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Chamala S, García N, Godden GT, et al. MarkerMiner 1.0: A new application for phylogenetic marker development using angiosperm transcriptomes. Appl Plant Sci. 2015;3(4)doi: 10.3732/apps.1400115.
Chamala, S., García, N., Godden, G. T., Krishnakumar, V., Jordon-Thaden, I. E., De Smet, R., Barbazuk, W. B., Soltis, D. E., & Soltis, P. S. (2015). MarkerMiner 1.0: A new application for phylogenetic marker development using angiosperm transcriptomes. Applications in plant sciences, 3(4), . https://doi.org/10.3732/apps.1400115
Chamala, Srikar, et al. "MarkerMiner 1.0: A new application for phylogenetic marker development using angiosperm transcriptomes." Applications in plant sciences vol. 3,4 (2015). doi: https://doi.org/10.3732/apps.1400115
Chamala S, García N, Godden GT, Krishnakumar V, Jordon-Thaden IE, De Smet R, Barbazuk WB, Soltis DE, Soltis PS. MarkerMiner 1.0: A new application for phylogenetic marker development using angiosperm transcriptomes. Appl Plant Sci. 2015 Apr 06;3(4). doi: 10.3732/apps.1400115. eCollection 2015 Apr. PMID: 25909041; PMCID: PMC4406834.
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Appl Plant Sci. 2015 Apr 06;3(4). doi: 10.3732/apps.1400115. eCollection 2015 Apr.

MarkerMiner 1.0: A new application for phylogenetic marker development using angiosperm transcriptomes.

Applications in plant sciences

Srikar Chamala, Nicolás García, Grant T Godden, Vivek Krishnakumar, Ingrid E Jordon-Thaden, Riet De Smet, W Brad Barbazuk, Douglas E Soltis, Pamela S Soltis

Affiliations

  1. Department of Biology, University of Florida, Gainesville, Florida, USA.
  2. Department of Biology, University of Florida, Gainesville, Florida, USA ; Florida Museum of Natural History, University of Florida, Gainesville, Florida, USA ; Facultad de Ciencias Forestales y Conservación de la Naturaleza, Universidad de Chile, Santiago, Chile.
  3. Department of Biology, University of Florida, Gainesville, Florida, USA ; Florida Museum of Natural History, University of Florida, Gainesville, Florida, USA ; Rancho Santa Ana Botanic Garden, Claremont, California, USA.
  4. Plant Genomics, J. Craig Venter Institute, Rockville, Maryland, USA.
  5. Department of Biology, Bucknell University, Lewisburg, Pennsylvania, USA ; Jepson and University Herbaria, University of California, Berkeley, Berkeley, California, USA.
  6. Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, 9052 Ghent, Belgium ; Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium.
  7. Department of Biology, University of Florida, Gainesville, Florida, USA ; Genetics Institute, University of Florida, Gainesville, Florida, USA.
  8. Department of Biology, University of Florida, Gainesville, Florida, USA ; Florida Museum of Natural History, University of Florida, Gainesville, Florida, USA ; Genetics Institute, University of Florida, Gainesville, Florida, USA.
  9. Florida Museum of Natural History, University of Florida, Gainesville, Florida, USA ; Genetics Institute, University of Florida, Gainesville, Florida, USA.

PMID: 25909041 PMCID: PMC4406834 DOI: 10.3732/apps.1400115

Abstract

PREMISE OF THE STUDY: Targeted sequencing using next-generation sequencing (NGS) platforms offers enormous potential for plant systematics by enabling economical acquisition of multilocus data sets that can resolve difficult phylogenetic problems. However, because discovery of single-copy nuclear (SCN) loci from NGS data requires both bioinformatics skills and access to high-performance computing resources, the application of NGS data has been limited.

METHODS AND RESULTS: We developed MarkerMiner 1.0, a fully automated, open-access bioinformatic workflow and application for discovery of SCN loci in angiosperms. Our new tool identified as many as 1993 SCN loci from transcriptomic data sampled as part of four independent test cases representing marker development projects at different phylogenetic scales.

CONCLUSIONS: MarkerMiner is an easy-to-use and effective tool for discovery of putative SCN loci. It can be run locally or via the Web, and its tabular and alignment outputs facilitate efficient downstream assessments of phylogenetic utility, locus selection, intron-exon boundary prediction, and primer or probe development.

Keywords: data mining; introns; marker development; next-generation sequencing; phylogenetics; single-copy nuclear genes; transcriptomes

References

  1. BMC Evol Biol. 2010 Feb 24;10:61 - PubMed
  2. Proc Natl Acad Sci U S A. 2013 Feb 19;110(8):2898-903 - PubMed
  3. PLoS One. 2013 Oct 08;8(10):e76957 - PubMed
  4. Nucleic Acids Res. 2012 Jan;40(Database issue):D1202-10 - PubMed
  5. Appl Plant Sci. 2013 May 16;1(6):null - PubMed
  6. Mol Phylogenet Evol. 2013 Feb;66(2):526-38 - PubMed
  7. Nucleic Acids Res. 2002 Jul 15;30(14):3059-66 - PubMed
  8. Am J Bot. 2012 Feb;99(2):349-64 - PubMed
  9. Am J Bot. 2012 Feb;99(2):257-66 - PubMed
  10. Bioinformatics. 2012 Dec 1;28(23):3144-6 - PubMed
  11. J Mol Biol. 1990 Oct 5;215(3):403-10 - PubMed
  12. Methods Mol Biol. 2009;537:39-64 - PubMed
  13. BMC Genomics. 2011 May 04;12 :211 - PubMed
  14. Appl Plant Sci. 2014 Oct 02;2(10):null - PubMed
  15. Front Plant Sci. 2011 Jul 25;2:34 - PubMed
  16. Am J Bot. 2012 Feb;99(2):291-311 - PubMed
  17. Plant Physiol. 2012 Feb;158(2):590-600 - PubMed
  18. Appl Plant Sci. 2014 Aug 29;2(9):null - PubMed
  19. Mol Phylogenet Evol. 2014 Jan;70:37-46 - PubMed
  20. Plant Biol (Stuttg). 2010 Nov;12(6):831-41 - PubMed
  21. Nucleic Acids Res. 1997 Sep 1;25(17):3389-402 - PubMed

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