Collagen IV and basement membrane at the evolutionary dawn of metazoan tissues

1A pivotal event in metazoan evolution was the transition from single-cell organisms to multicellular tissues (Figure 1A). The cellular microenvironment is presumed to play an essential role in this transition, yet the mechanism remains obscure. The basement membrane (BM), a specialized form of extracellular matrix (ECM), is a hallmark morphological feature of the microenvironment of epithelial tissues, and its appearance within the non-bilaterian animal phyla suggests it was a prerequisite. The BM has numerous functions including maintaining tissue architecture and compartmentalization, organizing growth factor signaling gradients, guiding cell migration and adhesion, delineating apical-basal polarity modulating cell differentiation during development, orchestrating cell behavior in tissue repair after injury, and guiding organ regeneration.

2The basement membrane is a supramolecular scaffold, comprised of a toolkit of proteins including collagen IV, laminin, perlecan, and nidogen. Among these proteins, recent studies reveal collagen IV is an ancient protein with up to six distinct genes (COL4A1, COL4A2, COL4A3, COL4A4, COL4A5, COL4A6), essential for early development, that functions as a smart scaffold providing tensile strength to tissues, influencing cell behavior by tethering diverse macromolecules, including laminin, proteoglycans, growth factors, binding integrins. Disrupting collagen IV scaffolds causes BM destabilization and tissue dysfunction in mice, zebrafish, flies, and nematodes. Collectively, these findings reveal that collagen IV, a component of the cellular microenvironment, is essential for tissue architecture and function; yet, the origin and molecular evolution of collagen IV remains obscure.

3Knowledge of collagen IV evolution may shed light on the fundamental features of the cellular microenvironment that enabled the transition from single-cell organisms to multicellular tissues. Together, the non-bilaterian animal phyla (Ctenophora, Porifera, Placozoa, and Cnidaria) represent this transition. Importantly, Ctenophora has recently emerged as one of the earliest-branching extant phyla, along with the sponges (Porifera). Here, we sought to identify ECM components in Ctenophora along with the other non-bilaterian animal phyla, and compared the components to Bilateria and the metazoan sister-groups, Choanozoa, Filasterea, Amoebozoa, and Apusozoa. Our findings reveal that collagen IV and its truncated variant, spongin, are associated with the transition to multicellularity, and further that collagen IV, as a component of BM scaffolds, enabled the genesis of multicellular epithelial tissues.

4We characterized the extracellular matrix in Ctenophora (comb jellies) and the other non-bilaterian animal phyla through a combination of immunohistochemistry (IHC), electron microscopy (EM), RNA sequencing, and genomic and transcriptomic analyses. Three ctenophore species, Mnemiopsis leidyi, Beroe ovata, and Pleurobrachia pileus, were used for EM and IHC experiments. Systematic assessment by EM of a number of sections from similar areas in Mnemiopsis was conducted, and no organized basement membrane was encountered. Furthermore, tight junctions between cells and cellular polarization were not observed, both hallmarks of epithelial basement membrane tissue structure (Figure 1B). IHC was congruent with this finding, indicating that collagen IV was dispersed throughout the tissue, surrounding and encompassing cells. In Beroe and Pleurobrachia, however, EM indicated an electron dense layer underlying cells along with cell polarization, and lateral tight junctions between cells, and IHC similarly showed a dense collagen IV layer underlying cells (Figure 1B). Together, these features are congruent with basement membrane architecture and epithelial tissue. Basement membrane structures are prevalent throughout metazoa, from Cnidaria to vertebrates, and we sought to compare the basement membrane architecture in Ctenophora to that of other non-bilaterian animal phyla and Bilateria. Nematostella, along with other cnidarians, have a bilayer body structure composed of endoderm and ectoderm layer with an intervening mesoglea; however, the general BM structure is congruent with that of bilaterian organisms, including mammals. Nematostella demonstrated presence of basement membrane, characterized by polarized cells apical to an electron dense layer by EM, and a concentrated region of collagen IV underlying cell nuclei by IHC (Figure 1C).

