title: Navigating the tip of the genomic iceberg: Next-generation sequencing for plant systematics.
abstract: OBJECTIVE
  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.
  
  
  METHODS
  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).
  
  
  RESULTS
  Paired-end reads performed better than single-end reads. Minimum sequencing depths for high quality rDNA and plastome assemblies were 40× and 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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Department of Botany and Plant Pathology, Oregon State University, 2082 Cordley Hall, Corvallis, Oregon 97331, USA. straubs@science.oregonstate.edu
authors.forename: Shannon C K
authors.initials: SC
authors.lastname: Straub
authors.forename: Matthew
authors.initials: M
authors.lastname: Parks
authors.forename: Kevin
authors.initials: K
authors.lastname: Weitemier
authors.forename: Mark
authors.initials: M
authors.lastname: Fishbein
authors.forename: Richard C
authors.initials: RC
authors.lastname: Cronn
authors.forename: Aaron
authors.initials: A
authors.lastname: Liston
mesh_terms: D031108:Asclepias / Q000145:classification* / Q000235:genetics; D003198:Computer Simulation; D018744:DNA, Plant / Q000235:genetics; D004275:DNA, Ribosomal / Q000235:genetics; D056426:Genetic Loci; D054629:Genome, Mitochondrial; D018745:Genome, Plant; D015698:Genomic Library; D023281:Genomics / Q000379:methods*; D010802:Phylogeny; D018087:Plastids / Q000235:genetics; D011110:Polymorphism, Genetic; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA / Q000379:methods
chemical_list: D018744:DNA, Plant; D004275:DNA, Ribosomal