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dc.contributor.authorStraub, SCK
dc.contributor.authorParks, M
dc.contributor.authorWeitemier, K
dc.contributor.authorFishbein, M
dc.contributor.authorCronn, RC
dc.contributor.authorListon, A
dc.date.accessioned2017-05-03T16:08:01Z
dc.date.available2017-05-03T16:08:01Z
dc.date.issued2012
dc.date.modified2013-09-17T23:07:47Z
dc.identifier.issn0002-9122
dc.identifier.doi10.3732/ajb.1100335
dc.identifier.urihttp://hdl.handle.net/10072/53171
dc.description.abstract堐remise of the study: Just as Sanger sequencing did more than 20 years ago, next-generation sequencing (NGS) is poised to revolutionize plant systematics. By combining multiplexing approaches with NGS throughput, systematists may no longer need to choose between more taxa or more characters. Here we describe a genome skimming (shallow sequencing) approach for plant systematics. 堍ethods: Through simulations, we evaluated optimal sequencing depth and performance of single-end and paired-end short read sequences for assembly of nuclear ribosomal DNA (rDNA) and plastomes and addressed the effect of divergence on reference-guided plastome assembly. We also used simulations to identify potential phylogenetic markers from low-copy nuclear loci at different sequencing depths. We demonstrated the utility of genome skimming through phylogenetic analysis of the Sonoran Desert clade (SDC) of Asclepias (Apocynaceae). 堋ey results: Paired-end reads performed better than single-end reads. Minimum sequencing depths for high quality rDNA and plastome assemblies were 40נand 30׬ respectively. Divergence from the reference significantly affected plastome assembly, but relatively similar references are available for most seed plants. Deeper rDNA sequencing is necessary to characterize intragenomic polymorphism. The low-copy fraction of the nuclear genome was readily surveyed, even at low sequencing depths. Nearly 160000 bp of sequence from three organelles provided evidence of phylogenetic incongruence in the SDC. 堃onclusions: Adoption of NGS will facilitate progress in plant systematics, as whole plastome and rDNA cistrons, partial mitochondrial genomes, and low-copy nuclear markers can now be efficiently obtained for molecular phylogenetics studies.
dc.description.peerreviewedYes
dc.description.publicationstatusYes
dc.languageEnglish
dc.language.isoeng
dc.publisherBotanical Society of America
dc.publisher.placeUnited States
dc.relation.ispartofstudentpublicationN
dc.relation.ispartofpagefrom349
dc.relation.ispartofpageto364
dc.relation.ispartofissue2
dc.relation.ispartofjournalAmerican Journal of Botany
dc.relation.ispartofvolume99
dc.rights.retentionY
dc.subject.fieldofresearchEvolutionary Biology not elsewhere classified
dc.subject.fieldofresearchTechnology not elsewhere classified
dc.subject.fieldofresearchEcology
dc.subject.fieldofresearchEvolutionary Biology
dc.subject.fieldofresearchPlant Biology
dc.subject.fieldofresearchcode060399
dc.subject.fieldofresearchcode109999
dc.subject.fieldofresearchcode0602
dc.subject.fieldofresearchcode0603
dc.subject.fieldofresearchcode0607
dc.titleNavigating the tip of the genomic iceberg: Next-generation sequencing for plant systematics
dc.typeJournal article
dc.type.descriptionC1 - Articles
dc.type.codeC - Journal Articles
gro.date.issued2012
gro.hasfulltextNo Full Text
gro.griffith.authorParks, Matthew


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