Male and female adult zebra finch (Taeniopygia guttata) gonad RNAseq associated with: Relaxed purifying selection maintains a sex-linked supergene polymorphism in zebra finches

Recent years have seen an explosion in examples of inversion polymorphisms, where recombination is suppressed between haplotypes, acting as supergenes to control complex traits. However, an enduring problem in evolutionary biology is understanding how these inversion polymorphisms are maintained, often for long periods of time. Here, we test alternate theories for how balancing selection maintains supergenes and explore the molecular evolution and expression of a large, sex-linked inversion polymorphism in a passerine bird, the zebra finch (Taeniopygia guttata) responsible for most of the genetic variation in sperm morphology. We find evidence for degeneration within the supergene characterised by relaxed purifying selection and an excess of nonsynonymous differences which, combined with signatures of balancing selection, is indicative of associative overdominance protecting heterozygotes from deleterious recessive alleles. Furthermore, we find that the transcriptome acts to mitigate th..., 10 adult gonad samples (five male and five female), were sequenced with Illumina NovaSeq (Paired-end, 2x150bp sequencing). No post-processing performed., , # Zebra Finch (Taeniopygia guttata) gonad RNAseq

[https://doi.org/10.5061/dryad.7pvmcvf1p](https://doi.org/10.5061/dryad.7pvmcvf1p)

RNA-seq data were obtained from a captive population of zebra finches at Queen Mary University of London. Individuals were in their first breeding season, having formed breeding pairs and produced fertile eggs. Samples were collected in accordance with national guidelines. The left gonad was dissected from five males and five females, homogenised and stored in RNA later until preparation. We used the Animal Tissue RNA Kit (Qiagen) to extract RNA. Dual-indexed, strand-specific RNASeq libraries were prepared at the NERC Environmental Omics Facility (NEOF) - Liverpool using the NEBNext polyA selection and Ultra II Directional RNA library preparation kits. RNA was sequenced on the Illumina NovaSeq using S4 chemistry, resulting in an average of 74 million 150bp paired-end reads per sample. 

## Description of the data and file structure

**Fastq Reads**

For e...