Unraveling land plant evolution through comparative transcriptomics of bryophytes, ferns and flowering plants

Abstract

Ferns, despite their complex and large genomes, provide valuable models for studying vascular evolution and plant cell walls. We have created gene expression atlases for 22 fern species, covering 12 major divisions, and constructed an accurate species tree that highlights several whole genome duplication events across ~400 million years of fern evolution. Comparative analysis between ferns and flowering plants revealed distinct differences in their hormonal systems and a negative correlation between gene age and organ-specific expression. Biochemical comparisons of cell walls and lignin indicated that ferns possess most polysaccharides found in flowering plants, alongside a novel cell wall sugar, and show evidence of independent evolution in cell wall biosynthesis. Extending our analysis to other land plants, we generated gene expression atlases for various organs and gametes from bryophytes, vascular plants, gymnosperms, and flowering plants. This revealed conserved organ- and gamete-specific orthogroups, with co-option of existing genes driving the evolution of new organs. Male gametes, particularly pollen, exhibited high specificity and conservation in gene expression, highlighting the specialization of male reproductive processes. These findings underscore the conserved and unique genetic mechanisms underpinning land plant organogenesis and reproduction.

Publications

https://pubmed.ncbi.nlm.nih.gov/34253868/(link is external)
https://pubmed.ncbi.nlm.nih.gov/31988262/(link is external)
https://pubmed.ncbi.nlm.nih.gov/36344371/