Characterization of microsatellite markers for the duckweed Spirodela polyrhiza and Lemna minor tested on samples from Europe and the United States of America
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Abstract
Microsatellite primers are a valuable tool to use for both observational and experimental studies in numerous taxa. Here, we develop 18 and 16 microsatellite markers for the widespread duckweeds Lemna minor and Spirodela polyrhiza, respectively. Only four primers were not polymorphic when tested on samples from Europe and Western Pennsylvania, USA.
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Acosta, K et al. (2020). “Duckweed hosts a taxonomically similar bacterial assemblage as the terrestrial leaf microbiome”. PLOS ONE 15. DOI: https://doi.org/10.1371/journal.pone.0228560. DOI: https://doi.org/10.1371/journal.pone.0228560
Agrawal, A A et al. (2013). “A field experiment demonstrating plant life-history evolution and its eco-evolutionary feedback to seed predator populations”. The American Naturalist 181. DOI: https://doi.org/10.1086/666727. DOI: https://doi.org/10.1086/666727
Anneberg, T J et al. (2023). “Polyploidy impacts population growth and competition with diploids: multigenerational experiments reveal key life history tradeoffs”. New Phytologist 238, pp. 1294–1304. DOI: https://doi.org/10.1111/nph.18794. DOI: https://doi.org/10.1111/nph.18794
Barks, P M et al. (2018). “Among-strain consistency in the pace and shape of senescence in duckweed”. Journal of Ecology 106, pp. 2132–2145. DOI: https://doi.org/10.1111/1365-2745.12937. DOI: https://doi.org/10.1111/1365-2745.12937
Bog, M, K S Sree, et al. (2020). “A taxonomic revision of Lemna sect. Uninerves (Lemnaceae)”. TAXON 69, pp. 56–66. DOI: https://doi.org/10.1002/tax.12188. DOI: https://doi.org/10.1002/tax.12188
Bog, M, U Lautenschlager, et al. (2015). “Genetic characterization and barcoding of taxa in the genera Landoltia and Spirodela (Lemnaceae) by three plastidic markers and amplified fragment length polymorphism (AFLP)”. Hydrobiologia 749, pp. 169–182. DOI: https://doi.org/10.1007/s10750-014-2163-3. DOI: https://doi.org/10.1007/s10750-014-2163-3
Boutin-Ganache, I et al. (2001). “M13-tailed primers improve the readability and usability of microsatellite analyses performed with two different allele-sizing methods”. BioTechniques 31, pp. 25–28. DOI: https://doi.org/10.2144/01311bm02. DOI: https://doi.org/10.2144/01311bm02
Braglia, L et al. (2021). “Duckweed species genotyping and interspecific hybrid discovery by tubulin-based polymorphism fingerprinting”. Frontiers in Plant Science 12, pp. 625670–625670. DOI: https://doi.org/10.3389/fpls.2021.625670. DOI: https://doi.org/10.3389/fpls.2021.625670
Cao, X H, P Fourounjian, and W Wang, eds. (2020). The Duckweed Genomes. Switzerland: Springer Cham, p. 185. DOI: https://doi.org/10.1007/978-3-030-11045-1. DOI: https://doi.org/10.1007/978-3-030-11045-1
Chapuis, M - P and A Estoup (2007). “Microsatellite null alleles and estimation of population differentiation”. Molecular Biology and Evolution 24, pp. 621–631. DOI: https://doi.org/10.1093/molbev/msl191. DOI: https://doi.org/10.1093/molbev/msl191
Chen, D et al. (2020). “Intraspecific variations in cadmium tolerance and phytoaccumulation in giant duckweed (Spirodela polyrhiza)”. J Hazard Mater 395, pp. 122672–122672. DOI: https://doi.org/10.1016/j.jhazmat.2020.122672. DOI: https://doi.org/10.1016/j.jhazmat.2020.122672
Cheng, J J and A M Stomp (2009). “Growing duckweed to recover nutrients from wastewaters and for production of fuel ethanol and animal Feed”. CLEAN - Soil, Air, Water 37, pp. 17–26. DOI: https://doi.org/10.1002/clen.200800210. DOI: https://doi.org/10.1002/clen.200800210
Cui, W and J J Cheng (2015). “Growing duckweed for biofuel production: a review”. Plant Biology 17, pp. 16–23. DOI: https://doi.org/10.1111/plb.12216. DOI: https://doi.org/10.1111/plb.12216
Fazekas, A J et al. (2012). “DNA Barcoding Methods for Land Plants”. In: DNA Barcodes. Methods in Molecular Biology. Ed. by W Kress and D Erickson. Vol. 858. Humana Press, pp. 223–252. DOI: https://doi.org/10.1007/978-1-61779-591-6_11. DOI: https://doi.org/10.1007/978-1-61779-591-6_11
