Mobile DNA shapes fern plastome evolution

Grusz lab research, published in the October 2018 issue of Genome Biology and Evolution, uncovers a suite of mobile DNA sequences shaping plastome evolution in ferns. Collaborating with Utah State University (Paul Wolf, Tanner Robison), Duke University (Karla Sosa), and the Smithosonian Institution (Eric Schuettpelz), we generated genome skimming data to assemble and annotate 26 new chloroplast genomes from the fern family Pteridaceae.

Figure 1: Distribution of MORFFO elements across the Pteridaceae phylogeny.  Topology results from ML analysis of plastome data (−ln  L =609991.403586); thickened branches indicate bootstrap/posterior probability support=100/1.0. Symbols highlight shared insertion sites, with empty squares signifying evident lack of a MORFFO insertion. Short arrows flanking  morffo1  indicate short inverted repeats. Novel insertions and losses, as inferred by maximum parsimony, are depicted as arrows or crossed-out circles, respectively. Robison et al. 2018  GBE.

Figure 1: Distribution of MORFFO elements across the Pteridaceae phylogeny. Topology results from ML analysis of plastome data (−ln L=609991.403586); thickened branches indicate bootstrap/posterior probability support=100/1.0. Symbols highlight shared insertion sites, with empty squares signifying evident lack of a MORFFO insertion. Short arrows flanking morffo1 indicate short inverted repeats. Novel insertions and losses, as inferred by maximum parsimony, are depicted as arrows or crossed-out circles, respectively. Robison et al. 2018 GBE.

Undergraduate researcher Blake Fauskee contributed his expertise to the identification of RNA editing sites across the newly generated chloroplast genomes. This interest stemmed from his time investigating the evolution of RNA editing in fern mitochondrial genomes (Field Museum REU, 2017).

 
figure 2: Detected insertion sites in plastomes of Pteridaceae, relative to  Adiantum capillus-veneris .  Light gray bar denotes inverted repeat region. Robison et al. 2018  GBE.

figure 2: Detected insertion sites in plastomes of Pteridaceae, relative to Adiantum capillus-veneris. Light gray bar denotes inverted repeat region. Robison et al. 2018 GBE.

FIGURE 3: Major inversion events uncovered in fern plastomes.  ( A ) Depiction of the two inversion events necessary to explain gene order differences between  Angiopteris  and  Adiantum  and their relationship to morffo1. ( B ) Depiction of the inversion events seen in early leptosporangiate and vittarioid ferns, highlighting relationship of  morffo1  to the event. Robison et al. 2018  GBE.

FIGURE 3: Major inversion events uncovered in fern plastomes. (A) Depiction of the two inversion events necessary to explain gene order differences between Angiopteris and Adiantum and their relationship to morffo1. (B) Depiction of the inversion events seen in early leptosporangiate and vittarioid ferns, highlighting relationship of morffo1 to the event. Robison et al. 2018 GBE.

Currently, the Grusz lab is examining the behavior of MORFFO elements in closely-related and/or sister species within the xeric-adapted genus Myriopteris. We look forward to sharing our findings soon!