Niklas KJ. The evolutionary-developmental origins of multicellularity. Am J Bot. 2014;101:6–25.
Article
PubMed
CAS
Google Scholar
Parfrey LW, Lahr DJG. Multicellularity arose several times in the evolution of eukaryotes (response to DOI 10.1002/bies.201100187). BioEssays. 2013;35:339–47.
Article
PubMed
CAS
Google Scholar
Abedin M, King N. Diverse evolutionary paths to cell adhesion. Trends Cell Biol. 2010;20:734–42.
Article
PubMed
PubMed Central
CAS
Google Scholar
Leys SP, Riesgo A. Epithelia, an evolutionary novelty of metazoans. J Exp Zoolog B Mol Dev Evol. 2012;318:438–47.
Article
Google Scholar
Miller PW, Clarke DN, Weis WI, Lowe CJ, Nelson WJ. The evolutionary origin of epithelial cell-cell adhesion mechanisms. Curr Top Membr. 2013;72:267–311.
Article
PubMed
PubMed Central
CAS
Google Scholar
Tyler S. Epithelium—the primary building block for metazoan Complexity1. Integr Comp Biol. 2003;43:55–63.
Article
PubMed
Google Scholar
Adamska M. Sponges as models to study emergence of complex animals. Curr Opin Genet Dev. 2016;39:21–8.
Article
PubMed
CAS
Google Scholar
Le Bivic A. Evolution and cell physiology. 4. Why invent yet another protein complex to build junctions in epithelial cells? Am J Physiol - Cell Physiol. 2013;305:C1193–201.
Article
PubMed
CAS
Google Scholar
Lanna E. Evo-devo of non-bilaterian animals. Genet Mol Biol. 2015;38:284–300.
Article
PubMed
PubMed Central
CAS
Google Scholar
Jenner RA, Wills MA. The choice of model organisms in evo–devo. Nat Rev Genet. 2007;8:311–4.
Article
PubMed
CAS
Google Scholar
Boute N, et al. Type IV collagen in sponges, the missing link in basement membrane ubiquity. Biol Cell. 1996;88:37–44.
Article
PubMed
CAS
Google Scholar
Ereskovsky AV, et al. The Homoscleromorph sponge Oscarellalobularis, a promising sponge model in evolutionary and developmental biology. BioEssays. 2009;31:89–97.
Article
PubMed
Google Scholar
Ringrose JH, et al. Deep proteome profiling of Trichoplax adhaerens reveals remarkable features at the origin of metazoan multicellularity. Nat Commun. 2013;4:1408.
Article
PubMed
CAS
Google Scholar
Fidler AL, et al. Collagen IV and basement membrane at the evolutionary dawn of metazoan tissues. elife. 2017;6. https://doi.org/10.7554/eLife.24176.
Adams EDM, Goss GG, Leys SP. Freshwater sponges have functional, sealing epithelia with high Transepithelial resistance and negative Transepithelial potential. PLoS One. 2010;5:e15040.
Article
PubMed
PubMed Central
CAS
Google Scholar
Leys SP, Hill A. The physiology and molecular biology of sponge tissues. Adv Mar Biol. 2012;62:1-56. https://doi.org/10.1016/B978-0-12-394283-8.00001-1.
Leys SP, Nichols SA, Adams EDM. Epithelia and integration in sponges. Integr Comp Biol. 2009;49:167–77.
Article
PubMed
Google Scholar
Smith CL, Reese TS. Adherens junctions modulate diffusion between epithelial cells in Trichoplax adhaerens. Biol Bull. 2016;231:216–24.
Article
PubMed
Google Scholar
Oda H, Takeichi M. Structural and functional diversity of cadherin at the adherens junction. J Cell Biol. 2011;193:1137–46.
Article
PubMed
PubMed Central
CAS
Google Scholar
Smith CL, et al. Novel cell types, neurosecretory cells and body plan of the early-diverging metazoan, Trichoplax adhaerens. Curr. Biol. CB. 2014;24:1565–72.
Article
PubMed
CAS
Google Scholar
Srivastava M, et al. The Trichoplax genome and the nature of placozoans. Nature. 2008;454:955–60.
Article
PubMed
CAS
Google Scholar
Hulpiau P, van Roy F. New insights into the evolution of metazoan Cadherins. Mol Biol Evol. 2011;28:647–57.
Article
PubMed
CAS
Google Scholar
Fahey B, Degnan BM. Origin of animal epithelia: insights from the sponge genome: evolution of epithelia. Evol Dev. 2010;12:601–17.
Article
PubMed
CAS
Google Scholar
Riesgo A, Farrar N, Windsor PJ, Giribet G, Leys SP. The analysis of eight transcriptomes from all Poriferan classes reveals surprising genetic complexity in sponges. Mol Biol Evol. 2014;31:1102–20.
