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- Title
NAVIGATING THE TIP OF THE GENOMIC ICEBERG; NEXT-GENERATION SEQUENCING FOR PLANT SYSTEMATICS.
- Authors
Straub, Shannon C. K.; Parks, Matthew; Weitemier, Kevin; Fishbein, Mark; Cronn, Richard C.; Liston, Aaron
- Abstract
* Premise of the study: Just as Sanger sequencing did more than 20 years ago, next-generation sequencing (NGS) is poised to revolutionize plant systematic. By combining multiplexing approaches with NGS throughput, systematizes may no longer need to choose between more taxa or more characters. Here we describe a genome skimming (shallow sequencing) approach for plant systematic. * 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 pastimes 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 40x and 30x, 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 160 000 bp of sequence from three organelles provided evidence of phylogenetic incongruence in the SDC. * Conclusions: Adoption of NGS will facilitate progress in plant systematic, as whole plastome and rDNA citrons, partial mitochondria genomes, and low-copy nuclear markers can now be efficiently obtained for molecular phylogenetics studies.
- Subjects
NUCLEOTIDE sequence; GENETIC research; PLANT genetics; APOCYNACEAE; GENETIC polymorphisms in plants; GENETIC polymorphism research
- Publication
American Journal of Botany, 2012, Vol 99, Issue 2, p349
- ISSN
0002-9122
- Publication type
Article
- DOI
10.3732/ajb.1100335