Book Description

My thesis provides the first whole genome analysis of an aquatic plant, Spirodela polyrhiza and a reference genome for a new order among the monocotelydonous angiosperms. The Lemnoideae belong to the order of the Alismatales and are commonly known as duckweeds, the smallest, fastest growing, and simplest of aquatic plants, thus telling them apart is not a trivial task. Whereas a simple and accessible protocol has been established for land plants by the Consortium for the Barcode of Life with seven universal DNA barcoding markers, we found that atpF-atpH noncoding spacer is the most promising marker for duckweed species-level identification. Furthermore, our assembly and annotation of the Spirodela chloroplast and mitochondrial genomes open an opportunity of population-level classification. A key to our understanding of the evolution of a species and its potential use is the gene content of the organism. Therefore, we sequenced Spirodela polyrhiza 7498 that has one of the smallest genomes with 158 Mb within this subfamily of species. The genome contains 19,623 predicted protein-coding genes, sharing a total of 8,255 common gene families with Arabidopsis, tomato, banana, and rice despite a significantly reduced gene number. Reduced gene families and missing genes reflect changes consistent with its compact and reduced morphogenesis or forever-young life style, aquatic suspension, and suppression of juvenile-to-adult transition. Spirodela exhibits a remarkable phenotypic plasticity to adapt to cold weather in winter. We identified and functionally annotated 362 differentially expressed genes, which open a major step towards understanding the molecular network underlying vegetative frond dormancy. Moreover, the expression data for lipid and starch biosynthesis together with the turion-specific transcriptional genes from our RNA-Seq data could be ideal targets to develop duckweeds into oil crops. Thanks to its unique and fascinating biology, applications of duckweed in water remediation and as a renewable energy source are predicted to have a bright future. The genome sequence of Spirodela provides the first step to identify, understand, and improve relevant traits for specific target applications.