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BaitFisher: A Software Package for Multispecies Target DNA Enrichment Probe Design
Christoph Mayer1, Manuela Sann2, Alexander Donath1
1Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, Bonn, Germany.
Molecular Biology and Evolution
|March 25, 2016
Summary
A new algorithm designs DNA enrichment baits for multiple species, enabling broader genomic studies. This method efficiently probes more genetic targets across diverse insect groups, aiding phylogenetics and biodiversity research.
Area of Science:
- Genomics
- Bioinformatics
- Evolutionary Biology
Background:
- High-throughput sequencing and target DNA enrichment are crucial for genomic analysis.
- Existing software lacks methods for designing cross-species applicable enrichment baits using multiple reference genomes.
- Efficiently probing multiple loci across diverse species requires optimized bait design.
Purpose of the Study:
- To develop a novel algorithm for designing target DNA enrichment baits applicable across multiple species.
- To minimize the number of baits required for efficient target probing in diverse taxa.
- To create a user-friendly software package for broad taxonomic applicability of baits.
Main Methods:
- Developed an algorithm that infers DNA enrichment baits from multiple nucleotide sequence alignments.
- Applied clustering and combinatorial 1-center sequence optimization for efficient bait design.
- Tested baits on apoid wasps (Hymenoptera) using Illumina reduced-representation library sequencing.
Main Results:
- Inferred 57,650 baits for capturing 378 coding sequences in 282 genes across 24 apoid wasp species.
- Confirmed successful enrichment of target DNA in various apoid wasps.
- Demonstrated broad taxonomic applicability by enriching DNA in distantly related Hymenoptera (Formicidae, Chalcidoidea).
Conclusions:
- The developed algorithm and BaitFisher software enable the design of baits with broad taxonomic applicability.
- This approach significantly enhances the efficiency of probing multiple loci across species.
- The availability of such baits is valuable for phylogenetics, biodiversity monitoring, and other genomic research areas.
