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Novel Sequence Discovery by Subtractive Genomics
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discomark: nuclear marker discovery from orthologous sequences using draft genome data.

Sereina Rutschmann1,2,3, Harald Detering1,2,3, Sabrina Simon4,5

  • 1Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 301, 12587, Berlin, Germany.

Molecular Ecology Resources
|July 26, 2016
PubMed
Summary
This summary is machine-generated.

Discomark streamlines nuclear DNA (nDNA) marker development from sequencing data. This automated approach aids phylogenetic analysis in both closely and distantly related species.

Keywords:
marker discoverymayflynon-model organismphylogeneticsprimer design

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Area of Science:

  • Genomics
  • Bioinformatics
  • Evolutionary Biology

Background:

  • High-throughput sequencing enables rapid and cost-effective development of phylogenetic markers.
  • Existing methods for marker development can be time-consuming and complex.

Purpose of the Study:

  • To introduce discomark, a novel program for streamlined nuclear DNA (nDNA) marker development.
  • To demonstrate the utility of discomark for designing phylogenetic markers across diverse species.

Main Methods:

  • Discomark integrates local alignment, trimming, reference mapping, and primer design from orthologous sequences.
  • The program was tested on closely related *Cloeon dipterum* and distantly related Ephemeroptera species.
  • Developed markers were validated through amplification, Sanger sequencing, and phylogenetic reconstruction.

Main Results:

  • Discomark identified 78 nDNA markers for the *Cloeon dipterum* species complex.
  • Eight markers were successfully used to reconstruct a well-supported phylogeny and haplotype networks.
  • Twenty-three primer pairs were developed for broad amplification across Ephemeroptera families.

Conclusions:

  • Discomark provides an automated and efficient pipeline for genome-scale phylogenetic marker discovery.
  • The program facilitates the development of nDNA markers crucial for evolutionary studies.
  • Discomark enhances phylogenetic research by simplifying marker generation from sequencing data.