Ancient eudicot hexaploidy meets ancestral eurosid gene order

Area of Science:

• Evolutionary genomics
• Plant biology
• Bioinformatics

Background:

• The majority of flowering plants evolved from a hexaploidization event over 125 million years ago.
• Understanding gene retention and loss post-polyploidy is crucial for plant genome evolution.
• Rosids, a major subgroup, provide insights into hexaploid ancestor reconstruction.

Purpose of the Study:

• To quantitatively trace the fate of gene triples after hexaploidy in core eudicots.
• To reconstruct the ancestral gene order of the eurosid clade.
• To analyze the functional classes of retained and lost duplicate genes.

Main Methods:

• Quantitative tracing of gene triplication fate across seven core eudicot genomes.
• Development of a novel protocol for ancestral gene order reconstruction using Maximum Weight Matching.
• Analysis of duplicate orthologous gene loss dynamics in three rosid genomes.

Main Results:

• A two-stage model (pre- and post-radiation) was fitted to gene loss dynamics.
• The developed protocol successfully reconstructed the ancestor of the eurosid clade from three rosid genomes.
• Functional analysis revealed retention of regulatory genes and loss of metabolic genes.

Conclusions:

• Gene loss and ancestor reconstruction offer complementary views of post-hexaploidization evolution.
• The reconstructed eurosid ancestor retained signatures of the original seven chromosomes.
• Functional biases in gene retention/loss mirror those observed in more recent polyploidy events.