Please use this identifier to cite or link to this item: https://hdl.handle.net/11000/30807
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dc.contributor.authorWilson-Sánchez, David-
dc.contributor.authorLup, Samuel Daniel-
dc.contributor.authorSarmiento, Raquel-
dc.contributor.authorPonce, María Rosa-
dc.contributor.authorMicol, José Luis-
dc.contributor.otherDepartamentos de la UMH::Biología Aplicadaes_ES
dc.date.accessioned2024-01-26T22:54:13Z-
dc.date.available2024-01-26T22:54:13Z-
dc.date.created2019-09-23-
dc.identifier.citationNucleic Acids Research, 2019, Vol. 47, No. 21es_ES
dc.identifier.issn1362-4962-
dc.identifier.issn0305-1048-
dc.identifier.urihttps://hdl.handle.net/11000/30807-
dc.description.abstractForward genetic screens have successfully identified many genes and continue to be powerful tools for dissecting biological processes in Arabidopsis and other model species. Next-generation sequencing technologies have revolutionized the time-consuming process of identifying the mutations that cause a phenotype of interest. However, due to the cost of such mapping-by-sequencing experiments, special attention should be paid to experimental design and technical decisions so that the read data allows to map the desired mutation. Here, we simulated different mapping-by-sequencing scenarios. We first evaluated which short-read technology was best suited for analyzing gene-rich genomic regions in Arabidopsis and determined the minimum sequencing depth required to confidently call single nucleotide variants. We also designed ways to discriminate mutagenesis-induced mutations from background Single Nucleotide Polymorphisms in mutants isolated in Arabidopsis non-reference lines. In addition, we simulated bulked segregant mapping populations for identifying point mutations and monitored how the size of the mapping population and the sequencing depth affect mapping precision. Finally, we provide the computational basis of a protocol that we already used to map T-DNA insertions with paired-end Illumina-like reads, using very low sequencing depths and pooling several mutants together; this approach can also be used with single-end reads as well as to map any other insertional mutagen. All these simulations proved useful for designing experiments that allowed us to map several mutations in Arabidopsis.es_ES
dc.formatapplication/pdfes_ES
dc.format.extent14es_ES
dc.language.isoenges_ES
dc.publisherOxford University Presses_ES
dc.rightsinfo:eu-repo/semantics/openAccesses_ES
dc.rightsAttribution-NonCommercial-NoDerivatives 4.0 Internacional*
dc.rights.urihttp://creativecommons.org/licenses/by-nc-nd/4.0/*
dc.subject.classificationGenéticaes_ES
dc.subject.otherCDU::5 - Ciencias puras y naturales::57 - Biologíaes_ES
dc.titleNext-generation forward genetic screens: using simulated data to improve the design of mapping-by-sequencing experiments in Arabidopsises_ES
dc.typeinfo:eu-repo/semantics/articlees_ES
dc.relation.publisherversionhttps://doi.org/10.1093/nar/gkz806es_ES
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