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Development of microsatellite markers for Myracrodruon urundeuva (F.F. & M.F. Allemão), a highly endangered species from tropical forest based on next-generation sequencing

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Abstract

Myracrodruon urundeuva is a tree species of high economic importance due the strength and durability of its wood. Threatened of extinction in Brazil, it is present only in a few forest remnants, mostly in conservation units. Currently, there is little information on the genetic diversity of natural populations in Brazil and even less information about the genome of this species. Here, new species-specific microsatellite loci were developed based on next-generation sequencing (Illumina). More than 100,000 loci were identified in the run, with di- to hexanucleotides motifs. Of these, 20 loci were selected for validation in 30 individuals, with 15 successfully polymorphic loci detected. The number of alleles ranged among loci from 3 to 16, with an average of 7.73, expected (H e ) and observed (H o ) heterozygosity ranged from 0.246 to 0.902 and from 0.103 to 0.867, respectively. These results point out that these new set of markers has a great potential for use in population genetic studies for genetic conservation of the species.

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References

  1. Gaino APSC, Silva AM, Moraes MA et al (2010) Understanding the effects of isolation on seed and pollen flow, spatial genetic structure and effective population size of the dioecious tropical tree Myracrodruon urundeuva. Conserv Genet 11:1631–1643

    Article  Google Scholar 

  2. Santin DA, Leitão Filho HF (1991) Restabelecimento e revisão taxonômica do gênero Myracrodruon Freire Allemão (Anacardiaceae). Rev Bras Bot 14:133–145

    Google Scholar 

  3. Gaino APSC, Moraes MLT, Moreira JP et al (2011) Mating system in Myracrodruon urundeuva (Anarcadiaceae): implications for conservation genetics. Rev Bras Bot 34(4):545–551

    Article  Google Scholar 

  4. Viana G et al (2014) Myracrodruon urundeuva Allemão, a Brazilian medicinal species, presents neuroprotective effects on a Parkinson’s disease model, in rats. Eur Neuropsychopharmacol 24(2):230–231

    Article  Google Scholar 

  5. Instituto Brasileiro do Meio Ambiente e dos Recursos Naturais Renováveis (1992) Lista oficial de espécies da flora brasileira ameaçadas de extinção. Diário Oficial, Brasília

    Google Scholar 

  6. Carvalho PER (1994) Espécies florestais brasileiras: recomendações silviculturais, potencialidade e uso da madeira. Empresa Brasileira de Pesquisa Agropecuária, Colombo

    Google Scholar 

  7. Moraes MLT, Kageyama PY, Sebbenn AM (2004) Correlated mating in dioecious tropical tree species. Myracrodruon urundeuva Fr All. For Genet 11(4):53–59

    Google Scholar 

  8. Moraes MLT, Kageyama PY, Sebbenn AM (2005) Diversidade e estrutura espacial em duas populações de Myracrodruon urundeuva Fr. All. sob diferentes condições antrópicas. Rev Árvore 29(2):281–289

    Article  Google Scholar 

  9. Reis AMM, Grattapaglia D (2004) RAPD variation in a germplasm collection of Myracrodruon urundeuva (Anacardiaceae), an endangered tropical tree: recommendations for conservation. Genet Resour Crop Evol. https://doi.org/10.1023/B:GRES.0000024159.48644.e6

    Google Scholar 

  10. Santos CAF, Oliveira VR, Kiill LHP, Sá IIS (2007) Variabilidade genética, com base em marcadores RAPD, de três espécies arbóreas ameaçadas de extinção no semi-árido brasileiro. Sci For (74):37–44

  11. Freitas MLM, Sebbenn AM, Moraes MLT, Lemos EGM (2004) Mating system of a population of Myracrodruon urundeuva F.F. & M.F. Allemão using the fAFLP molecular marker. Genet Mol Biol. https://doi.org/10.1590/S1415-47572004000300019

    Google Scholar 

  12. Freitas MLM, Aukar APA, Sebbenn AM, Moraes MLT, Lemos EGM (2005) Variabilidade genética intrapopulacional em Myracrodruon urundeuva Fr. All. por marcador AFLP. Sci For 68:21–28

    Google Scholar 

  13. Caetano S, Silveira P, Spichiger R, Naciri-Graven Y (2005) Identification of microsatellite markers in a neotropical seasonally dry Forest tree, Astronium urundeuva (Anacardiaceae). Mol Ecol Notes 5(1):21–23

    Article  CAS  Google Scholar 

  14. Caetano S, Prado D, Pennington RT et al (2008) The history of seasonally dry tropical forests in eastern South America: inferences from the genetic structure of the tree Astronium urundeuva (Anacardiaceae). Mol Ecol 13(17):3147–3159

