Development, characterization, and cross-amplification of 17 microsatellite markers for Filipendula vulgaris

. 2019 Dec ; 7 (12) : e11307. [epub] 20191208

Status PubMed-not-MEDLINE Jazyk angličtina Země Spojené státy americké Médium electronic-ecollection

Typ dokumentu časopisecké články

Perzistentní odkaz   https://www.medvik.cz/link/pmid31890353

PREMISE: Polymorphic microsatellite markers were developed as a tool for genetic investigations of Filipendula vulgaris (Rosaceae) and related species. METHODS AND RESULTS: Seventeen new polymorphic microsatellite markers were developed for F. vulgaris using the Illumina MiSeq platform. Polymorphism of the 17 loci was tested in three populations. We identified a total of 203 alleles, ranging from four to 19 per locus, with levels of observed and expected heterozygosity ranging from 0.267 to 1.000 and 0.461 to 0.899, respectively. Primers were also tested for cross-amplification in three related species. Seven loci successfully cross-amplified in F. camtschatica and F. ulmaria, whereas we detected positive cross-amplification in only three loci in Geum urbanum. CONCLUSIONS: The newly developed microsatellite primers will serve as useful genetic tools for further population genetic studies on F. vulgaris and related species.

Zobrazit více v PubMed

Bączek, K. , Cygan M., Przybył J. L., Kosakowska O., and Węglarz Z.. 2012. Seasonal variation of phenolics content in above‐ and underground organs of dropwort (Filipendula vulgaris Moench). Herba Polonica 58: 24–32.

Ball, P. W. 1968. Filipendula In Tutin T. G., Heywood V. H., Burges N. A., Moore D. M., Valentine D. H., Walters S. M., and Webb D. A. [eds.], Flora Europaea, vol. 2, 6–7. Cambridge University Press, Cambridge, United Kingdom.

Belyayev, A. , Josefiová J., Jandová M., Kalendar R., Krak K., and Mandák B.. 2019. Natural history of a satellite DNA family: From the ancestral genome component to species‐specific sequences, concerted and non‐concerted evolution. International Journal of Molecular Sciences 20: 1201. PubMed PMC

Bolger, A. M. , Lohse M., and Usadel B.. 2014. Trimmomatic: A flexible trimmer for Illumina sequence data. Bioinformatics 30: 2114–2120. PubMed PMC

Chakraborty, R. , Zhong Y., Jin L., and Budowle B.. 1994. Nondetectability of restriction fragments and independence of DNA fragment sizes within and between loci in RFLP typing of DNA. American Journal of Human Genetics 55: 391–401. PubMed PMC

Faircloth, B. C. 2008. MSATCOMMANDER: Detection of microsatellite repeat arrays and automated, locus‐specific primer design. Molecular Ecology Resources 8: 92–94. PubMed

Keenan, K. , McGinnity P., Cross T. F., Crozier W. W., and Prodöhl P. A.. 2013. diveRsity: An R package for the estimation and exploration of population genetics parameters and their associated errors. Methods in Ecology and Evolution 4: 782–788.

Langmead, B. , and Salzberg S. L.. 2012. Fast gapped‐read alignment with Bowtie 2. Nature Methods 9: 357–359. PubMed PMC

Meusel, H. , Jäger E. J., and Weinert E.. 1965. Vergleichende Chorologie der Zentraleuropäischen Flora, Vol. 1–3 G. Fischer, Jena, Germany.

Miller, M. P. , Knaus B. J., Mullins T. D., and Haig S. M.. 2013. SSR_pipeline: A bioinformatic infrastructure for identifying microsatellites from paired‐end Illumina high‐throughput DNA sequencing data. Journal of Heredity 104: 881–885. PubMed

Schanzer, I. A. 1994. Taxonomical revision of the genus Filipendula Mill. (Rosaceae). Journal of Japanese Botany 69: 290–319.

Schanzer, I. A. 2016. Phylogenetic relationships of East Asian endemic species of Filipendula (Rosaceae‐Rosoideae) as revealed by nrITS markers. Journal of Japanese Botany 91: 250–256.

Schuelke, M. 2000. An economic method for the fluorescent labeling of PCR fragments. Nature Biotechnology 18: 233–234. PubMed

Untergasser, A. , Cutcutache I., Koressaar T., Ye J., Faircloth B. C., Remm M., and Rozen S. G.. 2012. Primer3—New capabilities and interfaces. Nucleic Acids Research 40: e115. PubMed PMC

van Oosterhout, C. , Hutchinson W. F., Wills D. P., and Shipley P.. 2004. MICRO‐CHECKER: Software for identifying and correcting genotyping errors in microsatellite data. Molecular Ecology Notes 4: 535–538.

Weidema, I. R. , Magnussen L. S., and Philipp M.. 2000. Gene flow and mode of pollination in a dry‐grassland species, Filipendula vulgaris (Rosaceae). Heredity 84: 311–320. PubMed

Weir, B. S. , and Cockerham C. C.. 1984. Estimating F‐statistics for the analysis of population structure. Evolution 38: 1358–1370. PubMed

Najít záznam

Citační ukazatele

Nahrávání dat ...

    Možnosti archivace