Article
PubMed
CAS
Google Scholar
Srivastava M, et al. The Amphimedon queenslandica genome and the evolution of animal complexity. Nat. 2010;466:720–6.
Article
CAS
Google Scholar
Dunn CW, Leys SP, Haddock SHD. The hidden biology of sponges and ctenophores. Trends Ecol Evol. 2015;30:282–91.
Article
PubMed
Google Scholar
Jager M, Manuel M. Ctenophores: an evolutionary-developmental perspective. Curr Opin Genet Dev. 2016;39:85–92.
Article
PubMed
CAS
Google Scholar
Leys SP. Elements of a ‘nervous system’ in sponges. J Exp Biol. 2015;218:581–91.
Article
PubMed
Google Scholar
Moroz LL. Convergent evolution of neural systems in ctenophores. J Exp Biol. 2015;218:598–611.
Article
PubMed
PubMed Central
Google Scholar
Moroz LL, Kohn AB. Independent origins of neurons and synapses: insights from ctenophores. Philos Trans R Soc B Biol Sci. 2016;371:20150041.
Article
CAS
Google Scholar
O’Malley MA, Wideman JG, Ruiz-Trillo I. Losing complexity: the role of simplification in macroevolution. Trends Ecol Evol. 2016;31:608–21.
Article
PubMed
Google Scholar
Ryan JF, Chiodin M. Where is my mind? How sponges and placozoans may have lost neural cell types. Philos Trans R Soc B Biol Sci. 2015;370. https://doi.org/10.1098/rstb.2015.0059.
Halanych KM, Whelan NV, Kocot KM, Kohn AB, Moroz LL. Miscues misplace sponges. Proc Natl Acad Sci U S A. 2016;113:E946–7.
Article
PubMed
PubMed Central
CAS
Google Scholar
Pisani D, et al. Genomic data do not support comb jellies as the sister group to all other animals. Proc Natl Acad Sci U S A. 2015;112:15402–7.
Article
PubMed
PubMed Central
CAS
Google Scholar
Telford MJ, Moroz LL, Halanych KM. Evolution: a sisterly dispute. Nat. 2016;529:286–7.
Article
CAS
Google Scholar
Murray PS, Zaidel-Bar R. Pre-metazoan origins and evolution of the cadherin adhesome. Biol Open. 2014;3:1183–95.
Article
PubMed
PubMed Central
Google Scholar
Assémat E, Bazellières E, Pallesi-Pocachard E, Le Bivic A, Massey-Harroche D. Polarity complex proteins. Biochim Biophys Acta BBA - Biomembr. 2008;1778:614–30.
Article
CAS
Google Scholar
Bazellieres E, Assemat E, Arsanto JP, Le Bivic A, Massey-Harroche D. Crumbs proteins in epithelial morphogenesis. Front Biosci. 2009;14:2149–69.
Article
CAS
Google Scholar
Chen J, Zhang M. The Par3/Par6/aPKC complex and epithelial cell polarity. Exp Cell Res. 2013;319:1357–64.
Article
PubMed
CAS
Google Scholar
Elsum I, Yates L, Humbert PO, Richardson HE. The scribble–Dlg–Lgl polarity module in development and cancer: from flies to man. Essays Biochem. 2012;53:141–68.
Article
PubMed
CAS
Google Scholar
Boggon TJ, et al. C-cadherin Ectodomain structure and implications for cell adhesion mechanisms. Sci. 2002;296:1308–13.
Article
CAS
Google Scholar
Nichols SA, Roberts BW, Richter DJ, Fairclough SR, King N. Origin of metazoan cadherin diversity and the antiquity of the classical cadherin/β-catenin complex. Proc Natl Acad Sci U S A. 2012;109:13046–51.
Article
PubMed
PubMed Central
Google Scholar
Shapiro L, Weis WI. Structure and biochemistry of Cadherins and catenins. Cold Spring Harb Perspect Biol. 2009;1:a003053.
Article
PubMed
PubMed Central
Google Scholar
Clarke DN, Miller PW, Lowe CJ, Weis WI, Nelson WJ. Characterization of the cadherin?Catenin complex of the sea Anemone Nematostella vectensis and implications for the evolution of metazoan cell?Cell adhesion. Mol Biol Evol. 2016;33:2016–29.
Article
PubMed
PubMed Central
Google Scholar
Ishiyama N, et al. Dynamic and static interactions between p120 catenin and E-cadherin regulate the stability of cell-cell adhesion. Cell. 2010;141:117–28.
