DOI: 10.5061/dryad.6hdr7sr6k
title: Data from: Impact of Z chromosome inversions on gene expression in testes and liver tissues in the zebra finch

description: Chromosomal inversions have been identified in many natural populations
 and can be responsible for novel traits and rapid adaptation. In zebra
 finch, a large region on the Z chromosome has been subject to multiple
 inversions, which have pleiotropic effects on multiple traits but
 especially on sperm phenotypes, such as midpiece and flagellum length. To
 understand the effect the Z inversion has on these traits, we examined
 testis and liver transcriptomes of young males at different maturation
 times. We compared gene expression differences among three inversion
 karyotypes: AA, B*B* and AB*, where B* denotes the inverted regions on Z
 with respect to A. In testis, 794 differentially expressed genes were
 found and most of them were located on chromosome Z. They were
 functionally enriched for sperm-related traits. We also identified
 clusters of co-expressed genes that matched with the inversion-related
 sperm phenotypes. In liver, there were some enriched functions and some
 overrepresentation on chromosome Z with similar location as in testis. In
 both tissues, the overrepresented genes were located near the distal end
 of Z but also in the middle of the chromosome. For the heterokaryotype, we
 observed several genes with one allele being dominantly expressed, similar
 to expression patterns in one or the other homokaryotype. This was
 confirmed with SNPs for three genes, and interestingly one gene, DMGDH,
 had allele-specific expression originating mainly from one inversion
 haplotype in the testis, yet both inversion haplotypes were expressed
 equally in the liver. This karyotype-specific difference in
 tissue-specific expression suggests a pleiotropic effect of the inversion
 and thus suggests a mechanism for divergent phenotypic effects resulting
 from an inversion.
description: Zebra finch with different inversion karyotypes were reared at Institute of Vertebrate Biology (Studenec, Czechia). These birds originate from the domesticated ‘Krakow’ population that was generated by hybridizing between Krakow  and Seewiesen populations (population 11 and 8 in (Forstmeier et al., 2007)). Crosses were made between individuals in order to produce AA, AB* and B*B* males and inversion genotyping for all samples was done using 6 tag SNPs (Knief et al., 2017). Male offspring from the crosses were sampled between 49-69 days of age to capture different timepoints of testis development from immature to fully mature. Birds were euthanized by using cervical dislocation, and both right testis and liver tissue were frozen in liquid nitrogen and stored at -80°C until further analysis. Left testis was fixed in Davidson’s Fixative, and later prepared for histological determination of testis development. RNA from right testis and liver tissue was extracted with a phenol- based phase separation (Tri-reagent, Ambion) following the Trizol-protocol from SIGMA.<br>
description: # Data from: Impact of Z chromosome inversions on gene expression in
 testes and liver tissues in the zebra finch
 [https://doi.org/10.5061/dryad.6hdr7sr6k](https://doi.org/10.5061/dryad.6hdr7sr6k) "TaeGut\_TrimmedTestis.tar" contains the trimmed fastq files for each of the sampled 32 individuals for testis tissue. "TaeGut\_TrimmedLiver.tar" contains the trimmed fastq files for each of the sampled 32 individuals for liver tissue. Each file is named after the sample name and read pair information separated by underscore. Forward reads end with "\_Tr1.fastq.gz" and reverse reads end with "\_Tr2.fastq.gz". "Sample\_information.xlsx" contains details about each sample ## Code/Software Reads in the tar files were produced from the raw reads with cutadapt v2.7 (Martin, 2011).