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A Bioinformatics Pipeline to Accurately and Efficiently Analyze the MicroRNA Transcriptomes in Plants
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MarkerMiner 1.0: A new application for phylogenetic marker development using angiosperm transcriptomes.

Srikar Chamala1, Nicolás García2, Grant T Godden3

  • 1Department of Biology, University of Florida, Gainesville, Florida, USA.

Applications in Plant Sciences
|April 25, 2015
PubMed
Summary
This summary is machine-generated.

MarkerMiner 1.0 is a new automated tool that simplifies finding single-copy nuclear (SCN) loci from next-generation sequencing data. This bioinformatics workflow makes plant phylogenetic analysis more accessible and efficient.

Keywords:
data miningintronsmarker developmentnext-generation sequencingphylogeneticssingle-copy nuclear genestranscriptomes

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Area of Science:

  • Botany
  • Bioinformatics
  • Genomics

Background:

  • Next-generation sequencing (NGS) offers potential for plant systematics by providing multilocus data.
  • Discovering single-copy nuclear (SCN) loci from NGS data requires specialized bioinformatics skills and computing resources, limiting its application.

Purpose of the Study:

  • To develop an automated bioinformatics workflow for the discovery of SCN loci in angiosperms.
  • To overcome the limitations of accessing and processing NGS data for phylogenetic studies.

Main Methods:

  • Developed MarkerMiner 1.0, a fully automated, open-access bioinformatic workflow.
  • Applied the workflow to transcriptomic data from four independent test cases.

Main Results:

  • Identified up to 1993 SCN loci across the test cases.
  • MarkerMiner 1.0 is an effective tool for discovering putative SCN loci.

Conclusions:

  • MarkerMiner provides an easy-to-use solution for SCN loci discovery.
  • The tool facilitates downstream phylogenetic utility assessments, locus selection, and primer development.