DOI: 10.5061/dryad.8gtht770x
title: Data from: Seasonal brain regeneration and chromosome instability are linked to selection on DNA repair in Sorex araneus

description: 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.
description: # Data for "Selection on DNA repair underlies seasonal brain
 regeneration and chromosome instability in Sorex araneus" Dataset
 DOI: [10.5061/dryad.8gtht770x](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
 (&gt;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](https://github.com/wrthomas315/Sorex_Genome2)