Hydractinia strain 236-21 genome assembly and Alr domain predictions

This dataset is related to the preprint "A family of unusual A family of unusual immunoglobulin superfamily genes in an invertebrate histocompatibility complex" (https://www.biorxiv.org/content/10.1101/2022.03.04.482883v2). <strong>Preprint Abstract:</strong> Most colonial marine invertebrates are capable of allorecognition, the ability to distinguish between themselves and conspecifics. One long-standing question is whether invertebrate allorecognition genes are homologous to vertebrate histocompatibility genes. In the cnidarian <em>Hydractinia symbiolongicarpus, </em>allorecognition is controlled by at least two genes, <em>Allorecognition 1</em> (<em>Alr1</em>) and <em>Allorecognition 2 </em>(<em>Alr2</em>), which encode highly polymorphic cell surface proteins that serve as markers of self. Here, we show that <em>Alr1</em> and <em>Alr2</em> are part of a family of 41 <em>Alr </em>genes, all of which reside a single genomic interval called the Allorecognition Complex (ARC). Using sensitive homology searches and highly accurate structural predictions, we demonstrate that the Alr proteins are members of the immunoglobulin superfamily (IgSF) with V-set and I-set Ig domains unlike any previously identified in animals. Specifically, their primary amino acid sequences lack many of the motifs considered diagnostic for V-set and I-set domains, yet they adopt secondary and tertiary structures nearly identical to canonical Ig domains. Thus, the V-set domain, which played a central role in the evolution of vertebrate adaptive immunity, was present in the last common ancestor of cnidarians and bilaterians. Unexpectedly, several Alr proteins also have immunoreceptor tyrosine-based activation motifs (ITAMs) and immunoreceptor tyrosine-based inhibitory motifs (ITIMs) in their cytoplasmic tails, suggesting they could participate in pathways homologous to those that regulate immunity in humans and flies. This work expands our definition of the IgSF with the addition of a family of unusual members, several of which play a role in invertebrate histocompatibility. <strong>This dataset contains:</strong> <strong>Hsym-236-21-genome-assembly.fa.gz</strong>: A gzip-compressed FASTA-formatted file of the genome assembly generated in the paper. <strong>Alr-domain-structure-predictions.zip:</strong> a zip-compressed file with structural predictions produced with Colabfold for all domains of the Alr proteins described in that manuscript.本数据集关联于预印本论文《一类罕见的免疫球蛋白超家族基因存在于无脊椎动物组织相容性复合体中》（原文标题：*A family of unusual immunoglobulin superfamily genes in an invertebrate histocompatibility complex*，链接：https://www.biorxiv.org/content/10.1101/2022.03.04.482883v2）。 【预印本摘要】 多数群居海洋无脊椎动物具备同种异体识别（allorecognition）能力，即可区分自身与同种个体的特性。长期以来，学界存在一个核心科学问题：无脊椎动物的同种异体识别基因是否与脊椎动物的组织相容性基因同源。 在刺胞动物*Hydractinia symbiolongicarpus*中，同种异体识别至少受两个基因调控：**Allorecognition 1（Alr1）**与**Allorecognition 2（Alr2）**，二者编码高度多态的细胞表面蛋白，作为自身识别的分子标记。本研究证实，Alr1与Alr2隶属于包含41个Alr基因的基因家族，所有Alr基因均定位于一个被称为**同种异体识别复合体（Allorecognition Complex, ARC）**的单一基因组区域内。 通过高灵敏度同源性搜索与高精度结构预测，本研究证实Alr蛋白属于**免疫球蛋白超家族（immunoglobulin superfamily, IgSF）**，其含有V-set与I-set型免疫球蛋白结构域，这是此前在动物中未被发现的类型。具体而言，Alr蛋白的一级氨基酸序列缺失诸多被视为V-set与I-set结构域诊断特征的基序，但它们的二级与三级结构却与经典免疫球蛋白结构域几乎完全一致。由此可见，在脊椎动物适应性免疫进化中发挥核心作用的V-set结构域，其实早在刺胞动物与两侧对称动物的最后共同祖先中便已存在。 值得注意的是，部分Alr蛋白的胞质尾区还含有**免疫受体酪氨酸活化基序（immunoreceptor tyrosine-based activation motif, ITAMs）**与**免疫受体酪氨酸抑制基序（immunoreceptor tyrosine-based inhibitory motif, ITIMs）**，这提示它们可能参与与人类及果蝇免疫调控通路同源的信号通路。本研究拓展了免疫球蛋白超家族的定义，新增了一类罕见的成员，其中多个基因参与无脊椎动物的组织相容性调控。 【本数据集包含以下内容】 **Hsym-236-21-genome-assembly.fa.gz**：本文中生成的基因组组装文件，格式为FASTA并经gzip压缩。 **Alr-domain-structure-predictions.zip**：经压缩的ZIP文件，内含针对本文手稿中所述全部Alr蛋白结构域的ColabFold预测结果。