Induced immune reaction in the acorn worm, Saccoglossus kowalevskii, informs the evolution of antiviral immunity
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The data present in this repository reflect intermediate and processed data presented in the manuscript, <em>Induced immune reaction in the acorn worm, Saccoglossus kowalevskii, informs the evolution of antiviral immunity. </em>This manuscript is still under review; as such, this page will be updated upon publication. <strong>Manuscript Abstract:</strong> Evolutionary perspectives on the deployment of immune factors following infection have been shaped by studies on a limited number of biomedical model systems with a heavy emphasis on vertebrate species. Though their contributions to contemporary immunology cannot be understated, a broader phylogenetic perspective is needed to understand the evolution of immune systems across Metazoa. In our study, we leverage differential gene expression analyses to identify genes implicated in the antiviral immune response of the acorn worm hemichordate, <em>Saccoglossus kowalevskii</em>, and place them in the context of immunity evolution within deuterostomes – the animal clade composed of chordates, hemichordates, and echinoderms. Following acute exposure to the synthetic viral dsRNA analog, poly(I:C), we show that <em>S. kowalevskii </em>responds by regulating the transcription of genes associated with canonical innate immunity signaling pathways (e.g., NF-κB and IRF signaling) and metabolic processes (e.g., lipid metabolism), as well as many genes without clear evidence of orthology with those of model species. Aggregated across all experimental time point contrasts, we identify 423 genes that are differentially expressed in response to poly(I:C). We also identify 147 genes with altered temporal patterns of expression in response to immune challenge. By characterizing the molecular toolkit involved in hemichordate antiviral immunity, our findings provide vital evolutionary context for understanding the origins of immune systems within Deuterostomia. <strong>Repository contents:</strong> ### Processed Data ### <em>Full_DESeq2_matrix.csv </em>--> DESeq2 results for each contrast (e.g., 2hpi treatment vs. control) <em>MaSigPro.Clusters.csv</em> --> Mean expression for each gene placed within a pDEG cluster <em>MaSigPro.SigGenes.TreatmentvsControl.Robj</em> --> T.fit() R-object output from MaSigPro pipeline. This can be opened in R using the load() function. ### Homology Assessment ### <em>Orthofinder.tar.gz</em> --> OrthoFinder results <em>Skowalevskii_Genome_Annotation.SPHuman_and_HOG.csv</em> --> Assignment of IDs to Skow1.1 genes conforming to "PANTHER-Human" and "HOG" output described in the main text of the paper <em>Skowalevskii_Genome_Annotation.SPPANTHER.csv </em>--> Assignment of IDs to Skow1.1 genes conforming to "PANTHER-SwissProt" output described in the main text of the paper ### Functional Annotation ### <em>Skow.HMMER_Pfam.domtblout.tsv</em> --> Pfam annotation of the Skow1.1 genome assembly in HMMER's domblout format <em>Skow.KofamKOALA.detail.tsv</em> --> KO annotation of the Skow1.1 genome assembly using KofamKOALA (detailed output) <em>Skow.KofamKOALA.detail.tsv </em>--> KO annotation of the Skow1.1 genome assembly using KofamKOALA (mapper output) <em>SkowAnnotations.GO.tsv</em> --> GO annotation of the Skow1.1 genome assembly <em>SkowAnnotations.PF.tsv</em> --> PF annotation of the Skow1.1 genome assembly <em>SkowAnnotations.PP.tsv</em> --> PP annotation of the Skow1.1 genome assembly ### Enrichment Data ### <em>DESeqEnrichments.tsv</em> --> Pearson's chi-squared enrichment calculations for every annotation present in the Skow1.1 genome assembly for genes resolved as significantly differentially expressed by DESeq2. <em>MaSigProEnrichments.tsv</em> --> Pearson's chi-squared enrichment calculations for every annotation present in the Skow1.1 genome assembly for genes resolved as significantly differentially expressed by MaSigPro.
