Salvinia cucullata: The Smallest Fern Genome Known

Ferns have notoriously high chromosome numbers (as high as 2n=1440 in Ophioglossum) and large genome sizes (up to 1C=71 Gb in Psilotum). We recently discovered, however, that the floating aquatic fern Salvinia cucullata (Salviniales) has an extremely reduced genome size — 1C=255 Mb­­­­ — more than 40 times smaller than the average fern genome.

We sequenced the S. cucullata genome with 40X PacBio and 200X Illumina HiSeq. The reads were assembled using PBcR (PacBio-only assembly) and MaSuRCA (hybrid assembly) into a 222 Mb draft genome containing 2,865 scaffolds and a N50 scaffold length of 757 Kb. Our initial characterization of the S. cucullata genome found it has relatively little repetitive DNA, suggesting that the reduced genome size can be partly attributed to the purge of repeat elements.

In addition to its small genome size, S. cucullata lacks true roots and its “root-like” structure is a highly modified leaf. Because of this, Salvinia appears to be an ideal study system for understanding the evolutionary fate of organ-specific genes when an organ is lost—do they become pseudogenes? gain new functions? or get co-opted by other organs? We aim to address these questions by comparing tissue-specific Salvinia transcriptomes with other close relatives that do have true roots.

Finally, Salvinia is sister to Azolla, another floating aquatic fern, but one that has an obligate cyanobacterial symbiosis. By contrasting these two fern genera, we can identify genes and genomic elements that are likely to be important for the plant-cyanobacterial symbiosis.