Custom methods to identify conserved genetic modules applied to novel transcriptomic data from Amborella trichopoda

Area of Science:

• Evolutionary Developmental Biology
• Comparative Genomics
• Transcriptomics

Background:

• Understanding the evolutionary history of gene expression is crucial for deciphering plant development.
• Comparing transcriptomic data across distantly related species presents significant methodological challenges.
• The ancestral gene regulatory networks of angiosperms remain largely uncharacterized.

Purpose of the Study:

• To develop a procedure for inter-species comparison of transcriptomic data.
• To reconstruct ancestral gene expression dynamics in the common ancestor of living angiosperms.
• To identify conserved genetic modules involved in early angiosperm evolution.

Main Methods:

• Generated novel transcriptomic data from *Amborella trichopoda* female flower tissues using laser-assisted microdissection.
• Employed gene-expression clustering and a custom orthology-based comparison procedure.
• Compared gene modules between *Amborella trichopoda* and *Arabidopsis thaliana*.

Main Results:

• Successfully identified nine major genetic modules with conserved expression dynamics.
• These modules date back at least 149 million years to the most recent common ancestor of living angiosperms.
• The identified genes, comprising over 5000 orthogroups, represent about one-third of genes controlling female reproductive development in *Arabidopsis thaliana*.

Conclusions:

• The study provides a proof of concept for comparing transcriptomic data across widely diverged plant species.
• This represents a foundational step towards large-scale analysis of gene expression dynamics in a macro-evolutionary context.
• Identified conserved genetic modules offer insights into the early evolution of angiosperm reproductive development.