Data from: Molecular responses to temperature changes across timescales in the Madagascar ground gecko (Paroedura picta)
Data files
Feb 17, 2026 version files 30.98 GB
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Annotation.tar.gz
18.70 MB
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ATACseq_results.tar.gz
30.78 GB
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Code.zip
31.34 KB
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README.md
4.01 KB
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RNAseq_results.tar.gz
174.76 MB
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Thermal_traits.zip
17.78 KB
Abstract
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.
Contact Information
- Fuku Sakamoto
Email: fukusakamoto29@gmail.com - Masakado Kawata
Email: 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 >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_traitsDirectory:
Contains thermal traits measurements (CTmin.csv,CTmax.csv,SprintSpeed.csv,Tsel.csv,Tsel_rev.csv).CodeDirectory:
Contains analysis scripts for behavioral experiments and RNA sequencing data. Detailed descriptions of each code file are provided in the README within this directory.AnnotationDirectory:
Contains the fileentap_results.tsv, which includes predicted functional annotations linked to the publicly available P. picta genome (Hara et al., 2018).ATACseq_resultsDirectory:
Contains ATAC-seq analysis results, including:- Identified peaks (
ATACseq_peak_positionsdirectory) - Transcription factor footprint analysis results (
ATACseq_TOBIAS_resultsdirectory)
- Identified peaks (
RNAseq_resultsDirectory:
Contains RNA-seq analysis results, including:- Gene expression levels (
RNAseq_expression_levelsdirectory) - Alternative splicing analysis results (
RNAseq_rMATS_resultsdirectory)
- Gene expression levels (
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.
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 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 >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.