5We then characterized the ECM composition through analysis of transcriptomic and genomic data across the non-bilaterian animal phyla in comparison with Bilateria and unicellular sister-groups. Ctenophore genomic and transcriptomic data were publicly available from the Pleurobrachia Genome Browser on Neurobase (http://neurobase.rc.ufl.edu/Pleurobrachia) and the Mnemiopsis Genome Project Portal on the National Human Genome Research Institute site (https://kona.nhgri.nih.gov/mnemiopsis/). The ECM components in Nematostella are very similar to that of most bilaterian species BMs, including human, mouse, zebrafish, Drosophila, and C. elegans, consisting of collagen IV, laminin, peroxidasin, collagen XV and XVIII, perlecan, nidogen, fibronectin, as well as spongin (Figure 1C and Figure 2). Ctenophora, however, revealed a simplified set of ECM proteins, with collagen IV and laminin as the only components identified across Beroe, Pleurobrachia, and Mnemiopsis (Figure 1B and Figure 2). Importantly, despite lacking the full gamut of bilaterian ECM proteins, ctenophore cells can still construct a prototypical basement membrane in Pleurobrachia and Beroe. Mnemiopsis, however, does not form a BM despite exhibiting the very same toolkit proteins and this may be a result of secondary loss event.

6Across Porifera and Placozoa, basement membranes are uncommon. Placozoa and the poriferan classes of calcareous and demosponges lack basement membranes (Figure 1C), suggesting the BM may have been secondarily lost in these lineages or that it is present only at specific stages during their life cycle. Alternatively, basement membranes may have independently evolved in Ctenophora, Porifera, and Bilateria, a phenomenon that could have occurred because of shared inheritance of ECM proteins and domains from the last common ancestor of the non-bilaterian animal phyla. Investigation of the non-bilaterian animal phyla for components of the BM toolkit suggests that many of the components are present. Specifically, Placozoa contains the necessary components for a BM, including collagen IV, laminin, perlecan, and nidogen and also exhibits spongin (Figure 1C and Figure 2) (vide infra). In Porifera, the ECM of homoscleromorph sponges contains basement membranes, with collagen IV and laminin, but no spongin (Figure 1C and Figure 2). Demosponges, on the other hand, lack any detectable collagen IV and only contain laminin-related domains and spongin. In contrast, the Demosponge and Hexactinellidae classes of Porifera, which both lack collagen IV, do not have basement membranes (Figure 1C).

7Laminin architecture appears to be present in choanoflagellates, and additionally laminin-related genes appear in all other unicellular species including Capsaspora owczarzaki, Dictyostelium discoideum, and Thecamonas trahens (Figure 2). Although no other complete ECM components exist in unicellular choanoflagellates, several domains and fragments of ECM components have been identified, including collagenous repeats, laminin G (globular) domains and LN (N-terminal) domains, and fibronectin type II and III domains (Figure 1D). Furthermore, no other complete ECM components exist in other unicellular organisms, including Salpingoeca rosetta (Choanozoa), Capsaspora owczarzaki (Filasterea), Dictyostelium discoideum (Amoebozoa), or Thecamonas trahens (Apusozoa); however, collagenous GXY repeats were identified in Monosiga, Salpingoeca, and Dictyostelium. Receptors for collagen binding, including integrin, dystrophin, and Discoidin domain receptors (DDRs) were analyzed across metazoa and unicellular protists (Figure 2). Integrins are highly conserved across metazoa and are found in the unicellular Capsaspora and Thecamonas. Dystrophin was identified in humans, fruit fly, Nematostella, Amphimedon, as well as in unicellular protists but is absent in Trichoplax, Oscarella, and ctenophores. DDR 1 and 2 was identified only in humans and fruit fly. Collectively, the ECM composition across the non-bilaterian animal phyla points to laminin and collagen IV as highly conserved components, and importantly, that they are associated with BM and epithelial tissue architecture.

