ORIGINAL ARTICLE Reconstruction of chromosome rearrangements between the two most ancestral duckweed species Spirodela polyrhiza and S. intermedia Phuong T. N. Hoang 1 & Ingo Schubert 1 Received: 31 May 2017 /Revised: 6 July 2017 /Accepted: 12 July 2017 # Springer-Verlag GmbH Germany 2017 Abstract The monophyletic duckweeds comprising five genera within the monocot order Alismatales are neotenic, free-floating, aquatic organisms with fast vegetative prop- agation. Some species are considered for efficient biomass production, for life stock feeding, and for (simultaneous) wastewater phytoremediation. The ancestral genus Spirodela consists of only two species, Spirodela polyrhiza and Spirodela intermedia, both with a similar small genome (~160 Mbp/1C). Reference genome drafts and a physical map of 96 BACs on the 20 chromosome pairs of S. polyrhiza strain 7498 are available and provide useful tools for further evolutionary studies within and between duckweed genera. Here we applied sequential comparative multicolor fluorescence in situ hybridization (mcFISH) to address homeologous chromosomes in S. intermedia (2n = 36), to detect chromosome rearrangements between both species and to elucidate the mechanisms which may have led to the chromosome number alteration after their evolutionary sepa- ration. Ten chromosome pairs proved to be conserved be- tween S. polyrhiza and S. intermedia, the remaining ones ex- perienced, depending on the assumed direction of evolution, translocations, inversion, and fissions, respectively. These results represent a first step to unravel karyotype evolution among duckweeds and are anchor points for future genome assembly of S. intermedia. Keywords Spirodela polyrhiza . Spirodela intermedia . Duckweeds . Comparative FISH . Chromosome homeology . Karyotype evolution Introduction The aquatic, monocotyledonous duckweeds are the smallest, fastest growing, and simplest seed plants. They comprise 37 species belonging to the five genera: Spirodela, Landoltia, Lemna, Wolffiella, and Wolffia. Duckweeds are of potential economic importance because of (i) fast vegetative propagation, (ii) farming in aquacul- ture without requirement for arable land, (iii) duckweed’ s ability to remediate wastewater, (iv) possible application for pharmaceutical purpose, and (v) a high concentration of protein and/or starch. The genome size of duckweed species displays a nearly 12-fold range from 160 Mbp/1C (Spirodela polyrhiza) to 1881 Mbp/1C (Wolffia arrhiza) (Bog et al. 2015; Wang et al. 2011). The nuclear DNA content of duckweeds correlates negatively with frond size. The chromosome numbers reported for duckweeds vary from 2n = 20 to 126 (Geber 1989; Urbanska-Worytkiewicz 1980). There is no obvious correlation between chromosome number and genome size. The phylogenetically basic genus Spirodela comprises two species, S. polyrhiza (L.) Schleid. and S. intermedia W. Koch, which have a similar genome size (~160 Mbp/ Electronic supplementary material The online version of this article (doi:10.1007/s00412-017-0636-7) contains supplementary material, which is available to authorized users. * Ingo Schubert schubert@ipk-gatersleben.de 1 Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Corrensstrasse 3, 06466 Stadt Seeland, Germany Chromosoma DOI 10.1007/s00412-017-0636-7