Duckweeds represent a small, free-floating aquatic family (Lemnaceae) of the monocot order Alismatales with the fastest growth rate among flowering plants. They comprise five genera (Spirodela, Landoltia, Lemna, Wolffiella, and Wolffia) varying in genome size and chromosome number. Spirodela polyrhiza had the first sequenced duckweed genome. Cytogenetic maps are available for both species of the genus Spirodela (S. polyrhiza and S. intermedia). However, elucidation of chromosome homeology and evolutionary chromosome rearrangements by cross-FISH using Spirodela BAC probes to species of other duckweed genera has not been successful so far. We investigated the potential of chromosome-specific oligo-FISH probes to address these topics. We designed oligo-FISH probes specific for one S. intermedia and one S. polyrhiza chromosome (Fig. 1a). Our results show that these oligo-probes cross-hybridize with the homeologous regions of the other congeneric species, but are not suitable to uncover chromosomal homeology across duckweeds genera. This is most likely due to too low sequence similarity between the investigated genera and/or too low probe density on the target genomes. Finally, we suggest genus-specific design of oligo-probes to elucidate chromosome evolution across duckweed genera.

Arbor Biosciences Ann Arbor MI 48 102 USA

Biology Centre Czech Academy of Sciences Institute of Plant Molecular Biology CZ 37005 České Budějovice Czech Republic

Biology Department Dalat University District 8 Dalat City Lamdong Province Vietnam

Chemical Engineering Department University of Michigan Ann Arbor MI USA

Leibniz Institute of Plant Genetics and Crop Plant Research Gatersleben 06466 Stadt Seeland Germany

Zobrazit více v PubMed

Appenroth KJ, Sree KS, Bohm V, Hammann S, Vetter W, Leiterer M, Jahreis G. Nutritional value of duckweeds (Lemnaceae) as human food. Food Chem. 2017;217:266–273. doi: 10.1016/j.foodchem.2016.08.116. PubMed DOI

Appenroth K-J, Teller S, Horn M. Photophysiology of turion formation and germination inSpirodela polyrhiza. Biol Plant. 1996;38:95–106. doi: 10.1007/bf02879642. DOI

Aurich-Costa J, Zamechek L, Keenan P, Bradley S. Oligo fluorescence in situ hybridization (oligo-fish), a new strategy for enumerating chromosomes in interphase nuclei. Fertil Steril. 2007;88:S86. doi: 10.1016/j.fertnstert.2007.07.287. DOI

Bog M, Sree KS, Fuchs J, Hoang PTN, Schubert I, Kuever J, Rabenstein A, Paolacci S, Jansen MAK, Appenroth KJ. A taxonomic revision of Lemna sect. Uninerves (Lemnaceae) Taxon. 2020;69:56–66. doi: 10.1002/tax.12188. DOI

Braz GT, et al. Comparative oligo-FISH mapping: an efficient and powerful methodology to reveal karyotypic and chromosomal evolution. Genetics. 2018;208:513–523. doi: 10.1534/genetics.117.300344. PubMed DOI PMC

Cao HX, Vu GT, Wang W, Appenroth KJ, Messing J, Schubert I. The map-based genome sequence of Spirodela polyrhiza aligned with its chromosomes, a reference for karyotype evolution. New Phytol. 2016;209:354–363. doi: 10.1111/nph.13592. PubMed DOI

de Beukelaar MFA, Zeinstra GG, Mes JJ, Fischer ARH. Duckweed as human food. The influence of meal context and information on duckweed acceptability of Dutch consumers. Food Qual Prefer. 2019;71:76–86. doi: 10.1016/j.foodqual.2018.06.005. DOI

Han Y, Zhang T, Thammapichai P, Weng Y, Jiang J. Chromosome-specific painting in Cucumis species using bulked oligonucleotides. Genetics. 2015;200:771–779. doi: 10.1534/genetics.115.177642. PubMed DOI PMC

Harkess A, McLaughlin F, Bilkey N, Elliot K, Emenecker R, Mattoon E, Miller K, Czymme KK, Vierstra R, Meyers BC, Michael TP (2020) A new Spirodela polyrhiza genome and proteome reveal a conserved chromosomal structure with high abundances of proteins favoring energy production. bioRxiv. 10.1101/2020.01.23.909457 PubMed

