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Appl Plant Sci. 2015 Apr 6;3(4). pii: apps.1400115. doi: 10.3732/apps.1400115. eCollection 2015 Apr.

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

Author information

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.

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

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