A composite genome approach to identify phylogenetically informative data from next-generation sequencing.
Rachel S Schwartz1, Kelly M Harkins2,3, Anne C Stone4
1The Biodesign Institute, Arizona State University, Tempe, AZ, USA. Rachel.Schwartz@asu.edu.
BMC Bioinformatics
|June 12, 2015
Summary
A new software, SISRS, rapidly analyzes genomic data for phylogenetic analysis without a reference genome. This method simplifies complex bioinformatics workflows, enabling accurate evolutionary relationship reconstruction.
Area of Science:
- Genomics
- Bioinformatics
- Evolutionary Biology
Background:
- Next-generation sequencing generates large datasets, posing challenges for phylogenetic analysis.
- Traditional methods require extensive steps like de novo assembly and genome alignment.
Purpose of the Study:
- To develop a novel method for rapid homologous genomic data acquisition for phylogenetics.
- To bypass the need for a reference genome in phylogenetic analyses.
Main Methods:
- Developed SISRS software for direct analysis of next-generation sequencing reads.
- SISRS avoids de novo whole genome assembly, multiple genome alignment, and annotation.
Main Results:
- SISRS identified numerous loci with phylogenetic signal in simulations.
- Generated an accurate phylogeny for apes using thousands of variable sites.
- Estimated placental mammal phylogeny, resolving basal relationships with varying data completeness.
Conclusions:
- SISRS can transform phylogenetic research by directly using whole genome shotgun data.
- Eliminates the need for costly marker development.
- SISRS is open-source and freely available.
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