Article
PubMed
CAS
Google Scholar
Huber AH, Weis WI. The structure of the β-catenin/E-cadherin complex and the molecular basis of diverse ligand recognition by β-catenin. Cell. 2001;105:391–402.
Article
PubMed
CAS
Google Scholar
Bao R, Fischer T, Bolognesi R, Brown SJ, Friedrich M. Parallel duplication and partial subfunctionalization of ?-catenin/Armadillo during insect evolution. Mol Biol Evol. 2012;29:647–62.
Article
PubMed
CAS
Google Scholar
Pai L-M, et al. Drosophila α-catenin and E-cadherin bind to distinct regions of Drosophila Armadillo. J Biol Chem. 1996;271:32411–20.
Article
PubMed
CAS
Google Scholar
Noda Y, et al. Molecular recognition in dimerization between PB1 domains. J Biol Chem. 2003;278:43516–24.
Article
PubMed
CAS
Google Scholar
Horikoshi Y, et al. Interaction between PAR-3 and the aPKC-PAR-6 complex is indispensable for apical domain development of epithelial cells. J Cell Sci. 2009;122:1595–606.
Article
PubMed
CAS
Google Scholar
Ganot P, et al. Structural molecular components of septate junctions in cnidarians point to the origin of epithelial junctions in eukaryotes. Mol Biol Evol. 2015;32:44–62.
Article
PubMed
CAS
Google Scholar
Su W-H, Mruk DD, Wong EWP, Lui W-Y, Cheng CY. Polarity protein complex scribble/Lgl/Dlg and epithelial cell barriers. Adv Exp Med Biol. 2012;763:149–70.
PubMed
PubMed Central
CAS
Google Scholar
Albertson R, Chabu C, Sheehan A, Doe CQ. Scribble protein domain mapping reveals a multistep localization mechanism and domains necessary for establishing cortical polarity. J Cell Sci. 2004;117:6061–70.
Article
PubMed
CAS
Google Scholar
Bulgakova NA, Knust E. The crumbs complex: from epithelial-cell polarity to retinal degeneration. J Cell Sci. 2009;122:2587–96.
Article
PubMed
CAS
Google Scholar
Pocha SM, Knust E. Complexities of crumbs function and regulation in tissue morphogenesis. Curr Biol CB. 2013;23:R289–93.
Article
PubMed
CAS
Google Scholar
Baines AJ, Lu H-C, Bennett PM. The protein 4.1 family: hub proteins in animals for organizing membrane proteins. Biochim Biophys Acta. 2014;1838:605–19.
Article
PubMed
CAS
Google Scholar
Bachmann A, Schneider M, Theilenberg E, Grawe F, Knust E. Drosophila stardust is a partner of crumbs in the control of epithelial cell polarity. Nat. 2001;414:638–43.
Article
CAS
Google Scholar
Lemmers C, et al. CRB3 binds directly to Par6 and regulates the morphogenesis of the tight junctions in mammalian epithelial cells. Mol Biol Cell. 2004;15:1324–33.
Article
PubMed
PubMed Central
CAS
Google Scholar
Wei Z, Li Y, Ye F, Zhang M. Structural basis for the phosphorylation-regulated interaction between the cytoplasmic tail of cell polarity protein crumbs and the actin-binding protein Moesin. J Biol Chem. 2015;290:11384–92.
Article
PubMed
PubMed Central
CAS
Google Scholar
Borowiec ML, Lee EK, Chiu JC, Plachetzki DC. Extracting phylogenetic signal and accounting for bias in whole-genome data sets supports the Ctenophora as sister to remaining Metazoa. BMC Genomics. 2015;16:987.
Article
PubMed
PubMed Central
CAS
Google Scholar
Simion P, et al. A large and consistent Phylogenomic dataset supports sponges as the sister group to all other animals. Curr Biol CB. 2017;27:958–67.
Article
PubMed
CAS
Google Scholar
Whelan NV, Kocot KM, Halanych KM. Employing Phylogenomics to resolve the relationships among cnidarians, ctenophores, sponges, Placozoans, and Bilaterians. Integr Comp Biol. 2015;55:1084–95.
Article
PubMed
Google Scholar
Magie CR, Martindale MQ. Cell-cell adhesion in the Cnidaria: insights into the evolution of tissue morphogenesis. Biol Bull. 2008;214:218–32.
Article
PubMed
Google Scholar
Nielsen C. Animal evolution: interrelationships of the living Phyla. Oxford: OUP; 2012.
Google Scholar
Martin M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnetJ. 2011;17:10.
Article
Google Scholar
Peng Y, Leung HCM, Yiu SM, Chin FYL. IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth. Bioinforma Oxf Engl. 2012;28:1420–8.
Article
CAS
Google Scholar
Kajitani R, et al. Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads. Genome Res. 2014;24:1384–95.
