Data from: Seasonal brain regeneration and chromosome instability are linked to selection on DNA repair in Sorex araneus
Data files
May 19, 2025 version files 2.33 GB
-
alignments4hp_taper2.zip
198.32 MB
-
Clean_chains.zip
1.69 GB
-
jsons_absExplore.zip
200.29 MB
-
jsons_absFore.zip
193.99 MB
-
jsons_MEME.zip
43.15 MB
-
README.md
2.88 KB
Abstract
Sorex araneus, the Eurasian common shrew, has seasonal brain size plasticity (Dehnel’s phenomenon) and abundant intraspecific chromosomal rearrangements, but genomic contributions to these traits remain unknown. We couple a chromosome-scale genome assembly with seasonal brain transcriptomes to discover relationships between molecular changes and both traits. Positively selected genes enriched the Fanconi anemia DNA repair pathway, which prevents the accumulation of chromosomal aberrations, and is likely involved in chromosomal rearrangements (FANCI, FAAP100). Genes involved in neurogenesis show either signatures of positive selection (PCDHA6), seasonal differential expression in the cortex and hippocampus (Notch signaling), or both (SOX9), suggesting a role for cellular proliferation in seasonal brain shrinkage and regrowth. Both positive selection and evolutionary upregulation in the shrew hypothalamus of VEGFA and SPHK2 indicate adaptations in hypothalamic metabolic homeostasis have evolved together with Dehnel’s phenomenon. These findings reveal genomic changes central to the evolution of both chromosomal instability and cyclical patterns in brain gene expression that characterizes mammalian brain size plasticity.
Dataset DOI: 10.5061/dryad.8gtht770x
Description of the data and file structure
Abstract
Sorex araneus, the Eurasian common shrew, has seasonal brain size plasticity (Dehnel’s phenomenon) and abundant intraspecific chromosomal rearrangements, but genomic contributions to these traits remain unknown. We couple a chromosome-scale genome assembly with seasonal brain transcriptomes to discover relationships between molecular changes and both traits. Positively selected genes enriched the Fanconi anemia DNA repair pathway, which prevents the accumulation of chromosomal aberrations, and is likely involved in chromosomal rearrangements (FANCI, FAAP100). Genes involved in neurogenesis show either signatures of positive selection (PCDHA6), seasonal differential expression in the cortex and hippocampus (Notch signaling), or both (SOX9), suggesting a role for cellular proliferation in seasonal brain shrinkage and regrowth. Both positive selection and evolutionary upregulation in the shrew hypothalamus of VEGFA and SPHK2 indicate adaptations in hypothalamic metabolic homeostasis have evolved together with Dehnel’s phenomenon. These findings reveal genomic changes central to the evolution of both chromosomal instability and cyclical patterns in brain gene expression that characterizes mammalian brain size plasticity.
Data overview
Data contained here are the cleaned genome alignments, cleaned gene alignments, and json files from foreground, exploratory, and site selection tests.
Files and variables
File: alignments4hp_taper2.zip
Description: Gene alignments used for test.
File: jsons_absFore.zip
Description: Absrel foreground analysis json outputs. Unzipped folder called jsons. Each file within is absrel output for each transcript, which has significance values within. Tested on all alignments containing foreground species.
File: jsons_absExplore.zip
Description: Absrel exploratory analysis json outputs. Unzipped folder called jsons. Each file within is absrel output for each transcript, which has significance values within. Tested on all alignments containing foreground species.
File: jsons_MEME.zip
Description: MEME analysis json outputs. Unzipped folder called jsons. Each file within is MEME output for each transcript, with Empirical Bayes Factors within (>100 indicates selected site). Only tested on sigificant transcripts from absrel results.
File: Clean_chains.zip
Description: Cleaned whole genome alignments used in analyses.
Code/software
Code for data and analyses can be found on https://github.com/wrthomas315/Sorex_Genome2