8We characterized the gene and protein structure of collagen IV in Ctenophora and the other non-bilaterian animal phyla. In Mnemiopsis, 11 full-length collagen IV genes were discovered, which contrasts with the two genes typically present throughout invertebrates and the six genes typically found in vertebrates. The head-to-head orientation is a distinguishing characteristic of collagen IV genes among other collagens of Bilateria. In Mnemiopsis, four genes occur on the same scaffold and exhibit a head-to-head orientation (ML17501a and ML17504a, ML17502a and ML17503a) (designated as Group I) (Figure 3A). Furthermore, ML17502a and ML17503a genes are oriented in opposite directions, separated by ~2879 bases, and do not share the same promoter. The other seven Mnemiopsis genes: ML166441a, ML18175a, ML18197a, ML18198a, ML034334a, ML0343336a, and ML0343337a (designated as Group II), are aligned individually on separate scaffolds or in a unidirectional tandem array. Transcriptomic analysis of adult Mnemiopsis reveals differential expression within each group of collagen IV genes. In Group I, the expression of ML17501a and ML17502a is significantly higher than other Group I genes. Similarly, ML034334a, ML0343336a, and ML0343337a show considerable increase in expression levels compared to the other Group II genes (Figure 3B).

9Mnemiopsis collagen IV genes are shorter in sequence length and typically have fewer exons and shorter intronic regions compared to their Bilaterian counterparts (Figure 3C). Whereas bilaterian fibrillar collagen genes are composed of multiple exons with a length of 54 base pairs, exons of Mnemiopsis collagen IV genes range in size from 40 to 4867 bp. Among the Mnemiopsis genes, exons of 108 bp in length were found in several genes, including ML17503a, ML17504a, and ML16441a, but no increased frequency of 54 bp exons in length or any variation was detected) (Figure 3—figure supplement 1). The presence of split glycine codons coding for the collagenous domain and codons on junctional exons (e.g. collagenous domain/NC1 domain encoding exons) are defining features of vertebrate collagen IV genes. Multiple genes from each group (Group I: ML17501a, ML17502a, and ML17503a; Group II: ML034334a, ML034336a, and ML034337a) possess split glycine codons on the collagenous domain/NC1 domain junction exon (Figure 3—figure supplement 2 and Supplementary file 1).

10We then determined the number of collagen IV genes in 10 other species from the Ctenophora phylum. Transcriptome analysis was conducted using in-house generated libraries for Mnemiopsis leidyi and Pleurobrachia pileus and publicly available libraries for Pleurobrachia bachei, Beroe ovata, Beroe abyssicola, Euplokamis sp., Dryodora sp., Vallicula sp., Coeloplana sp., and Bolinopsis sp. Across these ten species, a total of 118 unique collagen IV genes were detected. Each species contained a variable number of collagen IV genes, ranging between 4 and 20 genes each, as compared to the 2 to 6 genes in the other non-bilaterian animal phyla and Bilateria (Figure 4A and B). All species, apart from the two Beroe species surveyed, contain a combination of both Group I and II chains, with the two Beroe species exhibiting only Group II chains. In addition to full-length collagen IV genes, two genes, with signal peptides, encoding only the NC1 domain were identified across ten species of Ctenophora. Expression of NC1 domains without collagenous tails is novel (Figure 4C). Together, these findings show that the ECM of ctenophores contain both collagen IV and standalone NC1 genes, and that the number and diversity collagen IV genes exceeds that of any other metazoan group.

11We also determined the number, structure, and orientation of collagen IV genes in Nematostella vectensis (Cnidaria) and Trichoplax adhaerens (Placozoa). We found two genes in both species, and that they are homologous with Bilateria, with each demonstrating a ‘head-to-head’ orientation and homologous coding regions for both collagenous and non-collagenous domains (Figure 3D). Complete genomic data was unavailable to determine the orientation of the two collagen IV genes in homoscleromorph sponges. In contrast, unicellular protists (Choanozoa, Filasterea, Amoebozoa, Apusozoa) do not contain collagen IV as determined by genomic analyses (Figure 2). Together, our findings show that head-to-head orientation of collagen IV is conserved across Bilateria, Cnidaria, Placozoa, and Ctenophora, whereas Ctenophora exhibits both head-to-head and tandem orientations (Figure 3A).