Article
PubMed
PubMed Central
CAS
Google Scholar
Boetzer M, Pirovano W. Toward almost closed genomes with GapFiller. Genome Biol. 2012;13:R56.
Article
PubMed
PubMed Central
Google Scholar
Huang X, Madan A. CAP3: a DNA sequence assembly program. Genome Res. 1999;9:868–77.
Article
PubMed
PubMed Central
CAS
Google Scholar
Kim D, et al. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol. 2013;14:R36.
Article
PubMed
PubMed Central
CAS
Google Scholar
Hoff KJ, Lange S, Lomsadze A, Borodovsky M, Stanke M. BRAKER1: unsupervised RNA-Seq-based genome annotation with GeneMark-ET and AUGUSTUS. Bioinforma Oxf Engl. 2016;32:767–9.
Article
CAS
Google Scholar
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990;215:403–10.
Article
PubMed
CAS
Google Scholar
Langmead B, Salzberg SL. Fast gapped-read alignment with bowtie 2. Nat Methods. 2012;9:357–9.
Article
PubMed
PubMed Central
CAS
Google Scholar
Koren S, et al. Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Res. 2017;27:722–36.
Article
PubMed
PubMed Central
CAS
Google Scholar
Bankevich A, et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J. Comput. Biol. J. Comput. Mol Cell Biol. 2012;19:455–77.
CAS
Google Scholar
Zhu W, Lomsadze A, Borodovsky M. Ab initio gene identification in metagenomic sequences. Nucleic Acids Res. 2010;38:e132.
Article
PubMed
PubMed Central
CAS
Google Scholar
Boetzer M, Henkel CV, Jansen HJ, Butler D, Pirovano W. Scaffolding pre-assembled contigs using SSPACE. Bioinforma Oxf Engl. 2011;27:578–9.
Article
CAS
Google Scholar
Walker BJ, et al. Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS One. 2014;9:e112963.
Article
PubMed
PubMed Central
CAS
Google Scholar
Lukashin AV, Borodovsky M. GeneMark.Hmm: new solutions for gene finding. Nucleic Acids Res. 1998;26:1107–15.
Article
PubMed
PubMed Central
CAS
Google Scholar
Burge C, Karlin S. Prediction of complete gene structures in human genomic DNA. J Mol Biol. 1997;268:78–94.
Article
PubMed
CAS
Google Scholar
Stanke M, Morgenstern B. AUGUSTUS: a web server for gene prediction in eukaryotes that allows user-defined constraints. Nucleic Acids Res. 2005;33:W465–7.
Article
PubMed
PubMed Central
CAS
Google Scholar
Solovyev V, Kosarev P, Seledsov I, Vorobyev D. Automatic annotation of eukaryotic genes, pseudogenes and promoters. Genome Biol. 2006;7(Suppl 1):S10.1–12.
Article
Google Scholar
Finn RD, et al. The Pfam protein families database: towards a more sustainable future. Nucleic Acids Res. 2016;44:D279–85.
Article
PubMed
CAS
Google Scholar
Jones P, et al. InterProScan 5: genome-scale protein function classification. Bioinforma Oxf Engl. 2014;30:1236–40.
Article
CAS
Google Scholar
Schultz J, Milpetz F, Bork P, Ponting CP. SMART, a simple modular architecture research tool: identification of signaling domains. Proc Natl Acad Sci U S A. 1998;95:5857–64.
Article
PubMed
PubMed Central
CAS
Google Scholar
Katoh K, Misawa K, Kuma K, Miyata T. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res. 2002;30:3059–66.
Article
PubMed
PubMed Central
CAS
Google Scholar
Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004;32:1792–7.
Article
PubMed
PubMed Central
CAS
Google Scholar
Gouy M, Guindon S, Gascuel O. SeaView version 4: a multiplatform graphical user interface for sequence alignment and phylogenetic tree building. Mol Biol Evol. 2010;27:221–4.
Article
PubMed
CAS
Google Scholar
Waterhouse AM, Procter JB, Martin DMA, Clamp M, Barton GJ. Jalview version 2--a multiple sequence alignment editor and analysis workbench. Bioinforma Oxf Engl. 2009;25:1189–91.
Article
CAS
Google Scholar
Guindon S, et al. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol. 2010;59:307–21.
Article
PubMed
CAS
Google Scholar
Ronquist F, Huelsenbeck JP. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinforma Oxf Engl. 2003;19:1572–4.
Article
CAS
Google Scholar
Abascal F, Zardoya R, Posada D. ProtTest: selection of best-fit models of protein evolution. Bioinforma Oxf Engl. 2005;21:2104–5.
Article
CAS
Google Scholar