    Article  Google Scholar 

  15. Viegas MP, Silva CLSP, Moreira JP et al (2011) Diversidade genética e tamanho efetivo de duas populações de Myracrodruon urundeuva Fr. All., sob conservação ex situ. Rev Árvore 35(4):769–779

    Article  Google Scholar 

  16. Doyle JJ, Doyle JL (1990) Isolation of plant DNA from fresh tissue. Focus 12:13–15

    Google Scholar 

  17. Miller MP, Knaus BJ, Mullins TD, Haig SM (2013) SSR_pipelin: a bioinformatic infrastructure for identifying microsatellites from paired-end Illumina high-throughput DNA sequencing data. J Hered 104:881–885

    Article  CAS  PubMed  Google Scholar 

  18. You FM, Huo N, Gu YQ et al (2008) BatchPrimer3: a high throughput web application for PCR and sequencing primer design. BMC Bioinform. https://doi.org/10.1186/1471-2105-9-253. http://probes.pw.usda.gov/batchprimer3/. Accessed Nov 2016

  19. Schuelke M (2000) An economic method for the fluorescent labeling of PCR fragments. Nat Biotechnol 18:233–234

    Article  CAS  PubMed  Google Scholar 

  20. Kalinowsk ST, Taper ML, Marshall TC (2007) Revising how the computer program CERVUS accommodates genotyping error increases success in paternity assignment. Mol Ecol. https://doi.org/10.1111/j.1365-294x.2007.03089.x

    Google Scholar 

  21. Rousset F (2008) Genepop’007: a complete reimplementation of the Genepop software for Windows and Linux. Mol Ecol Resour 8:103–106

    Article  PubMed  Google Scholar 

  22. van Oosterhout C, Hutchinson WF, Wills DP, Shipley P (2004) Micro-checker: software for identifying and correcting genotyping errors in microsatellite data. Mol Ecol Notes 4:535–538

    Article  Google Scholar 

  23. Duan C-x, Li D-d, Sun S-l et al (2014) Rapid development of microsatellite markers for Callosobruchus chinensis using Illumina paired-end sequencing. PLoS ONE. https://doi.org/10.1371/journal.pone.0095458

    Google Scholar 

  24. Yang T, Fang L, Zhang X et al (2015) High-throughput development of SSR markers from pea (Pisum sativum L.) based on next generation sequencing of a Purified Chinese commercial variety. PLoS ONE. https://doi.org/10.1371/journal.pone.0139775

    Google Scholar 

  25. Zhou T, Li Z-H, Bai G-Q et al (2016) Transcriptome sequencing and development of genic SSR markers of an endangered Chinese endemic genus Dipteronia Oliver (Aceraceae). Molecules. https://doi.org/10.3390/molecules21030166

    PubMed Central  Google Scholar 

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Acknowledgments

The authors thank all the individuals who assisted in the collection of samples. This investigation was supported by FAPESP (Fundação de Amparo à Pesquisa do Estado de São Paulo; Grant Number for DCLS 2013/24503-1).

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Authors and Affiliations

  1. Faculty of Agronomy, UNESP - Univ Estadual Paulista, C.P. 237, CEP 18610-307, Botucatu, SP, Brazil

    Danilla Cristina Lemos Souza & Mário Luiz Teixeira de Moraes

  2. Biotechnology Institute (IBTEC), UNESP - Univ Estadual Paulista, CEP 18607-440, Botucatu, SP, Brazil

    Bruno César Rossini & Celso Luís Marino

  3. Department of Genetics, UNESP - Univ Estadual Paulista, CEP 18618-689, Botucatu, SP, Brazil

    Bruno César Rossini & Celso Luís Marino

  4. Faculty of Engineer, UNESP - Univ Estadual Paulista, CEP 15385-000, Ilha Solteira, SP, Brazil

    Francine Beatriz de Souza & Mário Luiz Teixeira de Moraes

  5. São Paulo Forestry Institute, C.P. 1322, CEP 01059-970, São Paulo, SP, Brazil

    Alexandre Magno Sebbenn

Authors
  1. Danilla Cristina Lemos Souza
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  2. Bruno César Rossini
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  3. Francine Beatriz de Souza
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  4. Alexandre Magno Sebbenn
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  5. Celso Luís Marino
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  6. Mário Luiz Teixeira de Moraes
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Correspondence to Bruno César Rossini.

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Souza, D.C.L., Rossini, B.C., de Souza, F.B. et al. Development of microsatellite markers for Myracrodruon urundeuva (F.F. & M.F. Allemão), a highly endangered species from tropical forest based on next-generation sequencing. Mol Biol Rep 45, 71–75 (2018). https://doi.org/10.1007/s11033-017-4142-z

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  • DOI: https://doi.org/10.1007/s11033-017-4142-z

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