Feng, B et al. (2017). “Development of a new marker system for identification of Spirodela polyrhiza and Landoltia punctata”. International Journal of Genomics. DOI: https://doi.org/10.1155/2017/5196763. DOI: https://doi.org/10.1155/2017/5196763
Fu, L et al. (2020). “De novo assembly, transcriptome characterization, and simple sequence repeat marker development in duckweed Lemna gibba”. Physiol Mol Biol Plants 26, pp. 133–142. DOI: https://doi.org/10.1007/s12298-019-00726-9. DOI: https://doi.org/10.1007/s12298-019-00726-9
Gupta, C and D Prakash (2013). “Duckweed: an effective tool for phyto-remediation”. Toxicological & Environmental Chemistry 95, pp. 1256–1266. DOI: https://doi.org/10.1080/02772248.2013.879309. DOI: https://doi.org/10.1080/02772248.2013.879309
Hart, S P, M M Turcotte, and J M Levine (2019). “Effects of rapid evolution on species coexistence”. Proceedings of the National Academy of Sciences 116, pp. 2112–2117. DOI: https://doi.org/10.1073/pnas.1816298116. DOI: https://doi.org/10.1073/pnas.1816298116
Healey, A et al. (2014). “Protocol: a simple method for extracting next-generation sequencing quality genomic DNA from recalcitrant plant species”. Plant Methods 10. DOI: https://doi.org/10.1186/1746-4811-10-21. DOI: https://doi.org/10.1186/1746-4811-10-21
Hillman, W S (1961). “The Lemnaceae, or duckweeds”. Bot. Rev 27, pp. 221–287. DOI: https://doi.org/10.1007/BF02860083. DOI: https://doi.org/10.1007/BF02860083
Ho, E K H et al. (2019). “Population genomics of the facultatively asexual duckweed Spirodela polyrhiza”. New Phytologist 224, pp. 1361–1371. DOI: https://doi.org/10.1111/nph.16056. DOI: https://doi.org/10.1111/nph.16056
Jacobs, D L (1947). “An ecological life-history of Spirodela polyrhiza (greater duckweed) with emphasis on the turion phase”. Ecological Monographs 17, pp. 437–469. DOI: https://doi.org/10.2307/1948596. DOI: https://doi.org/10.2307/1948596
Kearse, M et al. (2012). “Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data”. Bioinformatics 28, pp. 1647–1649. DOI: https://doi.org/10.1093/bioinformatics/bts199. DOI: https://doi.org/10.1093/bioinformatics/bts199
Laird, R A and P M Barks (2018). “Skimming the surface: duckweed as a model system in ecology and evolution”. Am J Bot 105, pp. 1962–1966. DOI: https://doi.org/10.1002/ajb2.1194. DOI: https://doi.org/10.1002/ajb2.1194
Landolt, E (1986). “Biosystematic investigations in the family of duckweeds (Lemnaceae), Vol. 2”. In: The family of Lemnaceae—A Monographic Study, vol. 1. ETH Zürich.
Landolt, E (1992). “Lemnaceae duckweed family”. Journal of the Arizona-Nevada Academy of Science 26, pp. 10–14.
Markoulatos, P, N Siafakas, and M Moncany (2002). “Multiplex polymerase chain reaction: A practical approach”. J Clin Lab Anal 16, pp. 47–51. DOI: https://doi.org/10.1002/jcla.2058. DOI: https://doi.org/10.1002/jcla.2058
Morgante, M and A M Olivieri (1993). “PCR-amplified microsatellites as markers in plant genetics”. Plant J 3, pp. 175–182. DOI: https://doi.org/10.1046/j.1365-313X.1993.t01-9-00999.x
O Ekperusi, A, F D Sikoki, and E O Nwachukwu (2019). “Application of common duckweed (Lemna minor) in phytoremediation of chemicals in the environment: State and future perspective”. Chemosphere 223, pp. 285–309. DOI: https://doi.org/10.1016/j.chemosphere.2019.02.025. DOI: https://doi.org/10.1016/j.chemosphere.2019.02.025
O’Brien, A M et al. (2022). “Harnessing plant-microbiome interactions for bioremediation across a freshwater urbanization gradient”. Water Research 223, pp. 118926–118926. DOI: https://doi.org/10.1016/j.watres.2022.118926. DOI: https://doi.org/10.1016/j.watres.2022.118926
Powell, W, G C Machray, and J Provan (1996). “Polymorphism revealed by simple sequence repeats”. Trends in Plant Science 1, pp. 215–222. DOI: https://doi.org/10.1016/S1360-1385(96)86898-0
Schlötterer, C and D Tautz (1992). “Slippage synthesis of simple sequence DNA”. Nucleic Acids Res 20, pp. 211–215. DOI: https://doi.org/10.1093/nar/20.2.211
