The first draft genome of the aquatic model plant Lemna minor opens the route for future stress physiology research and biotechnological applications.

Arne Van Hoeck,Ronny Blust,Hieu Xuan Cao,Pieter Monsieurs,Nele Horemans,Hildegarde Vandenhove

doi:10.1186/s13068-015-0381-1

Abstract

BackgroundFreshwater 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.ResultsThe 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.ConclusionsThe genome sequence and annotation of L. minor protein-coding genes provide new insights in biological understanding and biomass production applications of Lemna species.Electronic supplementary materialThe online version of this article (doi:10.1186/s13068-015-0381-1) contains supplementary material, which is available to authorized users.

Highlights

Freshwater duckweed, comprising the smallest, fastest growing and simplest macrophytes has various applications in agriculture, phytoremediation and energy production
Duckweed species comprise a group of aquatic monocotyledons macrophytes consisting of floating plant bodies or “fronds.” The family Lemnaceae consists of five genera, Landoltia, Lemna, Spirodela, Wolffia and Wolffiella among which 37 species have been identified so far [1,2,3]
De novo assembly of L. minor genome with greater 100× of Illumina coverage Genome of L. minor clone 5500 was estimated as 481 Mbp by flow cytometry (Fig. 1b) and is compacted in 20 chromosome pairs (2n = 40, Fig. 1c)

Summary

Introduction

Freshwater duckweed, comprising the smallest, fastest growing and simplest macrophytes has various applications in agriculture, phytoremediation and energy production. L. minor (Fig. 1a) was put forward as a model system to study fundamental plant research and has been shown to contribute to the understanding of the photoperiodic control of flowering [15, 16] and the discovery of auxin biosynthesis and sulfur assimilation pathways [17, 18] Their variety in growth habitats and their sensitivity to toxicants allowed the use of Lemna species in ecotoxicological research as representative of higher aquatic plants and standardized guidelines on how to perform a growth inhibition test were developed [19,20,21,22,23,24,25,26]. Studies focusing on physiological mechanisms and genetic improvements among duckweed species await support at molecular level [3, 29]

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Conclusion