Fern genomes elucidate land plant evolution and cyanobacterial symbioses

Abstract

Ferns are the closest sister group to all seed plants, yet little is known about their genomes other than that they are generally colossal. Here, we report on the genomes of Azolla filiculoides and Salvinia cucullata (Salviniales) and present evidence for episodic whole-genome duplication in ferns-one at the base of 'core leptosporangiates' and one specific to Azolla. One fern-specific gene that we identified, recently shown to confer high insect resistance, seems to have been derived from bacteria through horizontal gene transfer. Azolla coexists in a unique symbiosis with N-fixing cyanobacteria, and we demonstrate a clear pattern of cospeciation between the two partners. Furthermore, the Azolla genome lacks genes that are common to arbuscular mycorrhizal and root nodule symbioses, and we identify several putative transporter genes specific to Azolla-cyanobacterial symbiosis. These genomic resources will help in exploring the biotechnological potential of Azolla and address fundamental questions in the evolution of plant life.

PPR proteins – orchestrators of organelle RNA metabolism

“…This could provide a safety net for possible random mutations in the PPR transcripts or in the target mRNA. Despite the high correlation of editing and ‘no phenotype’ seen in our analysis, it is worth pointing out that editing can play a crucial role in plants, especially in ferns where it has been reported that editing for the creation of the start codon is conserved and poses a selective advantage over having a translatable sequence encoded in the genome (Li et al ).…”

Recurrent genome duplication events likely contributed to both the ancient and recent rise of ferns

“…However, the phylogeny used for their dating analysis included only one fern species (the giant horsetail), with all other taxa being angiosperms; such a sparse sampling of ferns might have limited the power to estimate the age of the event. Li et al () recently reported the first two genome sequence datasets in ferns ( Salvinia and Azolla sps. of water ferns, Salviniaceae) and their detection of signals for an ancient WGD event from pairs of syntenic paralogs in the Salvinia genome as a peak in Ks distribution at ~1.2–1.3 (Li et al ).…”

On the evolutionary significance of horizontal gene transfers in plants

“…Nevertheless, Li et al . () did find an HGT gene derived from cyanobacteria, but one that is shared with many other fern and lycophyte species (i.e. a more ancient HGT).…”

“…Because of the species’ intimate association, they were identified as probable candidates for HGT. Surprisingly, no gene was found to be horizontally transferred between Azolla and the cyanobiont (Li et al ., ). Nevertheless, Li et al .…”