Hoang PTN (2019) Comparative cytology and cytogenomics for representative species of the five duckweed genera., Halle/S., Martin-Luther-Universität Halle-Wittenberg

Hoang PTN, Fiebig A, Novák P, Macas J, Cao HX, Stepanenko A, Chen G, Borisjuk N, Scholz U, Schubert I. Chromosome-scale genome assembly for the duckweed Spirodela intermedia, integrating cytogenetic maps, PacBio and Oxford Nanopore libraries. Sci Rep. 2020;10:19230. doi: 10.1038/s41598-020-75728-9. PubMed DOI PMC

Hoang PTN, Schubert I. Reconstruction of chromosome rearrangements between the two most ancestral duckweed species Spirodela polyrhiza and S. intermedia. Chromosoma. 2017;126:729–739. doi: 10.1007/s00412-017-0636-7. PubMed DOI

Hoang PTN, Schubert V, Meister A, Fuchs J, Schubert I. Variation in genome size, cell and nucleus volume, chromosome number and rDNA loci among duckweeds. Sci Rep. 2019;9:3234. doi: 10.1038/s41598-019-39332-w. PubMed DOI PMC

Hoang PNT, et al. Generating a high-confidence reference genome map of the Greater Duckweed by integration of cytogenomic, optical mapping and Oxford Nanopore technologies. Plant J. 2018;96:670–684. doi: 10.1111/tpj.14049. PubMed DOI

Ijdo JW, Wells RA, Baldini A, Reeders ST. Improved telomere detection using a telomere repeat probe (TTAGGG)n generated by PCR. Nucleic Acids Res. 1991;19:4780. doi: 10.1093/nar/19.17.4780. PubMed DOI PMC

Jiang JM (2019) Fluorescent in situ hybridization in plants: recent developments and future directions. Chromosome Res 27:153-165. 10.1007/s10577-019-09607-z PubMed

Kaur M, Srikanth S, Kumar M, Sachdeva S, Puri SK. An integrated approach for efficient conversion of Lemna minor to biogas. Energy Convers Manag. 2019;180:25–35. doi: 10.1016/j.enconman.2018.10.106. DOI

Kreider AN, Fernandez Pulido CR, Bruns MA, Brennan RA. Duckweed as an agricultural amendment: nitrogen mineralization, leaching, and sorghum uptake. J Environ Qual. 2019;48:469–475. doi: 10.2134/jeq2018.05.0207. PubMed DOI

Landolt E (1986) The family of Lemnaceae – a monographic study (Vol 1) Veröffentlichungen des Geobotanischen Institutes der Eidg Techn Hochschule, Zürich

Liu X, et al. Dual-color oligo-FISH can reveal chromosomal variations and evolution in Oryza species. Plant J: Cell Mol Biol. 2020;101:112–121. doi: 10.1111/tpj.14522. PubMed DOI

Lysak MA, Berr A, Pecinka A, Schmidt R, McBreen K, Schubert I. Mechanisms of chromosome number reduction in Arabidopsis thaliana and related Brassicaceae species. Proc Natl Acad Sci U S A. 2006;103:5224–5229. doi: 10.1073/pnas.0510791103. PubMed DOI PMC

Ma L, Vu GT, Schubert V, Watanabe K, Stein N, Houben A, Schubert I. Synteny between Brachypodium distachyon and Hordeum vulgare as revealed by FISH. Chromosome Res: Int J Mol, Supramol Evol Asp Chromosome Biol. 2010;18:841–850. doi: 10.1007/s10577-010-9166-3. PubMed DOI

Mandakova T, Lysak MA. Chromosomal phylogeny and karyotype evolution in x=7 crucifer species (Brassicaceae) Plant Cell. 2008;20:2559–2570. doi: 10.1105/tpc.108.062166. PubMed DOI PMC

Michael TP et al (2017) Comprehensive definition of genome features in Spirodela polyrhiza by high-depth physical mapping and short-read DNA sequencing strategies. Plant J: Cell Mol Biol. 10.1111/tpj.13400 PubMed

