Abstract
Invasive giant hogweeds are infamous in Europe for causing ecological and economic damage, but genetic resources for their study are limited. We used next-generation sequencing to develop a microsatellite library for Heracleum persicum, a widespread invasive in Nordic countries. In addition, these markers were cross amplified with the closely related Heracleum mantegazzianum, Heracleum sosnowskyi, Heracleum sphondylium, and the putative hybrid H. persicum × H. sphondylium, as well as the more distantly related Anthriscus sylvestris. We designed and validated 164 primer pairs. A cost-effective PCR approach with modified forward primer, reverse primer, and fluorescently labeled universal tail was used to test the functionality of each marker. Twenty-five of thirty markers screened on eight geographically distant samples of H. persicum were polymorphic. The number of alleles was 2–4 whereas the expected and observed heterozygosity varied from 0.06 to 0.84 and 0.0 to 1.0 respectively. The cross-species amplification efficiency was 84–100 %, in which 60–76 % of the cross-species amplified markers were polymorphic for Heracleum taxa including H. persicum × sphondylium. Three out of eight of the cross-amplified markers were polymorphic in Anthriscus sylvestris. Ordination revealed a clear genetic structure of Heracleum taxa. Thus, these markers can serve as important genetic resources for understanding taxonomy, population genetics, and phylogeny of giant hogweeds and their hybrids, which in turn, is expected to contribute to invasive species management.
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References
Alm T (2013) Ethnobotany of Heracleum persicum Desf. ex Fisch., an invasive species in Norway, or how plant names, uses, and other traditions evolve. J Ethnobiol Ethnomed 9(42):1–12. doi:10.1186/1746-4269-9-42
Anonymous (2009) Type-it Microsatellite PCR hand book: for reliable multiplex PCR-based analysis of microsatellites without the need for optimization. Qiagen, Hilden, Germany. http://www.qiagen.com/resources/resourcedetail?id=d6135896-0466-4d9d-aeef-1c4f23f8964e&lang=en. Accessed 15 December 2012
Anonymous (2011) emPCR amplification method manual - Lib L LV. 454 Sequencing, Branford, Connecticut, USA. http://454.com/downloads/my454/documentation/gs-flx-plus/emPCR-Amp-Lib-L-LV-Method-Manual_XLPlus_May2011.pdf. Accessed 07 November 2014
Blacket MJ, Robin C, Good RT, Lee SF, Miller AD (2012) Universal primers for fluorescent labelling of PCR fragments—an efficient and cost-effective approach to genotyping by fluorescence. Mol Ecol Resour 12:456–463. doi:10.1111/j.1755-0998.2011.03104.x
Butler J (2005) Constructing STR multiplex assays. In: Carracedo A (ed) Forensic DNA Typing Protocols, vol 297. Methods in Molecular Biology. Humana Press, Totowa, New Jersey, pp 53–65
Downie SR, Katz-Downie DS, Watson MF (2000) A phylogeny of the flowering plant family Apiaceae based on chloroplast DNA rpl16 and rpoC1 intron sequences: towards a suprageneric classification of subfamily Apioideae. Am J Bot 87:273–292
Elvebakk A (1992) Has Heracleum laciniatum auct. scand. been introduced to North Norway through England? Polarflokken 16:313–316
EPPO (2009) Heracleum mantegazzianum, Heracleum sosnowskyi and Heracleum persicum. EPPO Bull 39:489–499. doi:10.1111/j.1365-2338.2009.02313.x
Excoffier L, Lischer HEL (2010) Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Mol Ecol Resour 10:564–567. doi:10.1111/j.1755-0998.2010.02847.x
Fading P, Watson MF (2005) Heracleum Linnaeus. In: Zhengyi W, Raven P (eds) Flora of China (Apiaceae through Ericaceae), vol 14. Missouri Botanical Garden Press, St. Louis, pp 194–202
Fan L et al (2013) Transferability of newly developed pear SSR markers to other Rosaceae species. Plant Mol Biol Rep 31:1271–1282. doi:10.1007/s11105-013-0586-z
Fröberg L (2010) Heracleum L. In: Jonsell B, Karlsson T (eds) Flora Nordica (Thymelaeaceae to Apiaceae), vol 6. The Swedish Museum of Natural History, Stockholm, pp 224–234
Guichoux E et al (2011) Current trends in microsatellite genotyping. Mol Ecol Resour 11:591–611. doi:10.1111/j.1755-0998.2011.03014.x
Hejda M, Pyšek P, Jarošík V (2009) Impact of invasive plants on the species richness, diversity and composition of invaded communities. J Ecol 97:393–403. doi:10.1111/j.1365-2745.2009.01480.x
Henry P, Provan J, Goudet J, Guisan A, JahodovÁ Š, Besnard G (2008) A set of primers for plastid indels and nuclear microsatellites in the invasive plant Heracleum mantegazzianum (Apiaceae) and their transferability to Heracleum sphondylium. Mol Ecol Resour 8:161–163. doi:10.1111/j.1471-8286.2007.01911.x
Henry P, Le Lay G, Goudet J, Guisan A, JahodovÁ Š, Besnard G (2009) Reduced genetic diversity, increased isolation and multiple introductions of invasive giant hogweed in the western Swiss Alps. Mol Ecol 18:2819–2831. doi:10.1111/j.1365-294X.2009.04237.x
