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Supplemental Information

RNA sequencing sample treatment summary

Table summarizes the experimental setup including the genotypes, time of treatment, and type of treatment used for samples used in RNA sequencing. There were three replicates for each sample for a total of 21 sequenced samples.

DOI: 10.7287/peerj.preprints.2289v1/supp-1

Differentially regulated gene expression table with clade number and putatuve function

DOI: 10.7287/peerj.preprints.2289v1/supp-2

Differentially regulated gene clade groups and GO term analysis

DOI: 10.7287/peerj.preprints.2289v1/supp-3

Marker gene summary and primer information

DOI: 10.7287/peerj.preprints.2289v1/supp-4

Additional Information

Competing Interests

The authors declare that they have no competing interests.

Author Contributions

Nicholas C Thomas performed the experiments, analyzed the data, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.

Benjamin Schwessinger conceived and designed the experiments, performed the experiments, analyzed the data, wrote the paper, reviewed drafts of the paper.

Furong Liu performed the experiments, reviewed drafts of the paper.

Huamin Chen performed the experiments, reviewed drafts of the paper.

Tong Wei analyzed the data, reviewed drafts of the paper.

Yen P Nguyen performed the experiments, reviewed drafts of the paper.

Isaac WF Shaker performed the experiments, reviewed drafts of the paper.

Pamela C Ronald conceived and designed the experiments, analyzed the data, contributed reagents/materials/analysis tools, reviewed drafts of the paper.

Data Deposition

The following information was supplied regarding data availability:

The National Center for Biotechnology Information Sequence Read Archive (SRA)

BioProject ID PRJNA250865

http://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA250865

Funding

This work was part of the DOE Joint BioEnergy Institute (http://www.jbei.org) and the DOE Joint Genome Institute and were supported by the U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research, through contract DE-AC02-05CH11231 between Lawrence Berkeley National Laboratory and the U.S. Department of Energy. The United States Government retains and the publisher, by accepting the article for publication, acknowledges that the United States Government retains a non-exclusive, paid-up, irrevocable, world-wide license to publish or reproduce the published form of this manuscript, or allow others to do so, for United States Government purposes. B. S. was supported by a Human Frontiers Science Program long-term postdoctoral fellowship (LT000674/2012) and a Discovery Early Career Award (DE150101897). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.


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