Michael TP, Ernst E, Hartwick N, Chu P, Bryant D, Gilbert S, Ortleb S, Baggs EL, Sree KS, Appenroth KJ, Fuchs J, Jupe F, Sandoval JP, Krasileva KV, Borisjuk L, Mockler TC, Ecker JR, Martiessen RA, Lam E (2020) Genome and time-of-day transcriptome of Wolffia australianalink morphologial extreme limitization with un-gated plant growth. bioRxiv 2020.03.31.018291. 10.1101/2020.03.31.018291 PubMed

Nahar K, Sunny SA. Duckweed-based clean energy production dynamics (ethanol and biogas) and phyto-remediation potential in Bangladesh. Model Earth Syst Environ. 2020;6:1–11. doi: 10.1007/s40808-019-00659-y. DOI

Novák P, Ávila Robledillo L, Koblížková A, Vrbová I, Neumann P, Macas J. TAREAN: a computational tool for identification and characterization of satellite DNA from unassembled short reads. Nucleic Acids Res. 2017;45:e111. doi: 10.1093/nar/gkx257. PubMed DOI PMC

Novák P, Neumann P, Pech J, Steinhaisl J, Macas J. RepeatExplorer: a galaxy-based web server for genome-wide characterization of eukaryotic repetitive elements from next-generation sequence reads. Bioinformatics. 2013;29:792–793. doi: 10.1093/bioinformatics/btt054. PubMed DOI

Simonikova D, Nemeckova A, Karafiatova M, Uwimana B, Swennen R, Dolezel J, Hribova E. Chromosome painting facilitates anchoring reference genome sequence to chromosomes in situ and integrated karyotyping in banana (Musa Spp.) Front Plant Sci. 2019;10:1503. doi: 10.3389/fpls.2019.01503. PubMed DOI PMC

Song X, Song R, Zhou J, Yan W, Zhang T, Sun H, Xiao J, Wu Y, Xi M, Lou Q, Wang H, Wang X. Development and application of oligonucleotide-based chromosome painting for chromosome 4D of Triticum aestivum L. Chromosom Res. 2020;28:171–182. doi: 10.1007/s10577-020-09627-0. PubMed DOI

Tippery NP, Les DH, Crawford DJ. Evaluation of phylogenetic relationships in Lemnaceae using nuclear ribosomal data. Plant Biol. 2015;17(Suppl 1):50–58. doi: 10.1111/plb.12203. PubMed DOI

Wang W, Haberer G, Gundlach H, Gläßer C, Nussbaumer T, Luo MC, Lomsadze A, Borodovsky M, Kerstetter RA, Shanklin J, Byrant DW, Mockler TC, Appenroth KJ, Grimwood J, Jenkins J, Chow J, Choi C, Adam C, Cao XH, Fuchs J, Schubert I, Rokhsar D, Schmutz J, Michael TP, Mayer KFX, Messing J. The Spirodela polyrhiza genome reveals insights into its neotenous reduction fast growth and aquatic lifestyle. Nat Commun. 2014;5:3311. doi: 10.1038/ncomms4311. PubMed DOI PMC

Wang W, Kerstetter RA, Michael TP. Evolution of genome size in Duckweeds (Lemnaceae) J Bot. 2011;2011:1–9. doi: 10.1155/2011/570319. DOI

Weisshart K, Fuchs J, Schubert V. Structured illumination microscopy (SIM) and photoactivated localization microscopy (PALM) to analyze the abundance and distribution of RNA polymerase II molecules on flow-sorted arabidopsis Nuclei. Bio-protocol. 2016;6:e1725. doi: 10.21769/BioProtoc.1725. DOI

Xin H, Zhang T, Wu Y, Zhang W, Zhang P, Xi M, Jiang J. An extraordinarily stable karyotype of the woody Populus species revealed by chromosome painting. Plant J : Cell Mol Biol. 2020;101:253–264. doi: 10.1111/tpj.14536. PubMed DOI

Yaskolka Meir A, et al. A green-mediterranean diet, supplemented with Mankai Duckweed, preserves iron-homeostasis in humans and is efficient in reversal of anemia in Rats. J Nutr. 2019;149:1004–1011. doi: 10.1093/jn/nxy321. PubMed DOI

Zhao Y, et al. Pilot-scale comparison of four duckweed strains from different genera for potential application in nutrient recovery from wastewater and valuable biomass production. Plant Biol. 2015;17(Suppl 1):82–90. doi: 10.1111/plb.12204. PubMed DOI