Fantastic beasts and how to sequence them: genomic approaches for obscure model organisms

Summary Application of genomic approaches to “obscure model organisms” (OMOs), meaning species with little or no genomic resources, enables increasingly sophisticated studies of genomic basis of evolution, acclimatization and adaptation in real ecological contexts. Here, I highlight sequencing solutions and data handling techniques most suited for genomic analysis of OMOs. Glossary- Allele Frequency Spectrum, AFS (same as Site Frequency Spectrum, SFS): histogram of the number of segregating variants depending on their frequency in one or more populations.- Restriction site-Associated DNA (RAD) sequencing: family of diverse genotyping methods that sequence short fragments of the genome adjacent to recognition site(s) for specific restriction endonuclease(s).- Linkage Disequilibrium (LD): in this review, correlation of genotypes at a pair of markers across individuals.- LD block: typical distance between markers in the genome across which their genotypes remain correlated.- Genome scan: profiling of genotypes along the genome looking for unusual patterns. Often used to look for signatures of natural selection or introgression.- “Denser-than-LD” genotyping: genotyping of several polymorphic markers per LD block.- Highly contiguous reference: genome or transcriptome reference sequence containing the least amount of fragmentation.- Phased data: data showing which SNP alleles belong to the same homologous chromosome copy.- Cross-tissue gene expression analysis: looking for individual-specific shifts in gene expression detectable across multiple tissues. Such shifts are predominantly genetic in nature.