Navigating the tip of the genomic iceberg: Next-generation sequencing for plant systematics.

By S. Straub, Matthew Parks, Kevin A. Weitemier, M. Fishbein, R. Cronn, A. Liston. American-Eurasian journal of botany, 2012

616 citations recorded by the source corpus.

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.

Subfields: Genetics, Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/df97ad5a0450e5b19a4086b80271f45c290e636d

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Citations in the corpus

Neotropical Plant Evolution: Assembling the Big Picture (2013, background): “More robustly supported phylogenetic resolution of species within rain forest clades, which has so far proved elusive using traditional DNA sequence loci, just as it has been for high elevation Andean clades is needed.”
Planetary Biodiversity Inventory (2008–2017): Tapeworms from Vertebrate Bowels of the Earth (2017, background): “Approaches that can provide multi-locus data from DNA or ethanol-fixed material would allow existing material to be revisited; for example, by means of genome skimming (Straub et al., 2012; Ripma et al., 2014; Dodsworth, 2015; Richter et al., 2015) and target-enrichment of ultraconserved elements (F”
Capturing single-copy nuclear genes, organellar genomes, and nuclear ribosomal DNA from deep genome skimming data for plant phylogenetics: A case study in Vitaceae (2021, methodology): “…the organellar genomes (plastome and mitogenome) only account for a small portion of the reads, e.g., only 4-5% of the data accounting for plastomes (Straub et al., 2012), indicating the underutilization of the genome skimming data, which may have potential for the discovery of nuclear markers.”
Validating the power of mitochondrial metagenomics for community ecology and phylogenetics of complex assemblages (2015, background): “Mitogenomes are readily amenable to ‘genome skimming’, by which the high-copy portion of the genome is assembled from libraries sequenced at low depth (Straub et al. 2012).”