Evolutionary mobility of MORFFO genes: shuttling in and out of plastomes in an ancient fern lineage

Leveraging Next-Generation Sequencing (NGS) techniques, we successfully de novo assembled the complete chloroplast genome for the principal genera within the order Schizaeales. A comparative analysis of these plastomes was conducted, focusing on their gene content, genomic architecture, and the prevalence of "mobile open reading frames in fern organelles" (MORFFOs). Particular attention was given to their dynamics of transposition and substitution. MORFFOs contribute to plastome expansion and are recurrently identified in various intergenic regions, characterized by their inconsistent genomic loci, divergent phylogenetic origins, and elevated substitution rates relative to canonical plastid protein-coding genes. The observed phylogenetic incongruence among MORFFOs, coupled with their accelerated substitution rates and inherent mobility, strongly suggests a potential for autonomous replication independent of the plastome and subsequent intergenomic shuttling. This evidence supports their origin via horizontal gene transfer (HGT) and potentially intracellular gene transfer (IGT). Collectively, our findings underscore that MORFFOs represent dynamic, potentially selfish genetic elements capable of independent transcription, translation, and replication from the host plastomes.