Data from: Characterization of the genome and transcriptome of the blue tit Cyanistes caeruleus: polymorphisms, sex-biased expression and selection signals

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.

解析基因组序列并明确种群内的基因组变异，有望揭示物种内的适应性演化进程，阐明与生态相关的性状变异的遗传基础。蓝山雀（Cyanistes caeruleus）作为长期应用的生态模型物种，此前被用于研究交配与繁殖行为变异的适合度效应。然而，目前对于这种鸣禽基因组中因自然选择与性选择产生的潜在遗传改变，所知甚少。为填补这一研究空白，本研究组装了首份单只蓝山雀的基因组草图，将5只雌性与5只雄性的转录组比对至该参考基因组，鉴定了全基因组范围内的变异，并对性腺、大脑及其他组织开展性别差异表达分析。在性腺中，我们检测到大量性别偏向性基因；其中，雄性与雌性的性别限制性基因（仅在单一性别中表达的基因）占比相近。但在大脑中，雌性偏向性基因类别内的雌性限制性基因占比（82%）显著高于雄性偏向性基因类别内的雄性限制性基因占比（6%）。这表明雌性限制性基因主要遵循“开-关”式的表达调控机制。此外，多数雄性偏向性基因位于Z染色体上，提示雄性偏向性基因的剂量补偿并不完全。我们从RNA测序（RNA-seq）数据中鉴定了超过50万个单核苷酸多态性（Single Nucleotide Polymorphism, SNP）位点。单只参考个体的杂合子检测结果在DNA测序（DNA-seq）与RNA测序的变异鉴定中高度一致。借助这些多态性位点的信息，我们鉴定了基因组中潜在的选择信号。我们列出了可用于后续测序与详细选择研究的候选基因，其中包括可能与减数分裂驱动演化相关的基因。包含上述研究信息的蓝山雀公共基因组浏览器可通过以下网址访问：http://public-genomes-ngs.molgen.mpg.de。