Sree, K S, M Bog, and K J Appenroth (2016). “Taxonomy of duckweeds (Lemnaceae), potential new crop plants”. Emirates Journal of Food and Agriculture, pp. 291–302. DOI: https://doi.org/10.9755/ejfa.2016-01-038. DOI: https://doi.org/10.9755/ejfa.2016-01-038
Subramanian, S K and M M Turcotte (2020). “Preference, performance, and impact of the water-lily aphid on multiple species of duckweed”. Ecological Entomology 45, pp. 1466–1475. DOI: https://doi.org/10.1111/een.12932. DOI: https://doi.org/10.1111/een.12932
Tan, J, J E Kerstetter, and M M Turcotte (2021). “Eco-evolutionary interaction between microbiome presence and rapid biofilm evolution determines plant host fitness”. Nat Ecol Evol 5, pp. 670–676. DOI: https://doi.org/10.1038/s41559-021-01406-2. DOI: https://doi.org/10.1038/s41559-021-01406-2
Tautz, D (1989). “Hypervariability of simple sequences as a general source for polymorphic DNA markers”. Nucleic Acids Res 17, pp. 6463–6471. DOI: https://doi.org/10.1093/nar/17.16.6463
Tautz, D and M Renz (1984). “Simple sequences are ubiquitous repetitive components of eukaryotic genomes”. Nucleic Acids Res 12, pp. 4127–4138. DOI: https://doi.org/10.1093/nar/12.10.4127
Turcotte, M M, D N Reznick, and J D Hare (2011). “The impact of rapid evolution on population dynamics in the wild: experimental test of eco-evolutionary dynamics”. Ecology Letters 14, pp. 1084–1092. DOI: https://doi.org/10.1111/j.1461-0248.2011.01676.x. DOI: https://doi.org/10.1111/j.1461-0248.2011.01676.x
U Schenk, R and A C Hildebrandt (1972). “Medium and techniques for induction and growth of monocotyledonous and dicotyledonous plant cell cultures”. Can. J. Bot 50, pp. 199–204. DOI: https://doi.org/10.1139/b72-026. DOI: https://doi.org/10.1139/b72-026
Van Steveninck, R F M, M E Van Steveninck, and D R Fernando (1992). “Heavy-metal (Zn, Cd) tolerance in selected clones of duck weed (Lemna minor)”. Plant and Soil 146, pp. 271–280. DOI: https://doi.org/10.1007/BF00012021
Vieira, M L C et al. (2016). “Microsatellite markers: what they mean and why they are so useful”. Genet Mol Biol 39, pp. 312–328. DOI: https://doi.org/10.1590/1678-4685-GMB-2016-0027. DOI: https://doi.org/10.1590/1678-4685-GMB-2016-0027
W Armitage, D and S E Jones (2019). “Negative frequency-dependent growth underlies the stable coexistence of two cosmopolitan aquatic plants”. Ecology 100, pp. 2657–2657. DOI: https://doi.org/10.1002/ecy.2657. DOI: https://doi.org/10.1002/ecy.2657
W Hitsman, H and A M Simons (2020). “Latitudinal variation in norms of reaction of phenology in the greater duckweed Spirodela polyrhiza”. Journal of Evolutionary Biology 33, pp. 1405–1416. DOI: https://doi.org/10.1111/jeb.13678. DOI: https://doi.org/10.1111/jeb.13678
Wang, W et al. (2014). “The Spirodela polyrhiza genome reveals insights into its neotenous reduction fast growth and aquatic lifestyle”. Nat Commun 5, pp. 3311–3311. DOI: https://doi.org/10.1038/ncomms4311. DOI: https://doi.org/10.1038/ncomms4311
Wani, G et al. (2014). “cpDNA microsatellite markers for lemna minor (ARACEAE ): Phylogeographic Implications”. Applications in plant sciences 2(7). DOI: https://doi.org/10.3732/apps.1300099. DOI: https://doi.org/10.3732/apps.1300099
Xu, N et al. (2018). “Characterization of 19 polymorphic SSR markers in Spirodela polyrhiza (Lemnaceae) and cross-amplification in Lemna perpusilla”. Applications in Plant Sciences 6. DOI: https://doi.org/http://dx.doi.org/10.1002/aps3.1153. DOI: https://doi.org/10.1002/aps3.1153
Xu, S et al. (2019). “Low genetic variation is associated with low mutation rate in the giant duckweed”. Nat Commun 10, pp. 1243–1243. DOI: https://doi.org/10.1038/s41467-019-09235-5. DOI: https://doi.org/10.1038/s41467-019-09235-5
Xu, Y et al. (2015). “Species distribution, genetic diversity and barcoding in the duckweed family (Lemnaceae)”. Hydrobiologia 743, pp. 75–87. DOI: https://doi.org/10.1007/s10750-014-2163-3. DOI: https://doi.org/10.1007/s10750-014-2014-2
Ziegler, P et al. (2015). “Relative in vitro growth rates of duckweeds (Lemnaceae) - the most rapidly growing higher plants”. Plant Biol 17, pp. 33–41. DOI: https://doi.org/10.1111/plb.12184. DOI: https://doi.org/10.1111/plb.12184
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