本仓库收录的数据对应尚未正式发表的手稿《棘头虫Saccoglossus kowalevskii的诱导免疫反应对抗病毒免疫演化的启示》（原标题：*Induced immune reaction in the acorn worm, Saccoglossus kowalevskii, informs the evolution of antiviral immunity*）中的中间处理数据。该手稿目前仍处于审稿阶段，待正式发表后本页面将进行更新。**手稿摘要：** 目前关于感染后免疫因子调控的演化研究，多基于数量有限的生物医学模式系统，且高度聚焦于脊椎动物类群。尽管这类研究对当代免疫学的贡献毋庸置疑，但要理解整个后生动物（Metazoa）免疫系统的演化历程，亟需更广泛的系统发育视角。在本研究中，我们借助差异基因表达分析，鉴定出与棘头虫半索动物（hemichordate）*Saccoglossus kowalevskii*抗病毒免疫反应相关的基因，并将其置于后口动物（deuterostomes）的免疫演化框架中进行分析——后口动物是由脊索动物、半索动物和棘皮动物共同构成的动物支系。在暴露于合成病毒双链RNA类似物聚肌胞苷酸（poly(I:C)）后，我们发现*S. kowalevskii*通过调控与经典先天免疫信号通路（如NF-κB和IRF信号通路）、代谢过程（如脂质代谢）相关基因的转录，以及大量与模式物种无明确直系同源关系的基因，来应对免疫刺激。整合所有实验时间点的对照数据，我们共鉴定出423个在poly(I:C)刺激下发生差异表达的基因，同时还识别出147个在免疫挑战下表达时序模式发生改变的基因。通过解析半索动物抗病毒免疫所涉及的分子工具箱，本研究的发现为理解后口动物门（Deuterostomia）免疫系统的起源提供了关键的演化背景。**仓库内容：** ### 处理后数据 ### *Full_DESeq2_matrix.csv*：对应各对照组合（如感染后2小时处理组 vs 对照组）的DESeq2分析结果 *MaSigPro.Clusters.csv*：各基因在pDEG聚类中的平均表达量数据 *MaSigPro.SigGenes.TreatmentvsControl.Robj*：MaSigPro分析流程中T.fit()函数生成的R对象结果，可通过R语言的load()函数加载读取 ### 同源性评估 ### *Orthofinder.tar.gz*：OrthoFinder分析结果 *Skowalevskii_Genome_Annotation.SPHuman_and_HOG.csv*：Skow1.1版本基因组注释的ID分配文件，对应论文正文中描述的“PANTHER-人类”和“HOG”输出结果 *Skowalevskii_Genome_Annotation.SPPANTHER.csv*：Skow1.1版本基因组注释的ID分配文件，对应论文正文中描述的“PANTHER-SwissProt”输出结果 ### 功能注释 ### *Skow.HMMER_Pfam.domtblout.tsv*：采用HMMER的domtblout格式对Skow1.1版本基因组组装结果进行的Pfam注释文件 *Skow.KofamKOALA.detail.tsv*：采用KofamKOALA对Skow1.1版本基因组组装结果进行的KO注释（详细输出版本） *Skow.KofamKOALA.detail.tsv*：采用KofamKOALA对Skow1.1版本基因组组装结果进行的KO注释（映射输出版本） *SkowAnnotations.GO.tsv*：对Skow1.1版本基因组组装结果进行的GO注释文件 *SkowAnnotations.PF.tsv*：对Skow1.1版本基因组组装结果进行的PF注释文件 *SkowAnnotations.PP.tsv*：对Skow1.1版本基因组组装结果进行的PP注释文件 ### 富集分析数据 ### *DESeqEnrichments.tsv*：针对经DESeq2鉴定为显著差异表达的基因，对其在Skow1.1版本基因组注释中的所有条目进行Pearson卡方富集分析的结果文件 *MaSigProEnrichments.tsv*：针对经MaSigPro鉴定为显著差异表达的基因，对其在Skow1.1版本基因组注释中的所有条目进行Pearson卡方富集分析的结果文件
