Hostname: page-component-76fb5796d-9pm4c Total loading time: 0 Render date: 2024-04-25T12:31:01.173Z Has data issue: false hasContentIssue false
  • English
  • Français

Development of nuclear microsatellite markers in Stizophyllum (Bignoniaceae) using next-generation sequencing

Published online by Cambridge University Press:  05 April 2019

Maila Beyer Open the ORCID record for Maila Beyer [Opens in a new window] ,
Alison Gonçalvez Nazareno Open the ORCID record for Alison Gonçalvez Nazareno [Opens in a new window]  and
Lúcia G. Lohmann Open the ORCID record for Lúcia G. Lohmann [Opens in a new window]
Maila Beyer*
Affiliation:
Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo (USP), Rua do Matão 277, 05508-090, SP, São Paulo, Brazil
Alison Gonçalvez Nazareno
Affiliation:
Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo (USP), Rua do Matão 277, 05508-090, SP, São Paulo, Brazil
Lúcia G. Lohmann*
Affiliation:
Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo (USP), Rua do Matão 277, 05508-090, SP, São Paulo, Brazil
*
*Corresponding authors. E-mail: maila.beyer@gmail.com, llohmann@usp.br
*Corresponding authors. E-mail: maila.beyer@gmail.com, llohmann@usp.br
Get access Rights & Permissions [Opens in a new window]

Abstract

Here we developed the first set of nuclear microsatellite markers (nSSRs) for Stizophyllum riparium (Bignoniaceae), a widespread species of Neotropical liana. Thirty-two sets of primers were isolated from a genomic dataset obtained with an Illumina HiSeq Platform, and characterized for 57 individuals of S. riparium from three populations. Nine nSSRs were polymorphic and the number of alleles ranged from eight to 29. The unbiased expected heterozygosity per locus ranged from 0.724 to 0.952 and the polymorphic information content values ranged from 0.717 to 0.944. All nine primer pairs also amplified for two closely related species (S. inaequilaterum and S. perforatum). The new set of nuclear markers will be useful for population genetics studies of Stizophyllum as a whole.

Keywords

cross-amplificationgenetic diversityStizophyllum inaequilaterumStizophyllum perforatum
Type
Short Communication
Information
Plant Genetic Resources , Volume 17 , Issue 4 , August 2019 , pp. 382 - 385
Copyright
Copyright © NIAB 2019 

