The Capsaspora genome reveals a complex unicellular prehistory of animals
10.1038/ncomms3325
Crossref journal-article
Springer Science and Business Media LLC
Nature Communications (297)
Bibliography

Suga, H., Chen, Z., de Mendoza, A., Sebé-Pedrós, A., Brown, M. W., Kramer, E., Carr, M., Kerner, P., Vervoort, M., Sánchez-Pons, N., Torruella, G., Derelle, R., Manning, G., Lang, B. F., Russ, C., Haas, B. J., Roger, A. J., Nusbaum, C., & Ruiz-Trillo, I. (2013). The Capsaspora genome reveals a complex unicellular prehistory of animals. Nature Communications, 4(1).

Authors 19
  1. Hiroshi Suga (first)
  2. Zehua Chen (additional)
  3. Alex de Mendoza (additional)
  4. Arnau Sebé-Pedrós (additional)
  5. Matthew W. Brown (additional)
  6. Eric Kramer (additional)
  7. Martin Carr (additional)
  8. Pierre Kerner (additional)
  9. Michel Vervoort (additional)
  10. Núria Sánchez-Pons (additional)
  11. Guifré Torruella (additional)
  12. Romain Derelle (additional)
  13. Gerard Manning (additional)
  14. B. Franz Lang (additional)
  15. Carsten Russ (additional)
  16. Brian J. Haas (additional)
  17. Andrew J. Roger (additional)
  18. Chad Nusbaum (additional)
  19. Iñaki Ruiz-Trillo (additional)
References 52 Referenced 282
  1. Putnam, N. et al. Sea anemone genome reveals ancestral eumetazoan gene repertoire and genomic organization. Science 317, 86–94 (2007). (10.1126/science.1139158) / Science by N Putnam (2007)
  2. Srivastava, M. et al. The Trichoplax genome and the nature of Placozoans. Nature 454, 955–960 (2008). (10.1038/nature07191) / Nature by M Srivastava (2008)
  3. Srivastava, M. et al. The Amphimedon queenslandica genome and the evolution of animal complexity. Nature 466, 720–726 (2010). (10.1038/nature09201) / Nature by M Srivastava (2010)
  4. Chapman, J. et al. The dynamic genome of Hydra. Nature 464, 592–596 (2010). (10.1038/nature08830) / Nature by J Chapman (2010)
  5. Lang, B. F., O’Kelly, C., Nerad, T., Gray, M. W. & Burger, G. The closest unicellular relatives of animals. Curr. Biol. 12, 1773–1778 (2002). (10.1016/S0960-9822(02)01187-9) / Curr. Biol. by BF Lang (2002)
  6. Ruiz-Trillo, I., Roger, A., Burger, G., Gray, M. & Lang, B. A phylogenomic investigation into the origin of metazoa. Mol. Biol. Evol. 25, 664–672 (2008). (10.1093/molbev/msn006) / Mol. Biol. Evol. by I Ruiz-Trillo (2008)
  7. Shalchian-Tabrizi, K. et al. Multigene phylogeny of choanozoa and the origin of animals. PLoS One 3, e2098 (2008). (10.1371/journal.pone.0002098) / PLoS One by K Shalchian-Tabrizi (2008)
  8. Torruella, G. et al. Phylogenetic relationships within the Opisthokonta based on phylogenomic analyses of conserved single-copy protein domains. Mol. Biol. Evol. 29, 531–544 (2012). (10.1093/molbev/msr185) / Mol. Biol. Evol. by G Torruella (2012)
  9. King, N. et al. The genome of the choanoflagellate Monosiga brevicollis and the origin of metazoans. Nature 451, 783–788 (2008). (10.1038/nature06617) / Nature by N King (2008)
  10. Manning, G., Young, S., Miller, W. & Zhai, Y. The protist, Monosiga brevicollis, has a tyrosine kinase signaling network more elaborate and diverse than found in any known metazoan. Proc. Natl Acad. Sci. USA 105, 9674–9679 (2008). (10.1073/pnas.0801314105) / Proc. Natl Acad. Sci. USA by G Manning (2008)
