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An efficient field and laboratory workflow for plant phylotranscriptomic projects.

Ya Yang1, Michael J Moore2, Samuel F Brockington3

  • 1Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, 830 North University Avenue, Ann Arbor, Michigan 48109 USA.

Applications in Plant Sciences
|March 25, 2017
PubMed
Summary
This summary is machine-generated.

This study presents a cost-effective workflow for plant phylotranscriptomics, enabling efficient RNA extraction from challenging tissues. The method ensures high-quality DNA sequencing reads for diverse plant taxa.

Keywords:
CaryophyllalesRNAcryogenic field samplingphylogenomicsphylotranscriptomics

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Area of Science:

  • Plant Science
  • Genomics
  • Molecular Biology

Background:

  • Phylotranscriptomic studies require robust methods for collecting and processing plant tissues.
  • Extracting high-quality RNA from diverse plant species, especially those with recalcitrant tissues, presents significant challenges.

Purpose of the Study:

  • To develop and present a streamlined field and laboratory workflow for plant phylotranscriptomic projects.
  • To provide recommendations for efficient sample curation in these projects.

Main Methods:

  • Cryogenic tissue collection in the field followed by laboratory-based RNA extraction and quality control.
  • Stranded messenger RNA (mRNA) library preparation and sequencing on Illumina HiSeq platforms.
  • Application of the workflow to diverse angiosperm taxa, including mucilaginous plants like Cactaceae and Droseraceae.

Main Results:

  • Successfully collected and processed 216 frozen tissue samples from various Caryophyllales and other angiosperm taxa.
  • Generated high-quality RNA and sequenced libraries from challenging plant tissues, including those rich in secondary compounds.
  • Demonstrated the workflow's applicability to difficult-to-process samples.

Conclusions:

  • The developed workflow is cost-effective, with an estimated cost of $270 per sample (as of August 2016).
  • The method is time-efficient, requiring less than 50 hours for 10-12 samples, including all laboratory work and curation.
  • The workflow is robust and effective for extracting RNA from difficult plant tissues, facilitating phylotranscriptomic analyses.