Holleley CE, Geerts PG (2009) Multiplex Manager 1.0: a cross-platform computer program that plans and optimizes multiplex PCR. BioTechniques 46:511–517. doi:10.2144/000113156
Jahodova S, Trybush S, Pysek P, Wade M, Karp A (2007) Invasive species of Heracleum in Europe: an insight into genetic relationships and invasion history. Divers Distrib 13:99–114. doi:10.1111/j.1472-4642.2006.00305.x
Malausa T et al (2011) High-throughput microsatellite isolation through 454 GS-FLX Titanium pyrosequencing of enriched DNA libraries. Mol Ecol Resour 11:638–644
Meglécz E, Costedoat C, Dubut V, Gilles A, Malausa T, Pech N, Martin J-F (2010) QDD: a user-friendly program to select microsatellite markers and design primers from large sequencing projects. Bioinformatics 26:403–404. doi:10.1093/bioinformatics/btp670
Nielsen C, Ravn HP, Nentwig W, Wade M (eds) (2005) The giant hogweed best practice manual. Guidelines for the management and control of an invasive weed in Europe. Forest and Landscape Denmark, Hoersholm, Denmark, p 44
Peakall R, Smouse PE (2012) GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research—an update. Bioinformatics 28:2537–2539. doi:10.1093/bioinformatics/bts460
Pimentel D, Zuniga R, Morrison D (2005) Update on the environmental and economic costs associated with alien-invasive species in the United States. Ecol Econ 52:273–288. doi:10.1016/j.ecolecon.2004.10.002
Sell P, Murrell G (2009) Flora of Great Britain and Ireland. Volume 3 (Mimosaceae-Lentibulariaceae) vol 3. Cambridge University Press, New York
Stace C (2010) New flora of the British Isles, 3rd edn. Cambridge University Press, Cambridge
Thiele J, Otte A (2007) Impact of Heracleum mantegazzianum on invaded vegetation and human activities. In: Pysek P, Cock MJW, Nentwig W, Ravn HP (eds) Ecology and management of giant hogweed (Heracleum mantegazzianum). CABI, Wallingford, pp 144–156
Van Oosterhout C, Hutchinson WF, Wills DPM, Shipley P (2004) Micro-checker: software for identifying and correcting genotyping errors in microsatellite data. Mol Ecol Notes 4:535–538. doi:10.1111/j.1471-8286.2004.00684.x
Walker NF, Hulme PE, Hoelzel AR (2003) Population genetics of an invasive species, Heracleum mantegazzianum: implications for the role of life history, demographics and independent introductions. Mol Ecol 12:1747–1756. doi:10.1046/j.1365-294X.2003.01866.x
Acknowledgments
We would like to thank Atefeh Pirany for collecting samples from Iran. We are grateful to Jens-Petter Kjemprud, Embassy of Norway in Iran, for delivering samples from Iran. We would also like to thank Sarka Jahodova for sample contribution. The authors are thankful to all the sample contributors listed in Tables 1 and 2. We would like to thank two anonymous reviewers for their constructive comments which were invaluable while preparing this manuscript. Finally, we would like to thank Matthew Perisin from Department of Ecology and Evolution, University of Chicago, for language correction. This project was funded by Tromsø Museum, UiT—the Arctic University of Norway.
Author Contributions
DPR, TA, and IGA designed the project, obtained funding, and performed the fieldwork. MFA instructed DPR during primer optimization and laboratory work. DPR performed the laboratory work and wrote the manuscript. All coauthors commented on the manuscript.
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The authors declare no conflict of interest.
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Online resource 1
Microsatellite library of H. persicum with 3904 sequences containing microsatellite motifs (TXT 1173 kb)
Online resource 2
List of 30 biologically and 134 bioinformatically validated microsatellite markers (XLSX 47 kb)
Fig. S1
Screen shot of some of the markers amplified in H. persicum in a singleplex. PET labeled marker Hp_02 with two alleles at 131.5 and 135.6, Hp_08 with two alleles at 170.6 and 173.5, and Hp_18 with single allele at 256.8 bp (base pair); HEX labeled marker Hp_19 with two alleles at 170 and 180.1, and Hp_05 with one allele at 125 bp; 6-FAM labeled marker Hp_09 with single allele at 159 bp; and NED labeled marker Hp_10 and Hp_16 with single allele each at 187.6 and 135.6 bp respectively (see Tables 3 and 4 of the paper for details) (PDF 81 kb)
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Rijal, D.P., Falahati-Anbaran, M., Alm, T. et al. Microsatellite Markers for Heracleum persicum (Apiaceae) and Allied Taxa: Application of Next-Generation Sequencing to Develop Genetic Resources for Invasive Species Management. Plant Mol Biol Rep 33, 1381–1390 (2015). https://doi.org/10.1007/s11105-014-0841-y
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DOI: https://doi.org/10.1007/s11105-014-0841-y