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PopFly: the Drosophila population genomics browser
Sergi Hervas1, Esteve Sanz2, Sònia Casillas1
1Institut de Biotecnologia i de Biomedicina and Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Cerdanyola del Vallès 08193, Spain.
Bioinformatics (Oxford, England)
|May 5, 2017
Summary
A new genome browser, PopFly, visualizes population genomics data from over 1100 wild fruit fly genomes. This resource aids in understanding evolutionary forces shaping genome variation.
Area of Science:
- Population genomics
- Evolutionary biology
- Bioinformatics
Background:
- Over 1100 wild-derived Drosophila melanogaster genome sequences were compiled into the Drosophila Genome Nexus (DGN).
- Understanding genome-wide variation and selection patterns requires accessible visualization tools.
Purpose of the Study:
- To present PopFly, a population genomics-oriented genome browser.
- To enable visualization and retrieval of population genomic parameters from DGN data.
Main Methods:
- PopFly is based on JBrowse software.
- It automatically analyzes and displays genetic variation data within and between D. melanogaster populations.
- It visualizes functional annotations, nucleotide diversity, linkage disequilibrium, recombination rates, neutrality tests, and population differentiation.
Main Results:
- PopFly provides a comprehensive inventory of population genomic parameters from DGN data.
- The browser allows detailed examination of genetic variation across the D. melanogaster genome.
- It facilitates the study of evolutionary forces shaping genome variation.
Conclusions:
- PopFly offers a valuable resource for population genomic studies of Drosophila melanogaster.
- Visualizing genome-wide variation and selection patterns enhances understanding of evolutionary processes.
- The browser is freely available for research use.