  11. Pincus, D., Letunic, I., Bork, P. & Lim, W. Evolution of the phospho-tyrosine signaling machinery in premetazoan lineages. Proc. Natl Acad. Sci. USA 105, 9680–9684 (2008). (10.1073/pnas.0803161105) / Proc. Natl Acad. Sci. USA by D Pincus (2008)
  12. Rokas, A. The origins of multicellularity and the early history of the genetic toolkit for animal development. Annu. Rev. Genet. 42, 235–251 (2008). (10.1146/annurev.genet.42.110807.091513) / Annu. Rev. Genet. by A Rokas (2008)
  13. Fairclough, S. R. et al. Premetazoan genome evolution and the regulation of cell differentiation in the choanoflagellate Salpingoeca rosetta. Genome Biol. 14, R15 (2013). (10.1186/gb-2013-14-2-r15) / Genome Biol. by SR Fairclough (2013)
  14. Zmasek, C. & Godzik, A. Strong functional patterns in the evolution of eukaryotic genomes revealed by the reconstruction of ancestral protein domain repertoires. Genome Biol. 12, R4 (2011). (10.1186/gb-2011-12-1-r4) / Genome Biol. by C Zmasek (2011)
  15. Hertel, L., Bayne, C. & Loker, E. The symbiont Capsaspora owczarzaki, nov. gen. nov. sp., isolated from three strains of the pulmonate snail Biomphalaria glabrata is related to members of the Mesomycetozoea. Int. J. Parasitol. 32, 1183–1191 (2002). (10.1016/S0020-7519(02)00066-8) / Int. J. Parasitol. by L Hertel (2002)
  16. Sebe-Pedros, A., Roger, A., Lang, F., King, N. & Ruiz-Trillo, I. Ancient origin of the integrin-mediated adhesion and signaling machinery. Proc. Natl Acad. Sci. USA 107, 10142–10147 (2010). (10.1073/pnas.1002257107) / Proc. Natl Acad. Sci. USA by A Sebe-Pedros (2010)
  17. Sebe-Pedros, A., de Mendoza, A., Lang, B., Degnan, B. & Ruiz-Trillo, I. Unexpected repertoire of metazoan transcription factors in the unicellular holozoan Capsaspora owczarzaki. Mol. Biol. Evol. 28, 1241–1254 (2011). (10.1093/molbev/msq309) / Mol. Biol. Evol. by A Sebe-Pedros (2011)
  18. Young, S. et al. Premetazoan ancestry of the Myc-Max network. Mol. Biol. Evol. 28, 2961–2971 (2011). (10.1093/molbev/msr132) / Mol. Biol. Evol. by S Young (2011)
  19. Sebe-Pedros, A., Zheng, Y., Ruiz-Trillo, I. & Pan, D. Premetazoan origin of the hippo signaling pathway. Cell Rep. 1, 13–20 (2012). (10.1016/j.celrep.2011.11.004) / Cell Rep. by A Sebe-Pedros (2012)
  20. Suga, H. et al. Genomic survey of premetazoans shows deep conservation of cytoplasmic tyrosine kinases and multiple radiations of receptor tyrosine kinases. Sci. Signal. 5, ra35 (2012). (10.1126/scisignal.2002733) / Sci. Signal. by H Suga (2012)
  21. Nichols, S. A., Roberts, B. W., Richter, D. J., Fairclough, S. R. & King, N. Origin of metazoan cadherin diversity and the antiquity of the classical cadherin/beta-catenin complex. Proc. Natl Acad. Sci. USA 109, 13046–13051 (2012). (10.1073/pnas.1120685109) / Proc. Natl Acad. Sci. USA by SA Nichols (2012)
  22. Carr, M., Nelson, M., Leadbeater, B. & Baldauf, S. Three families of LTR retrotransposons are present in the genome of the choanoflagellate Monosiga brevicollis. Protist 159, 579–590 (2008). (10.1016/j.protis.2008.05.001) / Protist by M Carr (2008)
  23. Kim, J., Vanguri, S., Boeke, J., Gabriel, A. & Voytas, D. Transposable elements and genome organization: a comprehensive survey of retrotransposons revealed by the complete Saccharomyces cerevisiae genome sequence. Genome Res. 8, 464–478 (1998). (10.1101/gr.8.5.464) / Genome Res. by J Kim (1998)
  24. Ohno, S. Evolution by Gene Duplication 160, (Springer (1970). (10.1007/978-3-642-86659-3)