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

References

Barbará, T, Martinelli, G, Fay, MF, Mayo, SJ and Lexer, C (2007) Population differentiation and species cohesion in two closely related plants adapted to neotropical high-altitude ‘inselbergs’, Alcantarea imperialis and Alcantarea geniculata (Bromeliaceae). Molecular Ecology 16: 1981–1992.Google Scholar
Beyer, M, Nazareno, AG and Lohmann, LG (2017) Using genomic data to develop chloroplast DNA SSRs for the neotropical liana Stizophyllum riparium (Bignonieae, Bignoniaceae). Application in Plants Science 5: 1–5.Google Scholar
Collevatti, RG, Terribile, LC, Lima-Ribeiro, MS, Nabout, JC, Oliveira, G, Rangel, TF, Rabelo, SG and Diniz-Filho, JAF (2012) A coupled phylogeographical and species distribution modelling approach recovers the demo-graphical history of a Neotropical seasonally dry forest tree species. Molecular Ecology 21: 5845–5863.Google Scholar
Figueira, GM, Ramelo, PR, Ogasawara, DC, Montanari, I, Zucchi, MI, Cavallari, MM and Foglio, MA (2010) A set of microsatellite markers for Arrabidaea chica (Bignoniaceae), a medicinal liana from the Neotropics. American Journal of Botany 97: 63–64.Google Scholar
Fonseca, LHM and Lohmann, LG (2015) Biogeography and evolution of Dolichandra (Bignonieae, Bignoniaceae). Botanical Journal of the Linnean Society 179: 403–420.Google Scholar
Gentry, AH (1974) Coevolutionary patterns in Central American Bignoniaceae. Annals of the Missouri Botanical Garden 61: 728–759.Google Scholar
Goudet, J (1995) FSTAT (version 1.2): a computer note computer program to calculate F-statistics. Journal of Heredity 86: 485–486.Google Scholar
Hmeljevski, KV, Nazareno, AG, Bueno, ML, dos Reis, MS and Forzza, RC (2017) Do plant populations on distinct inselbergs talk to each other? A case study of genetic connectivity of a bromeliad species in an Ocbil landscape. Ecology and Evolution 7: 4704–4716.Google Scholar
Holland, MM and Parson, W (2011) Genemarker® HID: a reliable software tool for the analysis of forensic STR data. Journal of Forensic Sciences 56: 29–35.Google Scholar
Kalia, RK, Rai, MK, Kalia, S, Singh, R and Dhawan, AK (2011) Microsatellite markers: an overview of the recent progress in plants. Euphytica 177: 309–334.Google Scholar
Lexer, C, Marthaler, F, Humbert, S, Martinelli, G and Versieux, LM (2016) Gene flow and diversification in a species complex of Alcantarea inselberg bromeliads. Botanical Journal of the Linnean Society 181: 505–520.Google Scholar
Lohmann, LG (2006) Untangling the phylogeny of neotropical lianas (Bignonieae, Bignoniaceae). American Journal of Botany 93: 304–318.Google Scholar
Lohmann, LG and Taylor, CM (2014) A new generic classification of tribe Bignonieae (Bignoniaceae). Annals of the Missouri Botanical Garden 99: 348–489.Google Scholar
Morgante, M and Olivieri, AM (1993) PCR-amplified microsatellites as markers in plant genetics. The Plant Journal 3: 175–182.Google Scholar
Nazareno, AG, Carlsen, M and Lohmann, LG (2015) Complete chloroplast genome of Tanaecium tetragonolobum: the first Bignoniaceae plastome. PLoS ONE 10: 1–18.Google Scholar
Palma-Silva, C, Lexer, C, Paggi, GM, Barbará, T, Bered, F and Bodanese-Zanettini, MH (2009) Range-wide patterns of nuclear and chloroplast DNA diversity in Vriesea gigantea (Bromeliaceae), a neotropical forest species. Heredity 103: 503–512.Google Scholar
Peakall, R and Smouse, PE (2006) GENALEX 6: genetic analysis in Excel. Population genetic software for teaching and research. Molecular Ecology Notes 6: 288–295.Google Scholar
Pinheiro, F, de Barros, F, Palma-Silva, C, Fay, MF, Lexer, C and Cozzolino, S (2011) Phylogeography and genetic differentiation along the distributional range of the orchid Epidendrum fulgens: a Neotropical coastal species not restricted to glacial refugia. Journal of Biogeography 38: 1923–1935.Google Scholar
Powell, W, Machray, GC and Provan, J. (1996) Polymorphism revealed by simple sequence repeats. Trends in Plant Science 1: 215–222.Google Scholar
Rice, WR (1989) Analyzing tables of statistical tests. Evolution 43: 223–225.Google Scholar
Rozen, S and Skaletsky, H (1999) Primer3 on the www for general users and for biologist programmers. Methods in Molecular Biology 132: 365–386.Google Scholar
Tóth, EG, Köbölkuti, ZA, Pedryc, A and Höhn, M (2017) Evolutionary history and phylogeography of Scots pine (Pinus sylvestris L.) in Europe based on molecular markers. Journal of Forestry Research 28: 637–651.Google Scholar
Van Oosterhout, C, Hutchinson, WF, Wills, DPM and Shipley, P (2004) Micro-Checker: software for identifying and correcting genotyping errors in microsatellite data. Molecular Ecology Notes 4: 535–538.Google Scholar
Supplementary material: File

Beyer et al. supplementary material

Appendices 1-4

Download Beyer et al. supplementary material(File)
File 140.3 KB