12Several prominent structural domains characterize Bilaterian collagen IV chains (Figure 5). These include an N-terminal non-collagenous domain rich in cysteine and lysine residues (NC3) (Figure 5—figure supplement 1), a large collagenous domain of Gly-Xaa-Yaa (GXY) repeats of ~1400 residues with interruptions in the GXY repeats (Figure 6), followed by a non-collagenous (NC1) domain at the C-terminus of approximately ~230 residues (Figure 5—figure supplement 2). NC1 domains are comprised of two C4 domains, each containing a short, highly conserved HSQ residue motif proximal to the N-terminal side. We sought to determine whether these structural domains are characteristic of Ctenophora and the other non-bilaterian animal phyla. Indeed, these domains are conserved across Cnidaria, Placozoa, Porifera, and Ctenophora (Figure 5). The NC1 domain also contains a chloride-binding motif, which functions in binding extracellular chloride to signal the assembly of collagen IV networks and is conserved from vertebrates to Cnidaria and Placozoa. The chloride-binding motif was identified in both Ctenophora (group II chains) as well as in the two Homoscleromorph sponges analyzed, suggesting the chloride signaling function of NC1 domains is also conserved in Ctenophora and Porifera (Figure 5—figure supplement 3). Together, these findings reveal that the conserved structural features of bilaterian collagen IV extend across the non-bilaterian animal phyla, including Ctenophora.

13The NC1 domain is the molecular recognition module that directs the assembly of collagen IV protomers and networks. NC1 modules function in selecting collagen IV chains for trimerization, forming triple-helical protomers, and for oligomerization of protomers into networks (Figure 5). The NC1 modules are stabilized by sulfilimine cross-links, which connect methionine-93 (Met-93) and lysine/hydroxylysine-211 (Lys/Hyl-211) between adjoining protomers. Sulfilimine cross-links are conserved throughout Bilateria, from Humans to C. elegans, and in Cnidaria, with the exception of Hydra. In contrast, this cross-link is absent in Ctenophora, owing to the absence of Met-93 and Lys/Hyl-211 residues (Figure 5—figure supplement 4). Thus, we sought to characterize the biochemical properties of ctenophore NC1 domains to ascertain whether they are stabilized by an alternative cross-linking mechanism. Uniquely, ctenophore collagen IV is distinguished from all other metazoans by the presence of two additional domains. One is a non-collagenous domain (NC2 domain) that is approximately 38–44 residues in length within the collagenous domain (Figure 5—figure supplement 5). The other domain is 11–13 residues in length and consists of 3–4 conserved cysteine residues, designated as the cysteine-loop, which is an extension of the canonical NC1 domain, and a candidate for an alternative cross-linking mechanism (Figure 5—figure supplement 6). As we previously established for bilaterian collagen IV, the presence of NC1 dimers after reduction of with mercaptoethanol, indicates cross-links. Analysis in the three ctenophore species, Mnemiopsis, Beroe and Pleurobrachia, by SDS-PAGE and gel filtration chromatography, revealed the presence of NC1 hexamers, which upon reduction dissociated into dimers (Figure 7A–D). Since the dimers lack Met-93 and Lys/Hyl-211, the results indicate that ctenophore dimers are stabilized by the cysteine-loop (Figure 7E). Hence, the cross-linking mechanism of ctenophores (cysteine-loop) is distinguished from that of Cnidaria and Bilateria (sulfilimine cross-links).