  25. Hunter, S. et al. InterPro in 2011: new developments in the family and domain prediction database. Nucleic Acids Res. 40, D306–D312 (2012). (10.1093/nar/gkr948) / Nucleic Acids Res. by S Hunter (2012)
  26. Wickstead, B. & Gull, K. The evolution of the cytoskeleton. J. Cell Biol. 194, 513–525 (2011). (10.1083/jcb.201102065) / J. Cell Biol. by B Wickstead (2011)
  27. Nichols, S. A., Dirks, W., Pearse, J. S. & King, N. Early evolution of animal cell signaling and adhesion genes. Proc. Natl Acad. Sci. USA 103, 1251–1256 (2006). (10.1073/pnas.0604065103) / Proc. Natl Acad. Sci. USA by SA Nichols (2006)
  28. Degnan, B., Vervoort, M., Larroux, C. & Richards, G. Early evolution of metazoan transcription factors. Curr. Opin. Genet. Dev. 19, 591–599 (2009). (10.1016/j.gde.2009.09.008) / Curr. Opin. Genet. Dev. by B Degnan (2009)
  29. Burger, G., Lavrov, D., Forget, L. & Lang, B. Sequencing complete mitochondrial and plastid genomes. Nat. Protoc. 2, 603–614 (2007). (10.1038/nprot.2007.59) / Nat. Protoc. by G Burger (2007)
  30. Jaffe, D. et al. Whole-genome sequence assembly for mammalian genomes: Arachne 2. Genome Res. 13, 91–96 (2003). (10.1101/gr.828403) / Genome Res. by D Jaffe (2003)
  31. Haas, B. J. et al. Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments. Genome Biol. 9, R7 (2008). (10.1186/gb-2008-9-1-r7) / Genome Biol. by BJ Haas (2008)
  32. Lomsadze, A., Ter-Hovhannisyan, V., Chernoff, Y. O. & Borodovsky, M. Gene identification in novel eukaryotic genomes by self-training algorithm. Nucleic Acids Res. 33, 6494–6506 (2005). (10.1093/nar/gki937) / Nucleic Acids Res. by A Lomsadze (2005)
  33. Stanke, M. & Waack, S. Gene prediction with a hidden Markov model and a new intron submodel. Bioinformatics 19, (Suppl 2): ii215–ii225 (2003). (10.1093/bioinformatics/btg1080) / Bioinformatics by M Stanke (2003)
  34. Majoros, W. H., Pertea, M. & Salzberg, S. L. TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-finders. Bioinformatics 20, 2878–2879 (2004). (10.1093/bioinformatics/bth315) / Bioinformatics by WH Majoros (2004)
  35. Birney, E., Clamp, M. & Durbin, R. GeneWise and Genomewise. Genome Res. 14, 988–995 (2004). (10.1101/gr.1865504) / Genome Res. by E Birney (2004)
  36. Haas, B. J. et al. Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies. Nucleic Acids Res. 31, 5654–5666 (2003). (10.1093/nar/gkg770) / Nucleic Acids Res. by BJ Haas (2003)
  37. Grabherr, M. G. et al. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat. Biotechnol. 29, 644–652 (2011). (10.1038/nbt.1883) / Nat. Biotechnol. by MG Grabherr (2011)
  38. Haas, B. J., Delcher, A. L., Wortman, J. R. & Salzberg, S. L. DAGchainer: a tool for mining segmental genome duplications and synteny. Bioinformatics 20, 3643–3646 (2004). (10.1093/bioinformatics/bth397) / Bioinformatics by BJ Haas (2004)
  39. Li, L., Stoeckert, C. J. Jr. & Roos, D. S. OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res. 13, 2178–2189 (2003). (10.1101/gr.1224503) / Genome Res. by L Li (2003)
  40. Katoh, K., Kuma, K., Toh, H. & Miyata, T. MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Res. 33, 511–518 (2005). (10.1093/nar/gki198) / Nucleic Acids Res. by K Katoh (2005)
  41. Castresana, J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol. Biol. Evol. 17, 540–552 (2000). (10.1093/oxfordjournals.molbev.a026334) / Mol. Biol. Evol. by J Castresana (2000)
