Diversity arrays technology (DArT) for pan-genomic evolutionary studies of non-model organisms.
<h4>Background</h4>High-throughput tools for pan-genomic study, especially the DNA microarray platform, have sparked a remarkable increase in data production and enabled a shift in the scale at which biological investigation is possible. The use of microarrays to examine evolutionary rel...
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2008
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oai:doaj.org-article:527c1a73fcc14e7c9d099520d7de65992021-11-25T06:13:16ZDiversity arrays technology (DArT) for pan-genomic evolutionary studies of non-model organisms.1932-620310.1371/journal.pone.0001682https://doaj.org/article/527c1a73fcc14e7c9d099520d7de65992008-02-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/18301759/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203<h4>Background</h4>High-throughput tools for pan-genomic study, especially the DNA microarray platform, have sparked a remarkable increase in data production and enabled a shift in the scale at which biological investigation is possible. The use of microarrays to examine evolutionary relationships and processes, however, is predominantly restricted to model or near-model organisms.<h4>Methodology/principal findings</h4>This study explores the utility of Diversity Arrays Technology (DArT) in evolutionary studies of non-model organisms. DArT is a hybridization-based genotyping method that uses microarray technology to identify and type DNA polymorphism. Theoretically applicable to any organism (even one for which no prior genetic data are available), DArT has not yet been explored in exclusively wild sample sets, nor extensively examined in a phylogenetic framework. DArT recovered 1349 markers of largely low copy-number loci in two lineages of seed-free land plants: the diploid fern Asplenium viride and the haploid moss Garovaglia elegans. Direct sequencing of 148 of these DArT markers identified 30 putative loci including four routinely sequenced for evolutionary studies in plants. Phylogenetic analyses of DArT genotypes reveal phylogeographic and substrate specificity patterns in A. viride, a lack of phylogeographic pattern in Australian G. elegans, and additive variation in hybrid or mixed samples.<h4>Conclusions/significance</h4>These results enable methodological recommendations including procedures for detecting and analysing DArT markers tailored specifically to evolutionary investigations and practical factors informing the decision to use DArT, and raise evolutionary hypotheses concerning substrate specificity and biogeographic patterns. Thus DArT is a demonstrably valuable addition to the set of existing molecular approaches used to infer biological phenomena such as adaptive radiations, population dynamics, hybridization, introgression, ecological differentiation and phylogeography.Karen E JamesHarald SchneiderStephen W AnsellMargaret EversLavinia RobbaGrzegorz UszynskiNiklas PedersenAngela E NewtonStephen J RussellJohannes C VogelAndrzej KilianPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 3, Iss 2, p e1682 (2008) |
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Medicine R Science Q Karen E James Harald Schneider Stephen W Ansell Margaret Evers Lavinia Robba Grzegorz Uszynski Niklas Pedersen Angela E Newton Stephen J Russell Johannes C Vogel Andrzej Kilian Diversity arrays technology (DArT) for pan-genomic evolutionary studies of non-model organisms. |
| description |
<h4>Background</h4>High-throughput tools for pan-genomic study, especially the DNA microarray platform, have sparked a remarkable increase in data production and enabled a shift in the scale at which biological investigation is possible. The use of microarrays to examine evolutionary relationships and processes, however, is predominantly restricted to model or near-model organisms.<h4>Methodology/principal findings</h4>This study explores the utility of Diversity Arrays Technology (DArT) in evolutionary studies of non-model organisms. DArT is a hybridization-based genotyping method that uses microarray technology to identify and type DNA polymorphism. Theoretically applicable to any organism (even one for which no prior genetic data are available), DArT has not yet been explored in exclusively wild sample sets, nor extensively examined in a phylogenetic framework. DArT recovered 1349 markers of largely low copy-number loci in two lineages of seed-free land plants: the diploid fern Asplenium viride and the haploid moss Garovaglia elegans. Direct sequencing of 148 of these DArT markers identified 30 putative loci including four routinely sequenced for evolutionary studies in plants. Phylogenetic analyses of DArT genotypes reveal phylogeographic and substrate specificity patterns in A. viride, a lack of phylogeographic pattern in Australian G. elegans, and additive variation in hybrid or mixed samples.<h4>Conclusions/significance</h4>These results enable methodological recommendations including procedures for detecting and analysing DArT markers tailored specifically to evolutionary investigations and practical factors informing the decision to use DArT, and raise evolutionary hypotheses concerning substrate specificity and biogeographic patterns. Thus DArT is a demonstrably valuable addition to the set of existing molecular approaches used to infer biological phenomena such as adaptive radiations, population dynamics, hybridization, introgression, ecological differentiation and phylogeography. |
| format |
article |
| author |
Karen E James Harald Schneider Stephen W Ansell Margaret Evers Lavinia Robba Grzegorz Uszynski Niklas Pedersen Angela E Newton Stephen J Russell Johannes C Vogel Andrzej Kilian |
| author_facet |
Karen E James Harald Schneider Stephen W Ansell Margaret Evers Lavinia Robba Grzegorz Uszynski Niklas Pedersen Angela E Newton Stephen J Russell Johannes C Vogel Andrzej Kilian |
| author_sort |
Karen E James |
| title |
Diversity arrays technology (DArT) for pan-genomic evolutionary studies of non-model organisms. |
| title_short |
Diversity arrays technology (DArT) for pan-genomic evolutionary studies of non-model organisms. |
| title_full |
Diversity arrays technology (DArT) for pan-genomic evolutionary studies of non-model organisms. |
| title_fullStr |
Diversity arrays technology (DArT) for pan-genomic evolutionary studies of non-model organisms. |
| title_full_unstemmed |
Diversity arrays technology (DArT) for pan-genomic evolutionary studies of non-model organisms. |
| title_sort |
diversity arrays technology (dart) for pan-genomic evolutionary studies of non-model organisms. |
| publisher |
Public Library of Science (PLoS) |
| publishDate |
2008 |
| url |
https://doaj.org/article/527c1a73fcc14e7c9d099520d7de6599 |
| work_keys_str_mv |
AT karenejames diversityarraystechnologydartforpangenomicevolutionarystudiesofnonmodelorganisms AT haraldschneider diversityarraystechnologydartforpangenomicevolutionarystudiesofnonmodelorganisms AT stephenwansell diversityarraystechnologydartforpangenomicevolutionarystudiesofnonmodelorganisms AT margaretevers diversityarraystechnologydartforpangenomicevolutionarystudiesofnonmodelorganisms AT laviniarobba diversityarraystechnologydartforpangenomicevolutionarystudiesofnonmodelorganisms AT grzegorzuszynski diversityarraystechnologydartforpangenomicevolutionarystudiesofnonmodelorganisms AT niklaspedersen diversityarraystechnologydartforpangenomicevolutionarystudiesofnonmodelorganisms AT angelaenewton diversityarraystechnologydartforpangenomicevolutionarystudiesofnonmodelorganisms AT stephenjrussell diversityarraystechnologydartforpangenomicevolutionarystudiesofnonmodelorganisms AT johannescvogel diversityarraystechnologydartforpangenomicevolutionarystudiesofnonmodelorganisms AT andrzejkilian diversityarraystechnologydartforpangenomicevolutionarystudiesofnonmodelorganisms |
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