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Navigating the tip of the genomic iceberg: Next‐generation sequencing for plant systematics
Author(s) -
Straub Shan C. K.,
Parks Matthew,
Weitemier Kevin,
Fishbein Mark,
Cronn Richard C.,
Liston Aaron
Publication year - 2012
Publication title -
american journal of botany
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.218
H-Index - 151
eISSN - 1537-2197
pISSN - 0002-9122
DOI - 10.3732/ajb.1100335
Subject(s) - biology , chloroplast dna , dna sequencing , systematics , evolutionary biology , genome , phylogenetic tree , illumina dye sequencing , nuclear gene , ribosomal dna , sanger sequencing , phylogenetics , deep sequencing , genetics , dna , taxonomy (biology) , gene , botany
• Premise 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. • 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). • Key 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.