14NC1 domains are distinguishing domains of collagen IV that function as recognition modules in the assembly of collagen IV networks. Uniquely, all 10 ctenophore species possess a gene encoding only the NC1 domain, a feature not found in any other phyla. We performed phylogenetic analysis to compare the NC1 domains of non-bilaterian animal phyla with that of Bilateria (Figure 8). The results placed the NC1 domain of ctenophore collagen IV into two major groups, which are consistent with genomic orientation of Group I and Group II (vida supra). We conducted additional phylogenetic analysis of the NC1 domain using RAxML to select the best tree from eleven models of evolution (DAYHOFF, DCMUT, JTT, MTREV, WAG, RTREV, CPREV, VT, BLOSUM62, MTMAM, and LG). Among these, the VT model yielded the tree with the best-fit (Figure 8—figure supplement 1). The distinction of the two groups coincides with the presence of the novel structural domains, NC2 and cysteine-loop, found exclusively in ctenophore Group II chains. Furthermore, these groups can be further subdivided into subgroups Group I (A-E) and Group II (A-D) based on phylogenetic affinity (Figure 8—figure supplement 1). RAxML phylogenetic analysis revealed a closer affinity between the ctenophore NC1 genes and collagen IV NC1 domain from the non-bilaterian animal phyla and Bilateria, as compared to ctenophore Group I and II chains (Figure 8). Furthermore, Group I and Group II ctenophore chains showed a much higher rate of divergence both within the phylum and as compared to the other non-bilaterian animal phyla and bilaterian collagen IV sequences. The unrooted tree topology illustrates the high phylogenetic affinity between ctenophore NC1 proteins and bilaterian NC1 domain that cluster closely.

15Spongins are a family of collagen IV-related proteins composed of a short collagenous domain attached to an NC1 domain. This protein family was first detected in the exoskeleton of demosponges and has been subsequently identified in cnidarians, across invertebrates (with the exception of ecdysozoans, e.g., C. elegans, Drosophila), and in basal chordates. Interestingly, spongins do not occur in vertebrates, and we did not detect them in Ctenophora. We examined the phylogenetic relationship of the NC1 domain of spongins to that of collagen IV NC1 domains (Figure 8 and Figure 8—figure supplement 1). Multiple sequence alignment showed conservation of seven cysteine residues between spongins and collagen IV, while the HSQ motif was absent in spongin sequences (Figure 9). Comparison of collagen IV sequences revealed four cysteine residues that are absent in spongin sequences. The spongin variants, however, do show conservation of three cysteines that are absent in collagen IV sequences. Collectively, the presence of collagenous domains and the conservation of collagen IV NC1 domain features within spongin NC1 domains, reveal that they are homologous to collagen IV protein domain structure, as previously noted.

16Within Ctenophora, collagen IV underwent numerous gene duplication events resulting in an unprecedented diversity in both gene sequence and organization in comparison to all other metazoans. Ctenophora contains between 4 and 20 collagen IV chains across species, and exhibits both head-to-head orientation and genes aligned individually on separate scaffolds or in a unidirectional tandem array. Interestingly, Ctenophora has both collagen IV genes and a standalone NC1 gene. In both Nematostella and Trichoplax, there are two collagen IV genes exhibiting head-to-head gene orientation, similar to that of Bilateria. In Porifera, the ECM of homoscleromorphs is composed of two collagen IV genes, while in demosponges, it is composed of spongin, a collagen IV variant. Spongin is absent in Ctenophora but is present in non-bilaterian animal phyla, invertebrates, and lower chordates along with collagen IV throughout invertebrates and lower chordates, with the exception of Drosophila and C. elegans. Structural and phylogenetic analysis of spongin shows it is homologous to collagen IV (Figures 8 and 9). Collectively, collagen IV genes are highly conserved across the non-bilaterian animal phyla and Bilateria; yet, in Ctenophora, these genes are more diverse and distinct including a novel cross-linking mechanism, with up to 20 distinct genes compared with six in vertebrates. Moreover, the collagen IV gene is absent in the unicellular sister-groups (choanoflagellates, filastereans, amoebozoans, and apusozoans), suggesting it was an early metazoan innovation.

