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Data processing scripts for polyploid A.thaliana transcriptome analysis.

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Gene balance predicts transcriptional responses immediately following ploidy change in Arabidopsis thaliana

Michael J. Song1,†, Barney I. Potter2,†, Jeff J. Doyle3, Jeremy E. Coate4,*

1University and Jepson Herbaria and Department of Integrative Biology, University of California, Berkeley, California, 2Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 3School of Integrative Plant Science, Cornell University, Ithaca, NY, 4Department of Biology, Reed College, Portland, OR, , *Corresponding Author: [email protected], , These authors contributed equally to this work.

Abstract

The Gene Balance Hypothesis postulates that there is selection on gene copy number (gene dosage) to preserve stoichiometric balance among interacting proteins. This presupposes that gene product abundance is governed by gene dosage, and that gene dosage responses are consistent for all genes in a dosage-sensitive network or complex. Gene dosage responses, however, have rarely been quantified and the available data suggest that they are highly variable. We sequenced the transcriptomes of two synthetic autopolyploid accessions of Arabidopsis thaliana and their diploid progenitors, as well as one natural tetraploid and its synthetic diploid produced via haploid induction, to estimate transcriptome size and dosage responses immediately following ploidy change. Overall transcriptome size does not exhibit a simple doubling in response to genome doubling, and individual gene dosage responses are highly variable in all three accessions, indicating that expression is not strictly coupled with gene dosage. Nonetheless, putatively dosage-sensitive gene groups (GO terms, metabolic networks, gene families, and predicted interacting proteins) exhibit smaller and more coordinated dosage responses than do putatively dosage-insensitive gene groups, suggesting that constraints on dosage balance operate immediately following whole genome duplication, and that duplicate gene retention patterns are shaped by selection to preserve dosage balance.

Contents

ploidy-seq ├── bioinformatic_methods ├── data │   ├── dosage_response │   ├── duplication_history │   ├── final_figures_input │   ├── networks │   └── ppt ├── env ├── figures ├── latex │   └── plant cell submission ├── notebooks └── scripts

bioinformatic_methods

Notes on how to run the bioinformatic methods used in this manuscript.

data

Contains all data used for analyses.

env

Environment file for conda for installing requirements.

figures

All figures used in the paper.

latex

Contains manuscript LaTeX files.

notebooks

Jupyter notebooks in which figures were generated.

scripts

Minor scripts used to set up analyses.

Citation

Potter BI, Song MJ, Doyle JJ, Coate JE 2019. Gene Balance Predicts Transcriptional Responses Immediately Following Ploidy Change In Arabidopsis thaliana. bioRxiv: 795328..

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Data processing scripts for polyploid A.thaliana transcriptome analysis.

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