BACKGROUND Comparative genomics studies are central in identifying the coding and non-coding elements associated with complex traits, and the functional annotation of genomes is a critical step to decipher the genotype-to-phenotype relationships in livestock animals. As part of the Functional Annotation of Animal Genomes (FAANG) action, the FR-AgENCODE project aimed to create reference functional maps of domesticated animals by profiling the landscape of transcription (RNA-seq), chromatin accessibility (ATAC-seq) and conformation (Hi-C) in species representing ruminants (cattle, goat), monogastrics (pig) and birds (chicken), using three target samples related to metabolism (liver) and immunity (CD4+ and CD8+ T cells). RESULTS RNA-seq assays considerably extended the available catalog of annotated transcripts and identified differentially expressed genes with unknown function, including new syntenic lncRNAs. ATAC-seq highlighted an enrichment for transcription factor binding sites in differentially accessible regions of the chromatin. Comparative analyses revealed a core set of conserved regulatory regions across species. Topologically associating domains (TADs) and epigenetic A/B compartments annotated from Hi-C data were consistent with RNA-seq and ATAC-seq data. Multi-species comparisons showed that conserved TAD boundaries had stronger insulation properties than species-specific ones and that the genomic distribution of orthologous genes in A/B compartments was significantly conserved across species. CONCLUSIONS We report the first multi-species and multi-assay genome annotation results obtained by a FAANG project. Beyond the generation of reference annotations and the confirmation of previous findings on model animals, the integrative analysis of data from multiple assays and species sheds a new light on the multi-scale selective pressure shaping genome organization from birds to mammals. Overall, these results emphasize the value of FAANG for research on domesticated animals and reinforces the importance of future meta-analyses of the reference datasets being generated by this community on different species.

中文翻译：

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家养动物转录组和染色质结构的多物种注释。

背景比较基因组学研究对于识别与复杂性状相关的编码和非编码元件至关重要，基因组的功能注释是破译家畜动物基因型与表型关系的关键步骤。作为动物基因组功能注释 (FAANG) 行动的一部分，FR-AgENCODE 项目旨在通过分析转录 (RNA-seq)、染色质可及性 (ATAC-seq) 和构象 (ATAC-seq) 的图谱来创建家养动物的参考功能图谱。 Hi-C）在代表反刍动物（牛、山羊）、单胃动物（猪）和鸟类（鸡）的物种中，使用与代谢（肝脏）和免疫（CD4+ 和 CD8+ T 细胞）相关的三个目标样本。结果 RNA-seq 检测极大地扩展了注释转录本的可用目录，并鉴定了功能未知的差异表达基因，包括新的同线 lncRNA。ATAC-seq 强调了染色质不同可及区域中转录因子结合位点的富集。比较分析揭示了跨物种的一组保守的调控区域。Hi-C 数据注释的拓扑关联域 (TAD) 和表观遗传 A/B 区室与 RNA-seq 和 ATAC-seq 数据一致。多物种比较表明，保守的 TAD 边界比物种特异性边界具有更强的绝缘特性，并且 A/B 区室中直系同源基因的基因组分布在物种间显着保守。结论 我们报告了 FAANG 项目获得的第一个多物种和多测定基因组注释结果。除了生成参考注释和确认先前关于模型动物的发现之外，对多种测定和物种的数据的综合分析为塑造从鸟类到哺乳动物的基因组组织的多尺度选择性压力提供了新的视角。总体而言，这些结果强调了 FAANG 对于家养动物研究的价值，并强调了未来对该群落针对不同物种生成的参考数据集进行荟萃分析的重要性。