DOI: 10.5061/dryad.7pvmcvf1p
title: Male and female adult zebra finch (Taeniopygia guttata) gonad RNAseq associated with: Relaxed purifying selection maintains a sex-linked supergene polymorphism in zebra finches

description: 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 the negative consequences of
 relaxed purifying selection through the more equal expression of those
 most highly diverged, and potentially degenerated, alleles.
description: 10 adult gonad samples (five male and five female), were
 sequenced with Illumina NovaSeq (Paired-end, 2x150bp sequencing). No
 post-processing performed.
description: # 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 each sample fastq files are formatted as below: x-${sample}_*xxxxxx*_L00x_Rx.fastq.gz e.g. for sample 3, there are reads: 1-3_201014_L001-R1.fastq.gz 1-3_201014_L001-R2.fastq.gz 1-3_201002_L002-R1.fastq.gz 1-3_201002_L002-R2.fastq.gz **Metadata and sequencing Information** File "Sample ID TGU raw untrimmed.xlsx" contains information on the sex, naming, md5 values and number of reads once trimmed File "ID22333_Indexes used.xlsx" contains information on sequencing concentrations and adapters used per sample **Extraction Information** File "TGU individuals RNA extractions.xlsx" contains information on sample collection, death, extraction, sex, and extractions per sample File "2100 expert_Eukaryote Total RNA Nano_DE24802221_2020-02-26_17-25-28.pdf" contains BioAnalyser output File "Bio_analyser_README.txt" contains formation on naming for bioanalyser output