The genomes and epigenomes of aquatic plants (Lemnaceae) promote triploid hybridization and clonal reproduction

Abstract

SummaryThe Lemnaceae (duckweeds) are the world’s smallest but fastest growing flowering plants. Prolific clonal propagation facilitates continuous micro-cropping for plant-based protein and starch production, and holds tremendous promise for sequestration of atmospheric CO2. Here, we present chromosomal assemblies, annotations, and phylogenomic analysis ofLemnagenomes that uncover candidate genes responsible for the metabolic and developmental traits of the family, such as anatomical reduction, adaxial stomata, lack of stomatal closure, and carbon sequestration via crystalline calcium oxalate. Lemnaceae have selectively lost genes required for RNA interference, including Argonaute genes required for reproductive isolation (the triploid block) and haploid gamete formation. Triploid hybrids arise commonly amongLemna, and we have found mutations in highly-conserved meiotic crossover genes that could support polyploid meiosis. Syntenic comparisons withWolffiaandSpirodelareveal that diversification of these genera coincided with the “Azolla event” in the mid-Eocene, during which aquatic macrophytes reduced high atmospheric CO2levels to those of the current ice age.Facile regeneration of transgenic fronds from tissue culture, aided by reduced epigenetic silencing, makesLemnaa powerful biotechnological platform, as exemplified by recent engineering of high-oilLemnathat outperforms oil seed crops.