DOI: 10.5061/dryad.dc56b
title: Data from: Characterization of the genome and transcriptome of the blue tit Cyanistes caeruleus: polymorphisms, sex-biased expression and selection signals

description: Decoding genomic sequences and determining their variation within
 populations has potential to reveal adaptive processes and unravel the
 genetic basis of ecologically relevant trait variation within a species.
 The blue tit Cyanistes caeruleus – a long-time ecological model species –
 has been used to investigate fitness consequences of variation in mating
 and reproductive behaviour. However, very little is known about the
 underlying genetic changes due to natural and sexual selection in the
 genome of this songbird. As a step to bridge this gap, we assembled the
 first draft genome of a single blue tit, mapped the transcriptome of five
 females and five males to this reference, identified genomewide variants
 and performed sex-differential expression analysis in the gonads, brain
 and other tissues. In the gonads, we found a high number of sex-biased
 genes, and of those, a similar proportion were sex-limited (genes only
 expressed in one sex) in males and females. However, in the brain, the
 proportion of female-limited genes within the female-biased gene category
 (82%) was substantially higher than the proportion of male-limited genes
 within the male-biased category (6%). This suggests a predominant on-off
 switching mechanism for the female-limited genes. In addition, most
 male-biased genes were located on the Z-chromosome, indicating incomplete
 dosage compensation for the male-biased genes. We called more than 500 000
 SNPs from the RNA-seq data. Heterozygote detection in the single reference
 individual was highly congruent between DNA-seq and RNA-seq calling. Using
 information from these polymorphisms, we identified potential selection
 signals in the genome. We list candidate genes which can be used for
 further sequencing and detailed selection studies, including genes
 potentially related to meiotic drive evolution. A public genome browser of
 the blue tit with the described information is available at
 http://public-genomes-ngs.molgen.mpg.de.
description: Tests for
 sex-differential expression in gonadsCuffdiff results files;
 differential expression of all gonadal genes between 5 male and 5 female
 blue titsCuffdiff_gonads_gene_exp.diffTests for sex-differential expression in pooled organsCuffdiff results file; Differential expression of all pooled organ genes between 5 male and 5 female blue titsCuffdiff_organs_gene_exp.diffTests for sex-differential expression in the brainCuffdiff results files; differential expression of all brain genes between 5 male and 5 female blue tits.Cuffdiff_brain_gene_exp.diffAnnotated SNPs in male-specifc transcriptomevcf file: annotated SNPs in male-specific transcriptome; annotated using SnpEff; based on 5 male blue titsRNAseq_5ind_mspeccuffsnpsel1_eff.zipAnnotated SNPs in female-specific transcriptomevcf file: annotated SNPs in female-specific transcriptome; annotated using SnpEff; based on 5 female blue titsRNAseq_5ind_fspeccuffsnpsel1_eff.zipAnnotated SNPs in transcriptome common to both sexesvcf file: annotated SNPs in transcriptome common to both sexes; annotated using SnpEff; based on 5 male and 5 female blue tits.RNAseq_10ind_mandfcuffsnpsel1_eff.zipTajima's D across all 25 kb windows of the blue tit genomebased on SNPs called from the transcriptome of 5 male and 5 female blue tits.RNAseq10ind_mandfcuff_25kb.Tajima.DiHS values across all informative scaffoldsbased on SNPs called from the transcriptome of 5 male and 5 female blue tits.resihs_allscaff2.txt