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7 results for “Saccoglossus”
Induced immune reaction in the acorn worm, Saccoglossus kowalevskii, informs the evolution of antiviral immunity
<p>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.</p> <p> </p> <p><strong>Manuscript Abstract:</strong></p> <p>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.</p> <p> </p> <p><strong>Repository contents:</strong></p> <p>### Processed Data ###</p> <ul> <li><em>Full_DESeq2_matrix.csv </em>--> DESeq2 results for each contrast (e.g., 2hpi treatment vs. control)</li> <li><em>MaSigPro.Clusters.csv</em> --> Mean expression for each gene placed within a pDEG cluster</li> <li><em>MaSigPro.SigGenes.TreatmentvsControl.Robj</em> --> T.fit() R-object output from MaSigPro pipeline. This can be opened in R using the load() function.</li> </ul> <p>### Homology Assessment ###</p> <ul> <li><em>Orthofinder.tar.gz</em> --> OrthoFinder results</li> <li><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</li> <li><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</li> </ul> <p>### Functional Annotation ###</p> <ul> <li><em>Skow.HMMER_Pfam.domtblout.tsv</em> --> Pfam annotation of the Skow1.1 genome assembly in HMMER's domblout format</li> <li><em>Skow.KofamKOALA.detail.tsv</em> --> KO annotation of the Skow1.1 genome assembly using KofamKOALA (detailed output)</li> <li><em>Skow.KofamKOALA.detail.tsv </em>--> KO annotation of the Skow1.1 genome assembly using KofamKOALA (mapper output)</li> <li><em>SkowAnnotations.GO.tsv</em> --> GO annotation of the Skow1.1 genome assembly</li> <li><em>SkowAnnotations.PF.tsv</em> --> PF annotation of the Skow1.1 genome assembly</li> <li><em>SkowAnnotations.PP.tsv</em> --> PP annotation of the Skow1.1 genome assembly</li> </ul> <p>### Enrichment Data ###</p> <ul> <li><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.</li> <li><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.</li> </ul>
FIGURE 4 in A revision of the genus Saccoglossus (Hemichordata: Enteropneusta: Harrimaniidae) with taxonomic descriptions of five new species from the Eastern Pacific
FIGURE 4. Light micrographs of transverse sections of Saccoglossus shumaginensis n. sp.: A, Proboscis. B, Proboscis with heart-kidney complex. C, Proboscis neck. D, Anterior region of the collar. E, Posterior region of the collar. Inset: Collar canal. F, Anterior pharyngeal region of the trunk. bs, branchial sac; bv, blood vessel; cc, collar canal; cl, collar lumen; clm, collar longitudinal muscles; cv, cardiac vesicle; g, glomerulus; gb, gill bar; go, gonad; nc, nerve cord; pc, proboscis coelom; phd, periheamal diverticulum; pl, pharynx lumen; plm, proboscis longitudinal muscles; pv, proboscis vesicle; s, stomochord; sc, skeletal cornua; sp, skeletal plate; tlm, trunk longitudinal muscles; vm, ventral mesentery. Scale bars A, B, D, E, F = 500 µm; C = 200 µm; E inset = 100 µm.
FIGURE 1 in A revision of the genus Saccoglossus (Hemichordata: Enteropneusta: Harrimaniidae) with taxonomic descriptions of five new species from the Eastern Pacific
FIGURE 1. Photographs of fixed specimens from the NMNH (Smithsonian). With the exception of A and F, all of the specimens have lost the anterior end of the proboscis. A, Photograph of a coiled specimen of Saccoglossus porochordus n. sp. showing the proboscis and dorsal side. B, Photograph of the ventral side of S. porochordus n. sp. C, Photograph of the dorsal side of S. rhabdorhynchus n. sp. D, Photograph of the lateral side of S. rhabdorhynchus n. sp. E, Photograph of the right side of S. shumaginensis n. sp. F, Photograph of the left side of S. shumaginensis n. sp. G, Photograph of the right side of S. sonorensis n. sp. H, Photograph of the left side of S. sonorensis n. sp. c, collar; p, proboscis; t, trunk. Scale bars = 5 mm.
