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3 Biotech

, 9:423 | Cite as

Repetitive genomic elements in Campomanesia xanthocarpa: prospection, characterization and cross amplification of molecular markers

  • Vanessa S. Petry
  • Valdir Marcos Stefenon
  • Lilian O. Machado
  • Gustavo H. F. Klabunde
  • Fábio O. Pedrosa
  • Rubens O. NodariEmail author
Original Article
  • 24 Downloads

Abstract

Repetitive genomic elements were prospected in Campomanesia xanthocarpa, aiming to characterize these elements in a non-model plant species and to develop species-specific microsatellite markers. Approximately 4.12% of the partial genome of C. xanthocarpa is composed of repetitive elements, being retrotransposons the most widely represented. A total of nine polymorphic microsatellite markers were obtained: four nuclear-neutral, two nuclear EST, two plastidial and one mitochondrial. Levels of population genetic diversity of four natural populations of C. xanthocarpa were characterized using these markers. In addition, the cross-species amplification of the microsatellite markers was tested in seven species of tribe Myrteae (Myrtaceae). The characterized microsatellite markers revealed low to moderate levels of genetic diversity (expected heterozygosity range: 0.33–0.57; observed heterozygosity: 0.26–0.74 and number of alleles: 2.25–4.25). Cross-species amplification was successful for all loci, except Cxant76. These nine markers will contribute for studies on genetic diversity, gene flow, plant selection and breeding of this species, towards the conservation of natural populations, as well as its commercial use.

Keywords

Guabiroba nSSRs ptSSRs mtSSRs Transferability Transposons 

Notes

Acknowledgements

The authors would like to thank Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) for the financial support (Proc. 307144/2013-5) and scholarships and grants awarded to V.M.S. (Process 113617/2018-6), V.S.P. and R.O.N. The authors would also like to thank CAPES for scholarships awarded to G.H.F.K. and L.O.M., and to the Nucleus of Nitrogen Fixation/UFPR for sequencing. We thank Ms. Yohan Fritsche (LFDGV, UFSC) for the help with the flow cytometry analysis.

Compliance with ethical standards

Ethical approval

This article does not include any studies with human participants or animals performed by any of the authors.

Informed consent

This article does not involve any informed consent.

Conflict of interest

All authors hereby declare that there is no conflict of interest.

Supplementary material

13205_2019_1953_MOESM1_ESM.pdf (554 kb)
Supplementary material 1 (PDF 553 kb)

