Non–model organisms

Next-generation sequencing is broadening the application of genetic and genomic studies to the panoply of life.

Model organisms satisfy a research need for genetic uniformity and live happily in the controlled hum of the laboratory. But existing models lack many interesting traits and are limited when it comes to answering evolutionary and ecological questions. Advances in sequencing have radically expanded the reach of genetic studies to non–model organisms and wild populations, making this an exciting area to watch.

Genomic approaches open a jungle of possibilities. Credit: Marina Corral

Much of evolutionary and ecological research attempts to zero in on sequence variation that leads to functional phenotypic variation. The key to finding associations is to assess multiple markers in many individuals: what next-generation sequencing can do cheaply and often in one experiment. One class of genotyping-by-sequencing approach generates markers en masse without the need for a reference sequence. Restriction site–associated DNA sequencing and complexity reduction of polymorphic sequences are examples that only sequence short stretches around a specific restriction site dispersed throughout the genome. Markers generated in this way can be used for quantitative trait locus mapping, examining phylogeography and tracking evolution in natural populations.

These approaches are revealing interesting insights into processes such as adaptive radiation—the evolution of phenotypic diversity within a lineage. Targeted or candidate gene sequencing can similarly be used to identify allelic variation driving processes such as mimicry in butterfly wings, a fascinating example of convergent evolution. Complementary de novo transcriptome-assembly tools and digital-tagging approaches allow studies of changes in coding sequences and gene expression in the absence of a reference sequence.

Plummeting costs and sophisticated bioinformatics are making whole-genome sequencing projects commonplace and enabling comparative genomic studies. Organisms with sequenced genomes in key phylogenetic positions can also be better exploited for developmental studies. For example, sequencing of spike moss, one of the earliest plants with true roots, can help to understand how these structures first evolved. Non–model organism methods benefit from having close relatives with well-annotated reference sequences. The promise of large-scale whole-genome sequencing projects such as the Genome 10K Project is to anchor investigation of relatives in a diversity of phylogenetic neighborhoods, including many that can be helped by conservation genomic studies.

Population genomic comparisons will soon be possible, and we look forward to seeing the benefits of genomic science applied to interesting organisms that have yet to share the spotlight.

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Nawy, T. Non–model organisms. Nat Methods 9, 37 (2012). https://doi.org/10.1038/nmeth.1824

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