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EvolMarkers: a database for mining exon and intron markers for evolution, ecology and conservation studies
Chenhong Li1, Jean-Jack M Riethoven, Gavin J P Naylor
1College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, China. chli@shou.edu.cn
Molecular Ecology Resources
|July 19, 2012
Summary
EvolMarkers is a new database for finding nuclear gene markers, offering a cost-effective alternative to whole-genome sequencing for ecological and evolutionary studies. It supports various marker types across diverse species.
Area of Science:
- Genomics
- Bioinformatics
- Evolutionary Biology
Background:
- Next-generation sequencing has reduced genome project costs, but whole-genome sequencing remains prohibitive for many ecological, evolutionary, and conservation studies.
- Targeting single-copy nuclear gene markers is a more cost-effective and efficient approach for these research areas.
- Existing tools for identifying nuclear markers often lack broad phylogenetic applicability.
Purpose of the Study:
- To develop a searchable database, EvolMarkers, for identifying single-copy coding sequence (CDS) and exon-primed-intron-crossing (EPIC) markers.
- To create a tool that works across a wide range of phylogenetic divergences and taxonomic groups.
- To provide a cost-effective and efficient alternative to whole-genome sequencing for molecular marker development.
Main Methods:
- Constructed a database of single-copy CDS derived from BLAST searches of metazoan genomes.
- Implemented search functionalities for CDS and EPIC markers common to user-specified species sets.
- Designed the database to accommodate varying phylogenetic divergence characteristics.
Main Results:
- EvolMarkers was populated with 82 genomes in its initial release.
- The database and methods demonstrated effectiveness across diverse taxa including Placozoa, Cnidaria, Arthropod, Nematoda, Annelida, Mollusca, Echinodermata, Hemichordata, Chordata, and plants.
- Effectiveness was shown for CDS marker identification in annelids and intronic marker discovery in lizards (Anolis).
Conclusions:
- EvolMarkers provides a versatile and efficient platform for developing nuclear gene markers applicable to a broad taxonomic range.
- The database facilitates cost-effective molecular marker discovery for ecological, evolutionary, and conservation research.
- This resource addresses the need for accessible and broadly applicable tools in comparative genomics.
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