# Evolutionary mobility and genetic dynamics of MORFFO genes: shuttling among ancient plant lineages

## TL;DR

This paper explores mobile genes in ferns called MORFFOs, which behave differently from typical plant genes and may spread through horizontal gene transfer.

## Contribution

The study reveals MORFFOs as dynamic, potentially selfish genetic elements with unique evolutionary patterns in ferns.

## Key findings

- MORFFOs show high substitution rates and distinct codon preferences compared to other plastid genes.
- Phylogenetic analysis suggests MORFFOs replicate outside plastids and may spread via horizontal gene transfer.
- MORFFOs are under purifying selection but exhibit dynamic locations and genealogies.

## Abstract

Plastid genomes (plastomes) of land plants are characterized by their architectural and genic content stability. However, fern plastomes exhibit unexpected dynamism, characterized by the presence of mobile protein‐coding genes (CDS) – Mobile Open Reading Frames in Fern Organelles (MORFFOs).We investigate the evolutionary dynamics of MORFFOs in 30 species of Anemiaceae (Schizaeales), an ancient lineage of ferns, focusing on their transposition, substitution patterns, codon usages, and RNA editing patterns.MORFFOs expand plastome size and occur in diverse intergenic regions, exhibiting dynamic locations, genealogies, and exceptionally high substitution rates compared with canonical plastid CDS. Sliding window and codon usage analyses demonstrate that MORFFOs are under purifying selection but exhibit distinct codon preferences that deviate from those of other plastid CDS, suggesting functional constraints. Phylogenetic incongruence between MORFFOs and other plastid CDS, along with their extraordinary substitution rates and mobility, implies their replication outside plastids.Our findings highlight that MORFFOs are dynamic, potentially selfish genetic elements capable of transcription, translation, and replication independently from plastomes, and fern plastomes might acquire these mobile CDS through frequent horizontal gene transfer and possibly intracellular gene transfer.

Plastid genomes (plastomes) of land plants are characterized by their architectural and genic content stability. However, fern plastomes exhibit unexpected dynamism, characterized by the presence of mobile protein‐coding genes (CDS) – Mobile Open Reading Frames in Fern Organelles (MORFFOs).

We investigate the evolutionary dynamics of MORFFOs in 30 species of Anemiaceae (Schizaeales), an ancient lineage of ferns, focusing on their transposition, substitution patterns, codon usages, and RNA editing patterns.

MORFFOs expand plastome size and occur in diverse intergenic regions, exhibiting dynamic locations, genealogies, and exceptionally high substitution rates compared with canonical plastid CDS. Sliding window and codon usage analyses demonstrate that MORFFOs are under purifying selection but exhibit distinct codon preferences that deviate from those of other plastid CDS, suggesting functional constraints. Phylogenetic incongruence between MORFFOs and other plastid CDS, along with their extraordinary substitution rates and mobility, implies their replication outside plastids.

Our findings highlight that MORFFOs are dynamic, potentially selfish genetic elements capable of transcription, translation, and replication independently from plastomes, and fern plastomes might acquire these mobile CDS through frequent horizontal gene transfer and possibly intracellular gene transfer.