Hieu X. Cao, Nele Horemans, Pieter Monsieurs, Hildegarde Vandenhove, Ronny Blust, Arne Van Hoeck, Van Hoeck, Arne, HOREMANS, Nele, Monsieurs, Pieter, Cao, Hieu Xuan, VANDENHOVE, Hildegarde, and Blust, Ronny
Background: Freshwater duckweed, comprising the smallest, fastest growing and simplest macrophytes has various applications in agriculture, phytoremediation and energy production. Lemna minor, the so-called common duckweed, is a model system of these aquatic plants for ecotoxicological bioassays, genetic transformation tools and industrial applications. Given the ecotoxic relevance and high potential for biomass production, whole-genome information of this cosmopolitan duckweed is needed. Results: The 472 Mbp assembly of the L. minor genome (2n = 40; estimated 481 Mbp; 98.1 %) contains 22,382 protein- coding genes and 61.5 % repetitive sequences. The repeat content explains 94.5 % of the genome size difference in comparison with the greater duckweed, Spirodela polyrhiza (2n = 40; 158 Mbp; 19,623 protein-coding genes; and 15.79 % repetitive sequences). Comparison of proteins from other monocot plants, protein ortholog identification, OrthoMCL, suggests 1356 duckweed-specific groups (3367 proteins, 15.0 % total L. minor proteins) and 795 Lemna-specific groups (2897 proteins, 12.9 % total L. minor proteins). Interestingly, proteins involved in biosynthetic processes in response to various stimuli and hydrolase activities are enriched in the Lemna proteome in comparison with the Spirodela proteome. Conclusions: The genome sequence and annotation of L. minor protein-coding genes provide new insights in biological understanding and biomass production applications of Lemna species. The authors thank the Research foundation-Flanders (FWO) (G.A040.11N) and the European Commission Contract Fission-2010-3.5.1-269672 Strategy for Allied Radioecology (http://www.star-radioecology.org) for financial support of this work. Belgian nuclear research institute (SCK.CEN) is further thanked for funding the PhD of AVH. HXC is supported by the German Research Foundation (SCH 951/18 1). The people from CALCUA at the University of Antwerp are acknowledged for assisting high performance computing (http://www.uantwerpen.be/calcua). The authors also thank L. Leus, ILVO, for estimating DNA genome size through flow cytometry.