Plastid genomes display remarkable organizational stability over evolutionary time. From green algae to angiosperms, most plastid genomes are largely collinear, with only a few cases of inversion, gene loss, or, in extremely rare cases, gene addition. These plastome insertions are mostly clade-specific and are typically of nuclear or mitochondrial origin. Here, we expand on these findings and present the first family-level survey of plastome evolution in ferns, revealing a novel suite of dynamic mobile elements. Comparative plastome analyses of the Pteridaceae expose several mobile open reading frames that vary in sequence length, insertion site, and configuration among sampled taxa. Even between close relatives, the presence and location of these elements is widely variable when viewed in a phylogenetic context.We characterize these elements and refer to them collectively as Mobile Open Reading Frames in Fern Organelles (MORFFO). We further note that the presence of MORFFO is not restricted to Pteridaceae, but is found across ferns and other plant clades. MORFFO elements are regularly associated with inversions, intergenic expansions, and changes to the inverted repeats. They likewise appear to be present in mitochondrial and nuclear genomes of ferns, indicating that they can move between genomic compartments with relative ease. The origins and functions of these mobile elements are unknown, but MORFFO appears to be a major driver of structural genome evolution in the plastomes of ferns, and possibly other groups of plants.
Bibliographical noteFunding Information:
Thanks to Jim Van Etten, Dan Sloan, Aaron Duffy, and Michael McKain for various fruitful discussions, Nico Devos (Duke University Center for Genomic and Computational Biology) for technical assistance, and Sally Chambers for providing the V. appalachiana sample. Thanks to Blaine Marchant for generously allowing us to use the Ceratopteris nuclear genome in our search for MORFFO. Thanks also to the University of Utah Center for High-Performance Computing, particularly Anita Orendt, for providing computational resources for data analyses, and to the Minnesota Supercomputing Institute. We further acknowledge the Smithsonian Laboratories of Analytical Biology. Funding for this research was provided in part by the United States National Science Foundation (award DEB-1405181 to E.S.) and the Smithsonian Institution.
- Horizontal gene transfer