FIGURE 5 in A revision of the genus Saccoglossus (Hemichordata: Enteropneusta: Harrimaniidae) with taxonomic descriptions of five new species from the Eastern Pacific
FIGURE 5. Light micrographs of transverse sections of Saccoglossus sonorensis n. sp.: A, Proboscis with heart-kidney complex. Inset: Anterior region of the proboscis coelom. B, Proboscis neck showing the skeletal spine of the proboscis skeleton. C, Proboscis neck showing the proboscis vesicle. D, Anterior region of the collar. Inset: Collar nerve cord showing a nerve root. E, Posterior region of the collar. Inset: Collar canal. F, Anterior pharyngeal region of the trunk. ac, amoeboid cells; bp, branchial pore; bv, blood vessel; cc, collar canal; cl, collar lumen; clm, collar longitudinal muscles; cv, cardiac vesicle; e, epithelia; g, glomerulus; gb, gill bar; go, gonad; nc, nerve cord; nr, nerve root; pc, proboscis coelom; phd, periheamal diverticulum; pl, pharynx lumen; plm, proboscis longitudinal muscles; pv, proboscis vesicle; s, stomochord; sc, skeletal cornua; sk, skeletal keel; sl, stomochord lumen; sp, skeletal plate; ss, skeletal spine; tlm, trunk longitudinal muscles. Scale bars A, E, F, G = 500 µm; B and F inset = 100 µm; C, D, E inset = 200 µm.
FIGURE 3 in A revision of the genus Saccoglossus (Hemichordata: Enteropneusta: Harrimaniidae) with taxonomic descriptions of five new species from the Eastern Pacific
FIGURE 3. Light micrographs of transverse sections of Saccoglossus rhabdorhynchus n. sp.: A, Proboscis with heartkidney complex. B, Proboscis neck showing the spine of the proboscis skeleton. C, Proboscis neck showing the proboscis vesicle. D, Anterior region of the collar. E, Posterior region of the collar. Inset: Collar canal. F, Anterior pharyngeal region of the trunk. bp, branchial pore; bs, branchial sac; bv, blood vessel; cc, collar canal; cl, collar lumen; clm, collar longitudinal muscles; cv, cardiac vesicle; dm, dorsal mesentery; g, glomerulus; gb, gill bar; nc, nerve cord; pc, proboscis coelom; np, neuropore; phd, periheamal diverticulum; pl, pharynx lumen; plm, proboscis longitudinal muscles; pv, proboscis vesicle; s, stomochord; sc, skeletal cornua; sk, skeletal keel; sl, stomochord lumen; sp, skeletal plate; ss, skeletal spine; tl, trunk lumen; tlm, trunk longitudinal muscles; vm, ventral mesentery. Scale bars A, B, C, D, E, F = 500 µm; E inset = 100 µm.
FIGURE 6 in A revision of the genus Saccoglossus (Hemichordata: Enteropneusta: Harrimaniidae) with taxonomic descriptions of five new species from the Eastern Pacific
FIGURE 6. Light micrographs of transverse sections of Saccoglossus palmeri n. sp.: A, Anterior region of the proboscis. B, Proboscis with heart-kidney complex. C, Proboscis neck. D, Anterior region of the collar. E, Anterior pharyngeal region of the trunk. bv, blood vessel; cv, cardiac vesicle; dm, dorsal mesentery; g, glomerulus; gb, gill bar; go, gonad; nc, nerve cord; pc, proboscis coelom; phd, periheamal diverticulum; pl, pharynx lumen; plm, proboscis longitudinal muscles; pv, proboscis vesicle; s, stomochord; sc, skeletal cornua; sk, skeletal keel; sp, skeletal plate; tlm, trunk longitudinal muscles. Scale bars A, B, D, E = 250 µm; C = 150 µm.
FIGURE 2 in A revision of the genus Saccoglossus (Hemichordata: Enteropneusta: Harrimaniidae) with taxonomic descriptions of five new species from the Eastern Pacific
FIGURE 2. Light micrographs of transverse sections of Saccoglossus porochordus n. sp.: A, Proboscis with heartkidney complex. B, Heart-kidney complex. C, Proboscis neck. D, Anterior region of the collar. Inset: Dorsal collar nerve cord and crest. E, Posterior region of the collar. F, Collar canal. G, Dorsal groove of the collar. H, Anterior pharyngeal region of the trunk. a, axons; bs, branchial sac; bv, blood vessel; cb, cell bodies; cc, collar canal; cl, collar lumen; clm, collar longitudinal muscles; cv, cardiac vesicle; dg, dorsal groove; g, glomerulus; gb, gill bar; go, gonad; mc, mucous cells; nc, nerve cord; ncc, nerve cord crest; pc, proboscis coelom; phd, periheamal diverticulum; pl, pharynx lumen; plm, proboscis longitudinal muscles; pp, proboscis pore; pv, proboscis vesicle; s, stomochord; sc, skeletal cornua; sk, skeletal keel; sp, skeletal plate; ss, skeletal spine; tlm, trunk longitudinal muscles; vm, ventral mesentery. Scale bars A, D and F = 750 µm; B and C = 300 µm; D inset and E inset = 200 µm.
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