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One thousand plant transcriptomes and the phylogenomics of green plants

  • James H. Michael S. Eric J. Michael K. Matthew A. Sean W Leebens-Mack Barker Carpenter Deyholos GitzendanneJ. Leebens-Mack G. Wong
  • Biology, Environmental Science
    Nature
  • 7 October 2019
It is found that large expansions of gene families preceded the origins of green plants, land plants and vascular plants, whereas whole-genome duplications are inferred to have occurred repeatedly throughout the evolution of flowering plants and ferns.
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Chemistry of Cirsium and Carduus: a role in ecological risk assessment for biological control of weeds?

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MarkerMiner 1.0: A new application for phylogenetic marker development using angiosperm transcriptomes1

MarkerMiner is an easy-to-use and effective tool for discovery of putative SCN loci and its tabular and alignment outputs facilitate efficient downstream assessments of phylogenetic utility, locus selection, intron-exon boundary prediction, and primer or probe development.
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Evaluating Methods for Isolating Total RNA and Predicting the Success of Sequencing Phylogenetically Diverse Plant Transcriptomes

Novel insight is provided into the methods that are most important in isolating high quality RNA for sequencing and assembling plant transcriptomes and the methods and recommendations provided here could increase the efficiency and decrease the cost of RNA sequencing for individual labs and genome centers.
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Modified CTAB and TRIzol protocols improve RNA extraction from chemically complex Embryophyta1

It is concluded that the use of TRIzol supplemented with sarkosyl and the TURBO DNA-free kit is an effective, efficient, and robust method for obtaining RNA from 100 mg of leaf tissue of land plant species (Embryophyta) examined.
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Non-coding nuclear DNA markers in phylogenetic reconstruction

This work reviews the application of several non-coding nuclear DNA marker systems for phylogenetic reconstructions and summarizes valuable information for future research.
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The potential of genomics in plant systematics

Next-generation sequencing has revolutionized molecular systematics as well as population and conservation genetics and had a big impact on population genetics, initially by dramatically simplifying microsatellite marker development, but more recently by opening new possibilities through GBS approaches that have great potential to expand on the types of questions that can be addressed at the population level.
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Are polyploids really evolutionary dead-ends (again)? A critical reappraisal of Mayrose et al. ().

Polyploidy is now viewed not as a mere side branch of evolution, but as a major mechanism of evolution and diversification.
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Next-generation sequencing and genome evolution in allopolyploids.

For the first time, the application of next-generation sequencing technologies to the study of three aspects of allopolyploid genome evolution are reviewed, making any evolutionarily provocative system a new "model" system.
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Species richness and polyploid patterns in the genus Draba (Brassicaceae): a first global perspective

High rates of speciation and polyploidy support the hypothesis that speciation in the genus Draba has accelerated, and it is hypothesised that frequent glaciation cycles during the Pleistocene were a cause of this acceleration.
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