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Using a butterflyfish genome as a general tool for RAD-Seq studies in specialized reef fish
Joseph D DiBattista1,2, Pablo Saenz-Agudelo1,3, Marek J Piatek4,5
1Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia.
Molecular Ecology Resources
|February 26, 2017
Summary
This study assessed the usefulness of a reference genome for butterflyfish using RAD-Seq data. Using genomic resources improved SNP annotation for closely related species, revealing genes involved in calcium transport.
Area of Science:
- Marine Biology
- Genomics
- Bioinformatics
Background:
- Restriction site-associated DNA sequencing (RAD-Seq) is a common method for identifying genetic markers in non-model organisms.
- The utility of a draft genome for improving RAD-Seq data quality and SNP annotation in butterflyfish (Chaetodontidae) was previously untested.
- Understanding genetic variation is crucial for studying adaptation in coral reef fish populations.
Purpose of the Study:
- To evaluate the effectiveness of a draft genome from Chaetodon austriacus in enhancing RAD-Seq data analysis across nine butterflyfish species.
- To assess potential biases in RAD-Seq methods for isolating nuclear loci.
- To identify single nucleotide polymorphism (SNP) markers and their functional annotations with and without a reference genome.
Main Methods:
- Processing of double-digest restriction site-associated DNA (ddRAD) sequencing data from nine butterflyfish species.
- Comparative analysis of SNP identification and annotation with and without the use of the Chaetodon austriacus reference genome.
- Functional annotation of identified SNPs to infer potential adaptive mechanisms.
Main Results:
- A notable proportion of identified SNPs remained unannotated across all species, regardless of genome usage.
- The reference genome significantly improved SNP annotation and functional assignment for closely related butterflyfish species, but not for distantly related ones.
- Enrichment analysis revealed genes associated with calcium transmembrane transport and binding among sister taxa.
Conclusions:
- Genomic resources offer advantages for RAD-Seq analysis, particularly for closely related species, by facilitating SNP functional annotation.
- The identified enrichment of calcium transport-related genes suggests potential adaptive mechanisms in butterflyfish inhabiting challenging environments like the Red Sea and Arabian Sea.
- This approach holds promise for uncovering adaptive strategies in coral reef fish populations facing environmental pressures.
