BACKGROUND The Japanese quail (Coturnix japonica) is a popular domestic poultry species and an increasingly significant model species in avian developmental, behavioural and disease research. RESULTS We have produced a high-quality quail genome sequence, spanning 0.93 Gb assigned to 33 chromosomes. In terms of contiguity, assembly statistics, gene content and chromosomal organisation, the quail genome shows high similarity to the chicken genome. We demonstrate the utility of this genome through three diverse applications. First, we identify selection signatures and candidate genes associated with social behaviour in the quail genome, an important agricultural and domestication trait. Second, we investigate the effects and interaction of photoperiod and temperature on the transcriptome of the quail medial basal hypothalamus, revealing key mechanisms of photoperiodism. Finally, we investigate the response of quail to H5N1 influenza infection. In quail lung, many critical immune genes and pathways were downregulated after H5N1 infection, and this may be key to the susceptibility of quail to H5N1. CONCLUSIONS We have produced a high-quality genome of the quail which will facilitate further studies into diverse research questions using the quail as a model avian species.

中文翻译：

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鹌鹑基因组：洞察社会行为，季节性生物学和传染病反应。

背景技术日本鹌鹑（Coturnix japonica）是一种流行的家禽物种，并且在禽类的发育，行为和疾病研究中正变得越来越重要。结果我们产生了一个高质量的鹌鹑基因组序列，跨越0.93 Gb，分配给33个染色体。在连续性，装配统计，基因含量和染色体组织方面，鹌鹑基因组显示出与鸡基因组的高度相似性。我们通过三个不同的应用程序证明了该基因组的实用性。首先，我们确定与鹌鹑基因组（一种重要的农业和驯养性状）中的社会行为相关的选择特征和候选基因。其次，我们研究了光周期和温度对鹌鹑内侧下丘脑转录组的影响和相互作用，揭示了光周期的关键机制。最后，我们调查了鹌鹑对H5N1流感感染的反应。在鹌鹑肺中，H5N1感染后许多关键的免疫基因和途径被下调，这可能是鹌鹑对H5N1易感性的关键。结论我们已经建立了鹌鹑的高质量基因组，这将有助于以鹌鹑为模型禽类物种进一步研究各种研究问题。