17To address the evolutionary origin of the collagen IV gene, we compared two scenarios, Ctenophora-first versus Porifera-first. In both scenarios, collagen IV appeared in an early metazoan ancestor or a unicellular ancestor but was secondarily lost in demosponges and hexactinellid sponges (Figure 10A and B). It is noteworthy that the NC1 gene is present only in Ctenophora (Figure 10C and D), suggesting that this gene is a remnant from an early metazoan ancestor, and a forerunner to the NC1 domain of the ancestral collagen IV gene. This NC1 gene encodes a key recognition module that directs the assembly of collagen IV suprastructures. In comparison, spongin appeared after the divergence of the Ctenophora phylum in the Ctenophora-first hypothesis, yet in the Porifera-first hypothesis it would have appeared alongside collagen IV in the early metazoan ancestor or unicellular ancestor. With either hypothesis, the collagen IV gene coincided with the appearance of multicellular animals. Although laminin genes appear to have arisen prior to the metazoan lineage, with laminin-related genes appearing in unicellular choanoflagellates (Figure 10A and B).

18Collectively, we propose a model for collagen IV gene evolution that incorporates both Ctenophora-first and Porifera-first hypotheses (Figure 11). The presence of Gly-X-Y collagenous repeats, in the absence of a collagen IV gene, in choanoflagellates and amoebozoa, and the presence of a NC1 gene in the Ctenophora phylum suggests that Gly-X-Y repeats combined with an NC1 domain gene in an early metazoan ancestor, or possibly in a unicellular ancestor, forming an ancestral collagen IV gene. This combination of domains is analogous to the domain shuffling events that gave rise to the developmental protein, hedgehog. Within Ctenophora, collagen IV genes underwent unprecedented experimentation with several duplication events resulting in up to twenty distinct genes with both tandem and head-to-head organization. Within Porifera, the collagen IV gene was duplicated with a head-to-head orientation. This head-to-head feature was conserved in both sequence and gene structure throughout non-bilaterian animals and Bilateria (Figure 11), with the known exception of C. elegans. Two additional rounds of genome duplication resulted in six collagen IV genes in the vertebrate subphylum. Spongin, a collagen IV variant, first appeared in Porifera and is conserved throughout invertebrates, with the exception of Ecdysozoa and is found in cephalochordates (Branchiostoma floridae) and tunicates (Ciona intestinalis). The spongin gene arose either by domain shuffling of Gly-X-Y repeats from a unicellular ancestor and the NC1 gene, analogous to the assembly of the ancestral collagen IV gene, or diverged from an ancestral collagen IV gene (Figure 11).

19Collagen IV protein, or its spongin variant, is a required ECM component for all extant multicellular animals, considering that all animals investigated contain either collagen IV or spongin, and that the essentiality of collagen IV during development has been established in several studies. The collagen IV protein is associated with two distinct organizations of cells; one in which the ECM contains collagen IV broadly dispersed between communities of cells (Mnemiopsis) and the other in which collagen IV is a component of a well-defined BM underlying a layer of cells (Beroe, Pleurobrachia, Homoscleromorph sponges, and Nematostella), a hallmark feature of epithelial bilaterian tissues (Figure 12). The absence of BMs in Trichoplax and Mnemiopsis suggests there is an unknown component that facilitates the assembly of collagen IV and laminin into a basement membrane.

20Collectively, we conclude that collagen IV and its spongin variant are primordial components of the extracellular microenvironment, and collagen IV, as a component of BM, enabled the assembly of a fundamental architectural unit for the genesis and evolution of multicellular tissues (Figure 12). This unit is characterized by a layer of apical/basal-polarized cells that are laterally connected by tight junctions between plasma membranes, which are basally anchored via integrin receptors embedded in plasma membranes to a basement membrane supra-scaffold. In turn, this architectural unit served as the building block that enabled the formation and evolution of epithelial tissues, the ever-increasing complexity and size of organisms, and for the expansion and diversity of the animal kingdom.

