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

Srikar Chamala, Nicolás García, Grant T Godden, Vivek Krishnakumar, Ingrid E Jordon-Thaden, Riet De Smet (UGent) , W Brad Berbazuk, Douglas E Soltis and Pamela S Soltis
(2015) APPLICATIONS IN PLANT SCIENCES. 3(4).
Author
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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, PLANT SYSTEMATICS, FLOWERING PLANTS, GENERATION, ALIGNMENT, MAFFT, ARABIDOPSIS, SEQUENCES, FAMILIES, GENOMICS, GENE

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MLA
Chamala, Srikar, et al. “MarkerMiner 1.0: A New Application for Phylogenetic Marker Development Using Angiosperm Transcriptomes.” APPLICATIONS IN PLANT SCIENCES, vol. 3, no. 4, 2015, doi:10.3732/apps.1400115.
APA
Chamala, S., García, N., Godden, G. T., Krishnakumar, V., Jordon-Thaden, I. E., De Smet, R., … 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
Chicago author-date
Chamala, Srikar, Nicolás García, Grant T Godden, Vivek Krishnakumar, Ingrid E Jordon-Thaden, Riet De Smet, W Brad Berbazuk, Douglas E Soltis, and Pamela S Soltis. 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.
Chicago author-date (all authors)
Chamala, Srikar, Nicolás García, Grant T Godden, Vivek Krishnakumar, Ingrid E Jordon-Thaden, Riet De Smet, W Brad Berbazuk, Douglas E Soltis, and Pamela S Soltis. 2015. “MarkerMiner 1.0: A New Application for Phylogenetic Marker Development Using Angiosperm Transcriptomes.” APPLICATIONS IN PLANT SCIENCES 3 (4). doi:10.3732/apps.1400115.
Vancouver
1.
Chamala S, García N, Godden GT, Krishnakumar V, Jordon-Thaden IE, De Smet R, et al. MarkerMiner 1.0: a new application for phylogenetic marker development using angiosperm transcriptomes. APPLICATIONS IN PLANT SCIENCES. 2015;3(4).
IEEE
[1]
S. Chamala et al., “MarkerMiner 1.0: a new application for phylogenetic marker development using angiosperm transcriptomes,” APPLICATIONS IN PLANT SCIENCES, vol. 3, no. 4, 2015.
@article{5930743,
  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.}},
  articleno    = {{1400115}},
  author       = {{Chamala, Srikar and García, Nicolás and Godden, Grant T and Krishnakumar, Vivek and Jordon-Thaden, Ingrid E and De Smet, Riet and Berbazuk, W Brad and Soltis, Douglas E and Soltis, Pamela S}},
  issn         = {{2168-0450}},
  journal      = {{APPLICATIONS IN PLANT SCIENCES}},
  keywords     = {{data mining,introns,marker development,next-generation sequencing,phylogenetics,single-copy nuclear genes,transcriptomes,PLANT SYSTEMATICS,FLOWERING PLANTS,GENERATION,ALIGNMENT,MAFFT,ARABIDOPSIS,SEQUENCES,FAMILIES,GENOMICS,GENE}},
  language     = {{eng}},
  number       = {{4}},
  pages        = {{8}},
  title        = {{MarkerMiner 1.0: a new application for phylogenetic marker development using angiosperm transcriptomes}},
  url          = {{http://dx.doi.org/10.3732/apps.1400115}},
  volume       = {{3}},
  year         = {{2015}},
}
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