DOI: 10.5061/dryad.prr4xgxz1
title: Data from: The role of auxin-mediated gene activation in the bryophyte, Physcomitrium patens

description: Perception and response to the hormone auxin are critical to plant growth
 and development. Expression of auxin-response genes is tightly regulated
 via known mechanisms of both activation and repression. Across the plant
 lineage, auxin-response gene induction is performed by AUXIN-RESPONSE
 FACTOR (ARF), activating transcription factors. Conversely, AUXIN/INDOLE
 ACETIC ACID proteins repress expression. Studies of gain-of-function
 constitutive-repression lines and ARF loss-of-function mutants have
 advanced the field. Yet, there is a need for a comparative study of
 aberrant auxin-signaling mutants to understand the developmental
 consequences of constitutive repression versus the absence of
 auxin-mediated gene induction. Using CRISPR/Cas9 gene-editing tools, we
 mutated each activating ARF gene in the model bryophyte, Physcomitrium
 patens. The resulting septuple loss-of-function mutant line (arfasept) has
 severe developmental phenotypes and a diminished ability to respond to
 exogenous auxin. However, phenotypic analysis revealed that the arfasept
 line is not as severely affected as the constitutive-repression lines.
 Expression analysis of several auxin-response genes demonstrates that
 auxin-mediated gene induction is abolished in both arfasept
 and constitutive-repression lines but that basal expression
 levels are higher in the arfasept lines. Our results suggest that the
 expression of auxin-regulated genes important for developmental
 progression is maintained, albeit at reduced levels, in the absence of
 ARFs.
description: # The role of auxin-mediated gene activation in the bryophyte,
 Physcomitrium patens
 [https://doi.org/10.5061/dryad.prr4xgxz1](https://doi.org/10.5061/dryad.prr4xgxz1) ## Description of the data and file structure ### Files and variables #### File: Mutant\_Sequences.zip **Description:** Recovered mutant alleles from CRISPR/Cas9 mutagenesis (.ape files, readable via A Plasmid Editor (ApE)). Includes a flow chart (.pdf) that illustrates how the septuple mutants were generated. #### File: Combined\_CellWallAngles.csv **Description:** Cross wall angles, relative to the angle of growth, for moss protonemal cells studied in this work. Arranged by genotype. Units are degrees. ##### Variables * genotype #### File: Chl\_Content.csv **Description:** Relative chlorophyll content after 21 days on medium +/- NAA supplementation. Tissue samples were soaked in methanol overnight, in the dark, at room temperature. Measured on a spectrophotometer. Reported values have been normalized to chlorophyll content of the genotype on standard medium. ##### Variables * genotype, 1-Naphthaleneacetic acid (NAA, a synthetic hormone) treatment #### File: Gametophore\_Counts.csv **Description:** Absolute number of gametophores that colonies developed after 21 days on medium +/- NAA supplementation. ##### Variables * genotype, 1-Naphthaleneacetic acid (NAA, a synthetic hormone) treatment #### File: qPCR\_DOXexp\_raw\.csv **Description:** Raw cycle threshold (CT) values for the housekeeping gene (APT) and test gene (DOX). Biological replicates are prepared from seperate RNA extraction. Technical replicates are duplicated biological replicates. ##### Variables * genotype, indole acetic acid (IAA, a naturally occurring hormone) treatment #### File: qPCR\_IAA2exp\_raw\.csv **Description:** Raw cycle threshold (CT) values for the housekeeping gene (APT) and test gene (IAA2). Biological replicates are prepared from seperate RNA extraction. Technical replicates are duplicated biological replicates. ##### Variables * genotype, indole acetic acid (IAA, a naturally occurring hormone) treatment #### File: qPCR\_RSL4exp\_raw\.csv **Description:** Raw cycle threshold (CT) values for the housekeeping gene (APT) and test gene (RSL4). Biological replicates are prepared from seperate RNA extraction. Technical replicates are duplicated biological replicates. ##### Variables * genotype, indole acetic acid (IAA, a naturally occurring hormone) treatment #### File: qPCR\_ZHLexp\_raw\.csv **Description:** Raw cycle threshold (CT) values for the housekeeping gene (APT) and test gene (ZHL). Biological replicates are prepared from seperate RNA extraction. Technical replicates are duplicated biological replicates. ##### Variables * genotype, indole acetic acid (IAA, a naturally occurring hormone) treatment ## Code/software Excel is most suitable for the .csv files, though can be read in any .csv-reading software. For .ape sequence files are openable with "A Plasmid Editor" (ApE).