21Transcriptomes used in this study were sequenced at the Vanderbilt Technologies for Advanced Genomics Core Facility (VANTAGE, Nashville, TN). The Illumina TruSeq mRNA Sample Preparation Kit was used to convert the mRNA in 100 ng of total RNA into a library of template molecules suitable for subsequent cluster generation and sequencing on the Illumina HiSeq 2500 using the rapid run setting. The pipeline established in VANTAGE was followed and is briefly described below. The first step was a quality check of the input total RNA by running an aliquot on the Agilent Bioanalyzer to confirm RNA integrity. The Qubit RNA fluorometry assay was used to measure sample concentrations. The input-to-library prep was 100 ng of total RNA (2 ng/ul). The poly-A containing mRNA molecules were concentrated using poly-T oligo-attached magnetic beads. Following purification, the eluted poly(A) RNA was cleaved into small fragments of 120–210 base pair (bp) using divalent cations under elevated temperature. The cleaved RNA fragments were copied into first strand cDNA using SuperScript II reverse transcriptase and random primers. This step was followed by second strand cDNA synthesis using DNA Polymerase I and RNase H treatment. The cDNA fragments then went through an end repair process, the addition of a single ‘A’ base, and then ligation of the Illumina multiplexing adapters. The products were then purified and enriched with PCR to create the final cDNA sequencing library. The cDNA library then undergoes quality control by running on the Agilent Bioanalyzer HS DNA assay to confirm the final library size and on the Agilent Mx3005P qPCR machine using the KAPA Illumina library quantification kit to determine concentration. A 2 nM stock was created and samples pooled by molarity for multiplexing. From the pool, 12 pmoles were loaded into each well for the flow cell on the Illumina cBot for cluster generation. The flow cell was then loaded onto the Illumina HiSeq 2500 utilizing v3 chemistry and HTA 1.8. The raw sequencing reads were processed through CASAVA-1.8.2 for FASTQ conversion and demultiplexing. The Illumina chastity filter was used and only the PF (passfilter) reads are retained for further analysis. Assembly of transcriptomes was performed using both Velvet/Oases and Trinity software packages with default settings (see list of commands subsection below).

22List of commands used in sequence search:

23Velvet/Oases.

24velveth $outDir $hash_length -fastq -shortPaired $in_shuffled_ sequence_file

25velvetg $outDir -read_trkg yes

26oases $outDir -ins_length 150

27Trinity

28Trinity.pl –output $outDir –seqType fq –JM 90G –left $file1 –right $file2 –CPU 16

29Animals were initially fixed whole in cold 2.5% glutaraldehyde in 0.1M cacodylate buffer, pH7.4 overnight in the refrigerator. After this initial fixation, the samples were stable enough so that small portions of selected areas could be dissected out and fixed for a further 24 hr at 4°C in 2.5% glutaraldehyde in 0.1M cacodylate. Following fixation, the samples were washed in 0.1M cacodylate buffer, incubated 1 hr in 1% osmium tetroxide at RT then washed with 0.1M cacodylate buffer, dehydrated through a graded ethanol series and embedded in epoxy resin. Semi-thin sections (0.5 microns) were cut, stained with toluidine blue and viewed by light microscopy to choose appropriate areas for study. Thin sections (70–80 nm) were cut from these selected areas and contrasted using 2% uranyl acetate and Reynold’s lead citrate, and imaged on an FEI Tecnai T12 electron microscope.

30Whole ctenophore tissues were frozen in liquid nitrogen, pulverized in a mortar and pestle and then homogenized in 2.0 ml g−1 digestion buffer and 0.1 mg ml−1 Worthington Biochemical bacterial collagenase and allowed to digest at 37°C, with spinning for 24 hr. Liquid chromatography purification of solubilized NC1 varied by species based on protein yield. All ctenophore NC1s were purified by gel-exclusion chromatography (GE Superdex 200 10/300 GL). For reduction and alkylation of collagen IV NC1 hexamers, fractions containing high-molecular-weight complex from size-exclusion chromatography were concentrated by ultrafiltration and reduced in TBS buffer with various concentrations of DTT. After incubation for 30 min at 37°C, samples were alkylated with twofold molar excess of iodoacetamide for 30 min at room temperature in the dark. After mixing with SDS loading buffer, samples were heated for 5 min in boiling water bath and analyzed by non-reducing SDS-PAGE. Collagenase-solubilized NC1 hexamers were analyzed by SDS-PAGE in 12% bis-acrylamide mini-cells with Tris-Glycine-SDS running buffer. Sample buffer was 62.5 mM Tris-HCl, pH 6.8, 2% SDS (w/v), 25% glycerol (w/v), 0.01% bromophenol blue (w/v). Western blotting of SDS-dissociated NC1 hexamer was developed with JK-2, rat monoclonal antibody (kindly provided by Dr. Yoshikazu Sado, Shigei Medical Research Institute, Okayama, Japan). All Western blotting in Figure 6 was done with Thermo-Scientific SuperSignal West Femto chemiluminescent substrate and digitally imaged with a Bio-Rad GelDoc.

