The Azolla Genome Project

Azolla filiculoides (Salviniales) is a floating aquatic fern capable of fixing nitrogen from the air because of its obligate symbiotic association with the cyanobacterium Nostoc azollae, allowing it to achieve high growth rates even in the absence of ammonium or nitrates in the medium. The Azolla genome fills a critical phylogenetic gap among the five major embryophyte lineages; reference genomes are already available for bryophytes (Physcomitrella), lycophytes (Selaginella), gymnosperms (Picea and Pinus), and flowering plants (several representatives). In addition, the Azolla genome will inform us about the plant-cyanobacterial symbiotic partnership and the accompanying bacteria in the leaf pocket. Azolla was sequenced using a PacBio-only strategy supplemented with genome sequencing and transcriptome sequencing by Illumina and IonTorrent. Reads from 43 SMRT cells (51x coverage) were error-corrected with PBcR resulting in 23.5 Gb to which 95.9% of the assembled transcripts could be mapped. Different assembly options were tested before corrected reads were reduced to 25x coverage and assembled with Celera resulting in 693Mb of the genome (estimated at 750Mb). The genome was assembled into 4737 contigs with an N50 of 0.89Mb, and an average contig length of 146kb with the longest contig at 1.65Mb. 97% of the Illumina genome reads and 95.9% of the assembled transcripts mapped to the assembly, which has been scaffolded using BioNano technology. We will report on the ongoing genome annotation, particularly gene content and duplication status, and its implications for the evolutionary dynamics that are fundamental to plant life, as well as to the plant-cyanobacterial symbiosis.