In Asteraceae, small-scale duplications (tandem and dispersed) expanded gene families related to secondary metabolism and stress response.
• Segmental duplicates in Asteraceae showed adaptive selection for regulating biosynthetic and metabolic processes.
• Selective pressures on flowering time regulators indicate a balance between flexibility and constraint in floral evolution.

Conclusions:

• Beyond ancient polyploidy, small-scale gene duplications and fine-tuning of regulatory networks were key drivers of Asteraceae's ecological versatility and diversification.
• Comparative genomics provides insights into the evolution of extreme species richness in flowering plants.