31Whole ctenophore tissues were placed in 150 mL beaker and as much liquid was removed as possible. Each tube with tissue was filled with 100 mL ice-cold ctenophore fixation buffer 1 [80ul Glutaraldehyde (25%), 0.02% final concentration; 25 mL Paraformaldehyde (16%), 4.0% final concentration; 75 mL 0.2um-filtered seawater (Red Sea Coral Pro Salt)], inverted a few times gently, and left at 4 degrees Celsius for 5 min. Buffer 1 was then removed, and 100 mL of ctenophore fixation buffer 2 was added [25 mL Paraformaldehyde (16%), 4.0% final concentration; 75 mL 0.2um-filtered seawater (Red Sea Coral Pro Salt)]. Buffer 2 was then removed and tissues were gently washed five times with cold 1X PBS. Fixation protocol adopted from Pang and Martindale, Ctenophore Whole-Mount Antibody Staining. Tissues were then embedded in parafilm and sectioned onto individual slides for IHC staining. After deparaffinization and rehydration, tissues underwent heat-induced epitope retrieval with DAKO and microwaved for 15 min. Cold tap water was then run over tissues for 10 min, followed by two washed with 1X PBS and stored in 1X PBS. Immunostaining occurred at room temperature, with blocking by a 5% serum blocking buffer (1X PBS pH 7.4/5% normal goat serum/0.1% Triton X-100) for 60 min. All IHC for collagen IV was conducted with the rat monoclonal antibody (mAb) JK-2, and antibody dilution was done in 5% serum blocking buffer accordingly. Alexa488 tagged anti-rat secondary was used for the fluorochrome-conjugated secondary antibody (RRID:AB_10893331), and dilution was also done in 5% serum blocking buffer. IHC images were taken on a Zeiss Axioplan microscope. Lenses used were a 20X lens (Plan-APOCHROMAT 20X/0,75; ∞/0,17) and a 40X lens (Plan-NEOFLUAR 40X/0,75; ∞/0,17). Images were taken at room temperature, approximately 20 degrees Celsius. All images were done in an imaging medium of air. Fluorochromes used were Alexa488 (green) for collagen IV, and Hoescht stain (blue) was used for nuclei staining. The Camera for imaging was a Photometrics CoolSnap HQ, using Metamorph 7.7.0.0 software (RRID:SCR_002368). Slight gamma correction of (< ± 0.2) after acquisition to adjust contrast. Images captured were merged with ImageJ64, 1.48v (RRID:SCR_003070).

32The evolutionary relationship between collagen IV and spongins was analyzed using the NC1 domains of each of the 139 sequences in our dataset. NC1 domains were aligned using the Geneious alignment tool within Geneious software package (RRID:SCR_010519), version 8.1.9 with default settings. The resulting sequence alignment, which was 881 amino acid sites in length, was used to reconstruct the phylogeny of NC1 domains under the maximum likelihood optimality criterion as implemented in the RAxML software (RRID:SCR_006086), version 8.2.3. The phylogenetic analysis was performed using the PROTGAMMAAUTO option, which selects the substitution model with the best fit to the alignment among a set of among a set of 11 models (these were: DAYHOFF, DCMUT, JTT, MTREV, WAG, RTREV, CPREV, VT, BLOSUM62, MTMAM, and LG). In the case of the NC1 domain phylogeny, the model with the best fit was the VT model. Robustness in phylogeny inference was assessed with 100 bootstrap replicates.