MarkerMiner 1.0: A New Application for Phylogenetic Marker Development Using Angiosperm Transcriptomes

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 (S...

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Published inApplications in plant sciences Vol. 3; no. 4
Main Authors Chamala, Srikar, García, Nicolás, Godden, Grant T, Krishnakumar, Vivek, Jordon-Thaden, Ingrid E, Smet, Riet De, Barbazuk, W. Brad, Soltis, Douglas E, Soltis, Pamela S
Format Journal Article
LanguageEnglish
Published United States Botanical Society of America 01.04.2015
John Wiley & Sons, Inc
Subjects
Angiospermae
Angiosperms
Automation
Bioinformatics
data collection
data mining
Development projects
Genes
Genomes
high-throughput nucleotide sequencing
introns
loci
Magnoliophyta
marker development
next-generation sequencing
Phylogenetics
Phylogeny
Plant sciences
plant taxonomy
prediction
Proteins
Researchers
single-copy nuclear genes
SOFTWARE NOTE
transcriptome
transcriptomes
transcriptomics
next-generation sequencing
data mining
marker development
phylogenetics
transcriptomes
introns
single-copy nuclear genes
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Summary: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.
Bibliography:http://dx.doi.org/10.3732%2Fapps.1400115
The authors thank all oneKP contributors, especially Gane Ka‐Shu Wong, and BGI. Funding for S.C. was provided by the National Science Foundation (NSF; grant IOS‐0922742 [P.S.S., D.E.S., W.B.B.]). Research funding for N.G. and G.T.G. was provided in part by NSF Doctoral Dissertation Improvement grants DEB‐1310839 (P.S.S. and N.G.) and DEB‐1210671 (P.S.S. and G.T.G.), respectively. The salary of I.J.T. was provided by the David Burpee Endowment and Chris Martine (Bucknell University).
Authors are listed alphabetically by surname and contributed equally.
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The authors thank all oneKP contributors, especially Gane Ka-Shu Wong, and BGI. Funding for S.C. was provided by the National Science Foundation (NSF; grant IOS-0922742 [P.S.S., D.E.S., W.B.B.]). Research funding for N.G. and G.T.G. was provided in part by NSF Doctoral Dissertation Improvement grants DEB-1310839 (P.S.S. and N.G.) and DEB-1210671 (P.S.S. and G.T.G.), respectively. The salary of I.J.T. was provided by the David Burpee Endowment and Chris Martine (Bucknell University).
ISSN:2168-0450
2168-0450
DOI:10.3732/apps.1400115