DOI: 10.5281/zenodo.7758058
title: Induced immune reaction in the acorn worm, Saccoglossus kowalevskii, informs the evolution of antiviral immunity

description: 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>--&gt; DESeq2 results for each contrast (e.g., 2hpi treatment vs. control) <em>MaSigPro.Clusters.csv</em> --&gt; Mean expression for each gene placed within a pDEG cluster <em>MaSigPro.SigGenes.TreatmentvsControl.Robj</em> --&gt; 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> --&gt; OrthoFinder results <em>Skowalevskii_Genome_Annotation.SPHuman_and_HOG.csv</em> --&gt; 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>--&gt; 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> --&gt; Pfam annotation of the Skow1.1 genome assembly in HMMER's domblout format <em>Skow.KofamKOALA.detail.tsv</em> --&gt; KO annotation of the Skow1.1 genome assembly using KofamKOALA (detailed output) <em>Skow.KofamKOALA.detail.tsv </em>--&gt; KO annotation of the Skow1.1 genome assembly using KofamKOALA (mapper output) <em>SkowAnnotations.GO.tsv</em> --&gt; GO annotation of the Skow1.1 genome assembly <em>SkowAnnotations.PF.tsv</em> --&gt; PF annotation of the Skow1.1 genome assembly <em>SkowAnnotations.PP.tsv</em> --&gt; PP annotation of the Skow1.1 genome assembly ### Enrichment Data ### <em>DESeqEnrichments.tsv</em> --&gt; 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> --&gt; 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.