Comprehensive Definition of Genome Features in Spirodela polyrhiza by High-Depth Physical Mapping and Short-Read DNA Sequencing Strategies

Summary Spirodela polyrhiza is a fast-growing aquatic monocot with highly reduced morphology, genome size and number of protein-coding genes. Considering these biological features of Spirodela and its basal position in the monocot lineage, understanding its genome architecture could shed light on plant adaptation and genome evolution. Like many draft genomes, however, the 158 Mbp Spirodela genome sequence has not been resolved to chromosomes and important genome characteristics have not been defined. Here we deployed rapid genome-wide physical maps combined with high-coverage short-read sequencing to resolve the 20 chromosomes of Spirodela and to empirically delineate its genome features. Our data revealed a dramatic reduction in the number of the rDNA repeat unit in Spirodela to less than 100, which is even fewer than that reported for yeast. Consistent with its unique phylogenetic position, small RNA sequencing revealed 29 Spirodela-specific miRNA, with only 2 being shared with oil palm and banana. Combining DNA methylation data and small RNA sequencing enabled accurate prediction of 20.5% Long Terminal Repeats (LTRs) that doubled the previous estimate, and revealed a high Solo:Intact LTR ratio of 8.2. Interestingly, we found that Spirodela has the lowest global DNA methylation levels (9%) of any tested plant species. Taken together our results reveal a genome that has undergone reduction likely through eliminating non-essential protein coding genes, rDNA and LTRs. In addition to delineating genome features of this unique plant, the methodologies described and large-scale genome resources from this work will enable future evolutionary and functional studies of this basal monocot family. This article is protected by copyright. All rights reserved.