References

  1. Barghini E, Natali L, Cossu RM, Giordani T, Pindo M, Cattonaro F, Scalabrin S, Velasco R, Morgante M, Cavallini A (2014) The Peculiar Landscape of Repetitive Sequences in the Olive (Olea europaea L.) Genome. Genome Biol Evol 6:776–791CrossRefGoogle Scholar
  2. Doyle JJ, Doyle JL (1990) Isolation of plant DNA from fresh tissue. Focus 12:13–15Google Scholar
  3. Flint-Garcia SA, Thornsberry JM, Buckler ES IV (2003) Structure of linkage disequilibrium in plants. Annu Rev Plant Biol 54:357–374CrossRefGoogle Scholar
  4. Góes BD, Ruas EA, Benício LM, Cassiano D, de Souza FP, Ruas PM (2019) Development and characterization of microsatellite loci for Campomanesia xanthocarpa (Myrtaceae) and cross amplification in related species. Acta Scientiarum. Biol Sci 41:e43454Google Scholar
  5. Goudet J (2001) FSTAT: a program to estimate and test gene diversities and fixation indices (Version 2.9.3.2). University of Lausanne, SwitzerlandGoogle Scholar
  6. Guzman F, Almerão MP, Körbes AP, Loss-Morais G, Margis R (2012) Identification of MicroRNAs from Eugenia uniflora by High-Throughput Sequencing and Bioinformatics Analysis. PLoS One 7(11):e49811CrossRefGoogle Scholar
  7. Guzman F, Kulcheski FR, Turchetto-Zolet AC, Margis R (2014) De novo assembly of Eugenia uniflora L. transcriptome and identification of genes from the terpenoid biosynthesis pathway. Plant Sci 229:238–246CrossRefGoogle Scholar
  8. Kalendar R, Grob T, Suoniemi A, Schulman AH (1999) IRAP and REMAP: Two new retrotransposon-based DNA fingerprinting techniques. Theor Appl Genet 98:704–711CrossRefGoogle Scholar
  9. Kalinowski ST, Taper ML, Marshall TC (2007) Revising how the computer program CERVUS accommodates genotyping error increases success in paternity assignment. Mol Ecol 16:1099–1106CrossRefGoogle Scholar
  10. Khodwekar S, Staton M, Coggeshall MV, Carlson JE, Gailing O (2015) Nuclear microsatellite markers for population genetic studies in sugar maple (Acer saccharum Marsh.). Annu For Res 58:193–204Google Scholar
  11. Klabunde GHF, Olkoski D, Vilperte V, Zucchi MI, Nodari RO (2014) Characterization of 10 new Nuclear Microsatellite Markers in Acca sellowiana (Myrtaceae). Appl Plant Sci 2:1400020CrossRefGoogle Scholar
  12. Legrand CD, Klein RM (1977) Mirtáceas. In: Reitz R (ed) Flora ilustrada catarinense. Herbário Barbosa Rodrigues, Itajaí, pp 596–602Google Scholar
  13. Lemos RPM, Matielo CBDO, Beise DC, Rosa VG, Sarzi DS, Roesch LFW, Stefenon VM (2018) Characterization of plastidial and nuclear SSR markers for understanding invasion histories and genetic diversity of Schinus molle L. Biology 7:43CrossRefGoogle Scholar
  14. Lisbôa GN, Kinupp VF, Barros IBI (2011) Campomanesia xanthocarpa (Guabiroba). In: Coradin L, Siminski A, Reis A (eds) Espécies nativas da flora brasileira de valor econômico atual ou potencial: plantas para o futuro: Região Sul. MMA, Brasília, pp 159–162Google Scholar
  15. Macas J, Neumann P, Navrátilová A (2007) Repetitive DNA in the pea (Pisum sativum L.) genome: comprehensive characterization using 454 sequencing and comparison to soybean and Medicago truncatula. BMC Genom 8(1):1471–2164.  https://doi.org/10.1186/1471-2164-8-427 CrossRefGoogle Scholar
  16. Macas J, Novák P, Pellicer J, Čížkov J, Koblížkov A, Neumann P, Fukov I, Doležel J, Kelly LJ, Leitch IJ (2015) In depth characterization of repetitive DNA in 23 plant genomes reveals sources of genome size variation in the legume tribe fabeae. PLoS One 10:e0143424CrossRefGoogle Scholar
  17. Machado LO (2017) Análise comparativa do genoma plastidial de Myrtaceae: Acca sellowiana (O. Berg) Burret, Eugenia uniflora L., Campomanesia xanthocarpa (Mart.) O.Berg, Plinia cauliflora (Mart.) Kausel, Plinia aureana (Mattos) Mattos e Plinia sp [Comparative analysis of the plastid genome of Myrtaceae: Acca sellowiana (O. Berg) Burret, Eugenia uniflora L., Campomanesia xanthocarpa (Mart.) O.Berg, Plinia cauliflora (Mart.) Kausel, Plinia aureana (Mattos) Mattos and Plinia sp]. Dissertation, Federal University of Santa CatarinaGoogle Scholar
  18. Marcon HS, Domingues DS, Silva JC, Borges RJ, Matioli FF, Fontes MRM, Marino CL (2015) Transcriptionally active LTR retrotransposons in Eucalyptus genus are differentially expressed and insertionally polymorphic. BMC Plant Biol 15:198.  https://doi.org/10.1186/s12870-015-0550-1 CrossRefPubMedPubMedCentralGoogle Scholar
  19. Mehrotra S, Goyal V (2014) Repetitive sequences in plant nuclear DNA: types, distribution, evolution and function. Genom Proteom Bioinf 12:164–171CrossRefGoogle Scholar
  20. Nagel JC, Ceconi DE, Poletto I, Stefenon VM (2015) Historical Gene Flow within and among Populations of Luehea divaricata in the Brazilian Pampa. Genetica 143:317–329CrossRefGoogle Scholar
