Chromosome-level Assembly of The Greater Duckweed Spirodela polyrhiza Reveals Novel Genomic Features of One of the Fastest Growing Plants

The floating aquatic plant Duckweed is a promising addition to a growing list bioremediation and biofuel crops. Duckweeds are some of the smallest and fastest growing plants, which make them ideal for biomass production on wastewater. A draft genome of the Greater Duckweed Spirodela polyrhiza (Sp7498) revealed that its small 150 Mb genome has only 19,623 protein-coding genes, the fewest of any known flowering plant. Since Spirodela primarily reproduces asexually, we generated a physical map with BioNano Genomics Irys Technology to resolve the genome into its 20 chromosomes. For two accessions Sp7498 and Sp9509, we generated 109x and 140x coverage of single molecules with N50 lengths of 253 and 250 kb, which enabled us to re-order and merge the draft assemblies into 27 and 23 super-scaffolds respectively. Leveraging the entire 250x coverage from both accessions, we generated enough map support to merge Sp9509 into its 20 chromosomes. While variation and heterozygosity levels are very low in Spirodela, we were able to leverage the physical maps to identify 96 high-confidence structural variations spanning 100 to 100,000 bp. In addition, northern analysis suggested Spirodela had less than 100 rDNA repeats (18S-ITS1-5.8S-ITS2-26S) in its genome, which is surprisingly low when compared to Arabidopsis and maize that have 570 and 1,200 respectively. Using the raw BioNano single molecule data we were able to identify 81 repeats at the end of the chromosome 2, with one single molecule spanning 45 repeats. A better understanding of the reduced rDNA repeats and gene count will shed light on how these small aquatic plants have adapted for fast growth. BioNano physicals maps provide a new opportunity to resolve genome features that are not resolvable with other physical map or sequencing technologies.