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MarkerMiner 1.0: A New Application for Phylogenetic Marker Development Using Angiosperm Transcriptomes

Authordc.contributor.authorChamala, Srikar 
Authordc.contributor.authorGarcía Berguecio, Nicolás 
Authordc.contributor.authorGodden, Grant 
Authordc.contributor.authorKrishnakumar, Vivek 
Authordc.contributor.authorJordon Thaden, Ingrid 
Authordc.contributor.authorSmet, Riet De 
Authordc.contributor.authorBarbazuk, William 
Authordc.contributor.authorSoltis, Douglas 
Authordc.contributor.authorSoltis, Pamela 
Admission datedc.date.accessioned2015-08-14T15:33:55Z
Available datedc.date.available2015-08-14T15:33:55Z
Publication datedc.date.issued2015
Cita de ítemdc.identifier.citationApplications in Plant Sciences 2015 3 ( 4 ): 1400115en_US
Identifierdc.identifier.issn2168-0450
Identifierdc.identifier.otherDOI: 10.3732/apps.1400115
Identifierdc.identifier.urihttp://repositorio.uchile.cl/handle/2250/132749
General notedc.descriptionArtículo de publicación ISIen_US
Abstractdc.description.abstract• Premise of the study: Targeted sequencing using next-generation sequencing (NGS) platforms offers enormous potential for plant systematics by enabling economical acquisition of multilocus data sets that can resolve diffi cult phylogenetic problems. However, because discovery of single-copy nuclear (SCN) loci from NGS data requires both bioinformatics skills and access to high-performance computing resources, the application of NGS data has been limited. • Methods and Results: We developed MarkerMiner 1.0, a fully automated, open-access bioinformatic workfl ow and application for discovery of SCN loci in angiosperms. Our new tool identifi ed as many as 1993 SCN loci from transcriptomic data sampled as part of four independent test cases representing marker development projects at different phylogenetic scales. • Conclusions: MarkerMiner is an easy-to-use and effective tool for discovery of putative SCN loci. It can be run locally or via the Web, and its tabular and alignment outputs facilitate effi cient downstream assessments of phylogenetic utility, locus selection, intron-exon boundary prediction, and primer or probe development.en_US
Lenguagedc.language.isoenen_US
Publisherdc.publisherBotanical Society of Americaen_US
Type of licensedc.rightsAtribución-NoComercial-SinDerivadas 3.0 Chile*
Link to Licensedc.rights.urihttp://creativecommons.org/licenses/by-nc-nd/3.0/cl/*
Keywordsdc.subjectData miningen_US
Keywordsdc.subjectIntronsen_US
Keywordsdc.subjectMarker developmenten_US
Keywordsdc.subjectNext-generation sequencingen_US
Keywordsdc.subjectPhylogeneticsen_US
Keywordsdc.subjectSingle-copy nuclear genesen_US
Keywordsdc.subjectTranscriptomeen_US
Títulodc.titleMarkerMiner 1.0: A New Application for Phylogenetic Marker Development Using Angiosperm Transcriptomesen_US
Document typedc.typeArtículo de revistaen_US


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Atribución-NoComercial-SinDerivadas 3.0 Chile
Except where otherwise noted, this item's license is described as Atribución-NoComercial-SinDerivadas 3.0 Chile