Ribosomal DNA (rDNA) repeats are situated in the nucleolus organizer regions (NOR) of chromosomes and transcribed into rRNA for ribosome biogenesis. Thus, they are an essential component of eukaryotic genomes. rDNA repeat units consist of rRNA gene clusters that are transcribed into single pre-rRNA molecules, each separated by intergenic spacers (IGS) that contain regulatory elements for rRNA gene cluster transcription. Because of their high repeat content, rDNA sequences are usually absent from genome assemblies. In this work, we used the long-read sequencing technology to describe the chicken IGS and fill the knowledge gap on rDNA sequences of one of the key domesticated animals. We used the long-read PacBio RSII technique to sequence the BAC clone WAG137G04 (Wageningen BAC library) known to contain chicken NOR elements and the HGAP workflow software suit to assemble the PacBio RSII reads. Whole-genome sequence contigs homologous to the chicken rDNA repetitive unit were identified based on the Gallus_gallus-5.0 assembly with BLAST. We used the Geneious 9.0.5 and Mega software, maximum likelihood method and Chickspress project for sequence evolution analysis, phylogenetic tree construction and analysis of the raw transcriptome data. Three complete IGS sequences in the White Leghorn chicken genome and one IGS sequence in the red junglefowl contig AADN04001305.1 (Gallus_gallus-5.0) were detected. They had various lengths and contained three groups of tandem repeats (some of them being very GC rich) that form highly organized arrays. Initiation and termination sites of rDNA transcription were located within small and large unique regions (SUR and LUR), respectively. No functionally significant sites were detected within the tandem repeat sequences. Due to the highly organized GC-rich repeats, the structure of the chicken IGS differs from that of IGS in human, apes, Xenopus or fish rDNA. However, the chicken IGS shares some molecular organization features with that of the turtles, which are other representatives of the Sauropsida clade that includes birds and reptiles. Our current results on the structure of chicken IGS together with the previously reported ribosomal gene cluster sequence provide sufficient data to consider that the complete chicken rDNA sequence is assembled with confidence in terms of molecular DNA organization.

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鸡核糖体DNA中基因间隔子的结构

核糖体DNA（rDNA）重复序列位于染色体的核仁组织区（NOR）中，并转录成rRNA进行核糖体生物发生。因此，它们是真核基因组的重要组成部分。rDNA重复单元由rRNA基因簇组成，这些rRNA基因簇被转录成单个pre-rRNA分子，每个分子之间被基因间隔子（IGS）隔开，其中基因间隔子（IGS）包含用于rRNA基因簇转录的调控元件。由于其高重复含量，通常在基因组组装中不存在rDNA序列。在这项工作中，我们使用了长测序技术来描述鸡的IGS，并填补了关键家畜之一的rDNA序列的知识空白。我们使用了已久的PacBio RSII技术对已知含有鸡NOR元素的BAC克隆WAG137G04（Wageningen BAC库）进行测序，并且使用HGAP工作流程软件来组装PacBio RSII读段。基于BLAST的Gallus_gallus-5.0装配体，鉴定了与鸡rDNA重复单元同源的全基因组序列重叠群。我们使用Geneious 9.0.5和Mega软件，最大似然法和Chickspress项目进行序列进化分析，系统树构建和原始转录组数据分析。在白色来亨鸡鸡基因组中检测到三个完整的IGS序列，在红色丛林禽重叠群AADN04001305.1（Gallus_gallus-5.0）中检测到一个IGS序列。它们的长度各不相同，包含三组串联重复序列（其中一些非常富含GC），形成了高度组织的阵列。rDNA转录的起始和终止位点分别位于较小和较大的唯一区域（SUR和LUR）内。在串联重复序列中未检测到功能上重要的位点。由于高度组织化的富含GC的重复序列，在人，猿，非洲爪蟾或鱼类rDNA中，鸡IGS的结构与IGS的结构不同。但是，鸡的IGS与乌龟具有一些分子组织特征，乌龟是包括鸟类和爬行动物在内的蜥脚类进化支的其他代表。