  42. Stamatakis, A. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics. 22, 2688–2690 (2006). (10.1093/bioinformatics/btl446) / Bioinformatics. by A Stamatakis (2006)
  43. Lartillot, N., Lepage, T. & Blanquart, S. PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating. Bioinformatics 25, 2286–2288 (2009). (10.1093/bioinformatics/btp368) / Bioinformatics by N Lartillot (2009)
  44. Lartillot, N. & Philippe, H. A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process. Mol. Biol. Evol. 21, 1095–1109 (2004). (10.1093/molbev/msh112) / Mol. Biol. Evol. by N Lartillot (2004)
  45. Eddy, S. R. A new generation of homology search tools based on probabilistic inference. Genome. Inform. 23, 205–211 (2009). / Genome. Inform. by SR Eddy (2009)
  46. Bauer, S., Grossmann, S., Vingron, M. & Robinson, P. N. Ontologizer 2.0--a multifunctional tool for GO term enrichment analysis and data exploration. Bioinformatics 24, 1650–1651 (2008). (10.1093/bioinformatics/btn250) / Bioinformatics by S Bauer (2008)
  47. Alexa, A., Rahnenfuhrer, J. & Lengauer, T. Improved scoring of functional groups from gene expression data by decorrelating GO graph structure. Bioinformatics 22, 1600–1607 (2006). (10.1093/bioinformatics/btl140) / Bioinformatics by A Alexa (2006)
  48. Quevillon, E. et al. InterProScan: protein domains identifier. Nucleic Acids Res. 33, W116–W120 (2005). (10.1093/nar/gki442) / Nucleic Acids Res. by E Quevillon (2005)
  49. Gentleman, R. C. et al. Bioconductor: open software development for computational biology and bioinformatics. Genome Biol. 5, R80 (2004). (10.1186/gb-2004-5-10-r80) / Genome Biol. by RC Gentleman (2004)
  50. Blake, J. A. & Harris, M. A. The Gene Ontology (GO) project: structured vocabularies for molecular biology and their application to genome and expression analysis. Curr. Protoc. Bioinformatics Chapter 7, Unit 7.2 (2008). (10.1002/0471250953.bi0702s23)
  51. Conesa, A. et al. Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21, 3674–3676 (2005). (10.1093/bioinformatics/bti610) / Bioinformatics by A Conesa (2005)
  52. Burge, S. et al. Manual GO annotation of predictive protein signatures: the InterPro approach to GO curation. Database (Oxford) 2012, bar068 (2012). / Database (Oxford) by S Burge (2012)
Dates
Type When
Created 12 years ago (Aug. 14, 2013, 7:48 a.m.)
Deposited 2 years, 8 months ago (Jan. 5, 2023, 8:28 p.m.)
Indexed 1 week, 1 day ago (Aug. 28, 2025, 8:30 a.m.)
Issued 12 years ago (Aug. 14, 2013)
Published 12 years ago (Aug. 14, 2013)
Published Online 12 years ago (Aug. 14, 2013)
Funders 0

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@article{Suga_2013, title={The Capsaspora genome reveals a complex unicellular prehistory of animals}, volume={4}, ISSN={2041-1723}, url={http://dx.doi.org/10.1038/ncomms3325}, DOI={10.1038/ncomms3325}, number={1}, journal={Nature Communications}, publisher={Springer Science and Business Media LLC}, author={Suga, Hiroshi and Chen, Zehua and de Mendoza, Alex and Sebé-Pedrós, Arnau and Brown, Matthew W. and Kramer, Eric and Carr, Martin and Kerner, Pierre and Vervoort, Michel and Sánchez-Pons, Núria and Torruella, Guifré and Derelle, Romain and Manning, Gerard and Lang, B. Franz and Russ, Carsten and Haas, Brian J. and Roger, Andrew J. and Nusbaum, Chad and Ruiz-Trillo, Iñaki}, year={2013}, month=aug }