DOI: 10.5061/dryad.pvmcvdnwm
title: Data from: Molecular responses to temperature changes across timescales in the Madagascar ground gecko (<em>Paroedura picta</em>)

description: Short-term responses to temperature stress, such as heat waves, and
 long-term acclimation to temperature changes, including seasonal shifts
 and global warming, are expected to be mediated by distinct molecular
 pathways. However, in ectotherms, such as reptiles, the effects of
 exposure duration on molecular responses to temperature change remain
 unclear. In this study, we investigated temperature-induced molecular
 changes across distinct timescales in a newly established reptilian model
 species, the Madagascar ground gecko (Paroedura picta). To determine
 temperature-responsive phenotypes and assess phenotypic plasticity under
 long-term temperature changes, we compared thermal traits in individuals
 acclimated to 25°C and 30°C. We found significant differences in the
 critical thermal minimum and maximum as well as sprint speed between the
 two groups. We then employed RNA sequencing and the assay for
 transposase-accessible chromatin using sequencing to analyze gene
 expression, splicing, and chromatin states across multiple temperature
 conditions and durations. Results revealed that abrupt temperature shifts
 activated known heat stress pathways, whereas prolonged temperature
 acclimation altered immune function. In the liver, predicted occupancy of
 some transcription factors diverged between short- and long-term
 temperature stimuli. These findings indicate that transient temperature
 stress responses and long-term temperature acclimation in P. picta involve
 distinct molecular mechanisms.
description: We first compared thermal traits in individuals acclimated to
 25°C (approximating the annual average habitat temperature) and 30°C
 (approximating the daily average habitat temperature during the warmest
 period). Four widely used thermal response traits were measured (Taylor et
 al. 2021): selected temperature, critical thermal minimum, critical
 thermal maximum, and sprint speed across various body temperatures. Using
 these measurements, we estimated the thermal performance curve (TPC),
 describing the relationship between body temperature and
 performance. Subsequently, we investigated how
 temperature and acclimation duration influence molecular thermal responses
 in <em>P. picta</em>. We employed RNA sequencing (RNA-seq) and
 the assay for transposase-accessible chromatin using sequencing (ATAC-seq)
 to analyze gene expression, splicing, and chromatin states across multiple
 temperature conditions and durations. Individuals were first acclimated at
 25°C ± 1°C for at least 30 days, before being subjected to the following
 treatments: for short-term treatments, individuals were exposed to 25°C,
 30°C, or 37°C (approximating the maximum habitat temperature) for 4 h
 (referred to as Short 25, Short 30, and Short 37, respectively); for
 long-term treatments, individuals were exposed to 25°C or 30°C for
 &gt;50 days (referred to as Long 25 and Long 30, respectively). All
 individuals used were adult males, and both brain and liver samples were
 collected. RNA-seq included 40 samples from 20 individuals, with 4 samples
 per temperature condition and tissue type. ATAC-seq included 20 samples
 from 10 individuals, with 2 samples per condition and tissue
 type.
description: # Data from: Molecular Responses to Temperature Changes Across Timescales
 in the Madagascar Ground Gecko (*Paroedura picta*) ## Contact Information
 1. **Fuku Sakamoto**\ Email:
 [fukusakamoto29@gmail.com](mailto:fukusakamoto29@gmail.com) 2. **Masakado
 Kawata**\ Email: [kawata@tohoku.ac.jp](mailto:kawata@tohoku.ac.jp) ##
 Description This study investigated temperature-induced molecular changes
 across distinct timescales in the Madagascar ground gecko (*Paroedura
 picta*). To determine temperature-responsive phenotypes and assess
 phenotypic plasticity under long-term temperature changes, we first
 compared thermal traits in individuals acclimated to 25°C (approximating
 the annual average habitat temperature) and 30°C (approximating the daily
 average habitat temperature during the warmest period). We measured four
 widely used thermal response indices (Taylor et al. 2021): selected
 temperature, critical thermal minimum, critical thermal maximum, and
 sprint speed across various body temperatures. Using these measurements,
 we estimated the thermal performance curve (TPC), describing the
 relationship between body temperature and performance. Subsequently, we
 investigated how temperature and acclimation duration influence molecular
 thermal responses in *P. picta*. We employed RNA sequencing (RNA-seq) and
 the assay for transposase-accessible chromatin using sequencing (ATAC-seq)
 to analyze gene expression, splicing, and chromatin states across multiple
 temperature conditions and durations. Individuals were first acclimated at
 25°C ± 1°C for at least 30 days, before being subjected to the following
 treatments: for short-term treatments, individuals were exposed to 25°C,
 30°C, or 37°C (approximating the maximum habitat temperature) for 4 h
 (referred to as Short 25, Short 30, and Short 37, respectively); for
 long-term treatments, individuals were exposed to 25°C or 30°C for &gt;50
 days (referred to as Long 25 and Long 30, respectively). All individuals
 used were adult males, and both brain and liver samples were collected.
 RNA-seq included 40 samples from 20 individuals, with 4 samples per
 temperature condition and tissue type. ATAC-seq included 20 samples from
 10 individuals, with 2 samples per condition and tissue type. ###
 Directory Structure Description * **`Thermal_traits`** **Directory**:\
 Contains thermal traits measurements (`CTmin.csv`, `CTmax.csv`,
 `SprintSpeed.csv`, `Tsel.csv`, `Tsel_rev.csv`). * **`Code`**
 **Directory**:\ Contains analysis scripts for behavioral experiments and
 RNA sequencing data. Detailed descriptions of each code file are provided
 in the README within this directory. * **`Annotation`** **Directory**:\
 Contains the file `entap_results.tsv`, which includes predicted functional
 annotations linked to the publicly available *P. picta* genome (Hara et
 al., 2018). * **`ATACseq_results`** **Directory**:\ Contains ATAC-seq
 analysis results, including: * Identified peaks (`ATACseq_peak_positions`
 directory) * Transcription factor footprint analysis results
 (`ATACseq_TOBIAS_results` directory) * **`RNAseq_results`**
 **Directory**:\ Contains RNA-seq analysis results, including: * Gene
 expression levels (`RNAseq_expression_levels` directory) * Alternative
 splicing analysis results (`RNAseq_rMATS_results` directory) For more
 details on each dataset, please refer to the `README.md` file within the
 respective directory. ## References Hara, Yuichiro, Miki Takeuchi, Yuka
 Kageyama, Kaori Tatsumi, Masahiko Hibi, Hiroshi Kiyonari, and Shigehiro
 Kuraku. 2018. “Madagascar Ground Gecko Genome Analysis Characterizes
 Asymmetric Fates of Duplicated Genes.” *BMC Biology* 16 (1): 40. Taylor,
 Emily N., Luisa M. Diele-Viegas, Eric J. Gangloff, Joshua M. Hall, Bálint
 Halpern, Melanie D. Massey, Dennis Rödder, et al. 2021. “The Thermal
 Ecology and Physiology of Reptiles and Amphibians: A User’s Guide.”
 *Journal of Experimental Zoology. Part A, Ecological and Integrative
 Physiology* 335 (1): 13–44.