  21. Owusu SA, Staton M, Jennings TN, Schlarbaum S, Coggeshall MV, Romero-Severson J, Carlson JE (2013) Gailing O (2013) development of genomic microsatellites in Gleditsia triacanthos (Fabaceae) using illumina sequencing. Appl Plant Sci 1:1300050CrossRefGoogle Scholar
  22. Peakall R, Smouse PE (2012) GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research—an update. Bioinformatics 28:2537–2539CrossRefGoogle Scholar
  23. Petit RJ, Duminil J, Fineschi S, Hampe A, Salvini D, Vendramin GG (2005a) Comparative organization of chloroplast, mitochondrial and nuclear diversity in plant populations. Mol Ecol 14:689–701CrossRefGoogle Scholar
  24. Petit RJ, Duminil J, Fineschi S, Hampe A, Slavini D, Vendramin GG (2005b) Comparative organization of chloroplast, mitochondrial and nuclear diversity in plant populations. Mol Ecol 14:689–701.  https://doi.org/10.1111/j.1365-294X.2004.02410.x CrossRefPubMedGoogle Scholar
  25. Raymond M, Rousset F (1995) GENEPOP (Version 1.2): population genetics software for exact tests and ecumenicism. J Hered 86:248–249CrossRefGoogle Scholar
  26. Rousset F (2008) Genepop’007: a complete re-implementation of the genepop software for windows and linux. Mol Ecol Resour 8:103–106CrossRefGoogle Scholar
  27. Rozen S, Skaletsky HJ (2000) Primer3 on the WWW for general users and for biologist programmers. In: Krawetz S, Misener S (eds) Bioinformatics methods and protocols: methods in molecular biology. Humana Press, Totowa, pp 365–386Google Scholar
  28. Santos KL, Santos MO, Laborda PR, Souza AP, Peroni N, Nodari RO (2008) Isolation and characterization of microsatellite markers in Acca sellowiana (Berg) Burret. Molecular Ecology Resources 8:998–1000CrossRefGoogle Scholar
  29. Sarzi DS, Justolin B, Silva C, Lemos RPM, Stefenon VM (2019) Discovery and characterization of SSR markers in Eugenia uniflora L. (Myrtaceae) using low coverage genome sequencing. An Acad Bras Ciênc 91:20180420CrossRefGoogle Scholar
  30. Shcherban AB (2015) Repetitive DNA sequences in plant genomes. Russ J Genet Appl Res 5:159–167.  https://doi.org/10.1134/S2079059715030168 CrossRefGoogle Scholar
  31. Staton M, Best T, Khodwekar S, Owusu S, Xu T, Xu Y, Jennings T, Cronn R, Arumuganathan AK, Coggeshall M et al (2015) Preliminary genomic characterization of ten hardwood tree species from multiplexed low coverage whole genome sequencing. PLoS ONE 10:e0145031CrossRefGoogle Scholar
  32. Stefenon VM, Nagel JC, Poletto I (2016) Evidences of genetic bottleneck and fitness decline in Luehea divaricata populations from Southern Brazil. Silvae Fennica 50:1566Google Scholar
  33. Stefenon VM, Sarzi DS, Roesch LFW (2019) High-throughput sequencing analysis of Eugenia uniflora: insights into repetitive DNA, gene content and potential biotechnological applications. 3 Biotech 9:200.  https://doi.org/10.1007/s13205-019-1729-1 CrossRefPubMedGoogle Scholar
  34. Thiel T, Michalek W, Varshney R, Graner A (2003) Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.). Theor Appl Genet 106:411–422CrossRefGoogle Scholar
  35. Van Oosterhout C, Hutchinson WF, Wills DPM, Shipley P (2004) MICRO-CHECKER: software for identifying and correcting genotyping errors in microsatellite data, version 2.2.4. Mol Ecol Notes 4:535–553CrossRefGoogle Scholar
  36. Viecili PRN, Borges DO, Kirsten K, Malheiros J, Viecili E, Melo RD, Trevisan G, Silva MA, Bochi GV, Moresco RN, Klafke JZ (2014) Effects of Campomanesia xanthocarpa on inflammatory processes, oxidative stress, endothelial dysfunction and lipid biomarkers in hypercholesterolemic individuals. Atherosclerosis 234:85–92CrossRefGoogle Scholar
  37. Vieira MLC, Santini L, Diniz AL, Munhoz CF (2016) Microsatellite markers: what they mean and why they are so useful. Genet Mol Biol 39(3):312–328CrossRefGoogle Scholar
  38. Wu Y, Zhang R, Staton M, Schlarbaum SE, Coggeshall MV, Romero-Severson J, Carlson JE, Liang H, Xu Y, Drautz-Moses DI et al (2017) Development of genic and genomic microsatellites in Gleditsia triacanthos L (Fabaceae) using illumina sequencing. Ann For Res 60(2):343–350Google Scholar

Copyright information

© King Abdulaziz City for Science and Technology 2019

Authors and Affiliations

  1. 1.Graduate Program in Plant Genetic ResourcesUniversidade Federal de Santa CatarinaFlorianópolisBrazil
  2. 2.Nucleus of Molecular Ecology and Plant MicropropagationUniversidade Federal do PampaSão GabrielBrazil
  3. 3.Empresa de Pesquisa Agropecuária e Extensão Rural de Santa Catarina (EPAGRI)ItajaíBrazil
  4. 4.Department of Biochemistry and Molecular Biology, Nucleus of Nitrogen FixationUniversidade Federal do ParanáCuritibaBrazil

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