Anonymous nuclear loci in non-model organisms: making the most of high-throughput genome surveys

Bioinformatics
Terry BertozziMichael G Gardner

Abstract

When working with non-model organisms, few if any species-specific markers are available for phylogenetic, phylogeographic and population studies. Therefore, researchers often try to adapt markers developed in distantly related taxa, resulting in poor amplification and ascertainment bias in their target taxa. Markers can be developed de novo and anonymous nuclear loci (ANL) are proving to be a boon for researchers seeking large numbers of fast-evolving, independent loci. However, the development of ANL can be laboratory intensive and expensive. A workflow is described to identify suitable low-copy anonymous loci from high-throughput shotgun sequences, dramatically reducing the cost and time required to develop these markers and produce robust multilocus datasets. By successively removing repetitive and evolutionary conserved sequences from low coverage shotgun libraries, we were able to isolate thousands of potential ANL. Empirical testing of loci developed from two reptile taxa confirmed that our methodology yields markers with comparable amplification rates and nucleotide diversities to ANLs developed using other methodologies. Our approach capitalizes on next-generation sequencing technologies to enable the development of ph...Continue Reading

References

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Citations

Oct 3, 2012·Molecular Phylogenetics and Evolution·Kate L SandersArne R Rasmussen
Oct 30, 2013·Molecular Ecology Resources·Carole P ElliottSiegfried L Krauss
Dec 5, 2013·Evolution; International Journal of Organic Evolution·Qixin HeL Lacey Knowles
Oct 10, 2012·Molecular Phylogenetics and Evolution·Kanishka D B UkuwelaKate L Sanders
Mar 20, 2013·Molecular Ecology·Kate L SandersMichael S Y Lee
Jul 21, 2016·Genome Research·Igor Rodrigues CostaW Bryan Jennings

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