Ryan, J. F. et al. The genome of the ctenophore Mnemiopsis leidyi and its implications for cell type evolution. Science 342, 1242592 (2013).
Halanych, K. M. The ctenophore lineage is older than sponges? That cannot be right! Or can it? J. Exp. Biol. 218, 592–597 (2015).
Jékely, G., Paps, J. & Nielsen, C. The phylogenetic position of ctenophores and the origin(s) of nervous systems. Evodevo 6, 1 (2015).
Ryan, J. F. & Chiodin, M. Where is my mind? How sponges and placozoans may have lost neural cell types. Philos. Trans. R. Soc. Lond. B 370, 20150059 (2015).
Moroz, L. L. et al. The ctenophore genome and the evolutionary origins of neural systems. Nature 510, 109–114 (2014).
Burkhardt, P. Ctenophores and the evolutionary origin(s) of neurons. Trends Neurosci. 45, 878–880 (2022).
Philippe, H. et al. Phylogenomics revives traditional views on deep animal relationships. Curr. Biol. 19, 706–712 (2009).
Simion, P. et al. A large and consistent phylogenomic dataset supports sponges as the sister group to all other animals. Curr. Biol. 27, 958–967 (2017).
Dunn, C. W. et al. Broad phylogenomic sampling improves resolution of the animal tree of life. Nature 452, 745–749 (2008).
Whelan, N. V. et al. Ctenophore relationships and their placement as the sister group to all other animals. Nat. Ecol. Evol. 1, 1737–1746 (2017).
Li, Y., Shen, X.-X., Evans, B., Dunn, C. W. & Rokas, A. Rooting the animal tree of life. Mol. Biol. Evol. 38, 4322–4333 (2021).
Simakov, O. et al. Deeply conserved synteny and the evolution of metazoan chromosomes. Sci. Adv. 8, eabi5884 (2022).
Dunn, C. W., Leys, S. P. & Haddock, S. H. D. The hidden biology of sponges and ctenophores. Trends Ecol. Evol. 30, 282–291 (2015).
Ryan, J. F. et al. The homeodomain complement of the ctenophore Mnemiopsis leidyi suggests that Ctenophora and Porifera diverged prior to the ParaHoxozoa. Evodevo 1, 9 (2010).
Musser, J. M. et al. Profiling cellular diversity in sponges informs animal cell type and nervous system evolution. Science 374, 717–723 (2021).
Harbison, G. R. in The Origins and Relationships of Lower Invertebrates Systematics Association Special Vol. 28 (eds Morris, S. C. et al.) 78–100 (Clarendon Press, 1985).
Tamm, S. L. Formation of the statolith in the ctenophore Mnemiopsis leidyi. Biol. Bull. 227, 7–18 (2014).
Burton, P. M. Insights from diploblasts; the evolution of mesoderm and muscle. J. Exp. Zool. B 310, 5–14 (2008).
Sachkova, M. Y. et al. Neuropeptide repertoire and 3D anatomy of the ctenophore nervous system. Curr. Biol. 31, 5274–5285 (2021).
Antcliffe, J. B., Callow, R. H. T. & Brasier, M. D. Giving the early fossil record of sponges a squeeze. Biol. Rev. Camb. Philos. Soc. 89, 972–1004 (2014).
O’Brien, L. J. & Caron, J.-B. A new stalked filter-feeder from the middle Cambrian Burgess Shale, British Columbia, Canada. PLoS ONE 7, e29233 (2012).
Mah, J. L. & Leys, S. P. Think like a sponge: the genetic signal of sensory cells in sponges. Dev. Biol. 431, 93–100 (2017).
Erives, A. & Fritzsch, B. A screen for gene paralogies delineating evolutionary branching order of early metazoa. G3 10, 811–826 (2020).
Shen, X.-X., Hittinger, C. T., Rokas, A., Minh, B. Q. & Braun, E. L. Contentious relationships in phylogenomic studies can be driven by a handful of genes. Nat. Ecol. Evol. 1, 0126 (2017).
Francis, W. R. & Canfield, D. E. Very few sites can reshape the inferred phylogenetic tree. PeerJ 8, e8865 (2020).
Kapli, P., Yang, Z. & Telford, M. J. Phylogenetic tree building in the genomic age. Nat. Rev. Genet. 21, 428–444 (2020).
Renwick, J. H. The mapping of human chromosomes. Annu. Rev. Genet. 5, 81–120 (1971).
Muller, H. J. in The New Systematics (ed. Huxley, J.) 185–268 (Oxford Univ. Press, 1940).
Drosophila 12 Genomes Consortium. Evolution of genes and genomes on the Drosophila phylogeny. Nature 450, 203–218 (2007).
Hane, J. K. et al. A novel mode of chromosomal evolution peculiar to filamentous Ascomycete fungi. Genome Biol. 12, R45 (2011).
Wright, S. On the probability of fixation of reciprocal translocations. Am. Nat. 75, 513–522 (1941).
Lv, J., Havlak, P. & Putnam, N. H. Constraints on genes shape long-term conservation of macro-synteny in metazoan genomes. BMC Bioinform. 12, S11 (2011).
Hillis, D. M. SINEs of the perfect character. Proc. Natl Acad. Sci. USA 96, 9979–9981 (1999).
Rokas, A. & Holland, P. W. Rare genomic changes as a tool for phylogenetics. Trends Ecol. Evol. 15, 454–459 (2000).
Okada, N. SINEs: Short interspersed repeated elements of the eukaryotic genome. Trends Ecol. Evol. 6, 358–361 (1991).
Martini, S., Schultz, D. T., Lundsten, L. & Haddock, S. H. D. Bioluminescence in an undescribed species of carnivorous sponge (Cladorhizidae) from the deep sea. Front. Mar. Sci. 7, 576476 (2020).
Kenny, N. J. et al. Tracing animal genomic evolution with the chromosomal-level assembly of the freshwater sponge Ephydatia muelleri. Nat. Commun. 11, 3676 (2020).
Schuster, A. et al. Divergence times in demosponges (Porifera): first insights from new mitogenomes and the inclusion of fossils in a birth-death clock model. BMC Evol. Biol. 18, 114 (2018).
McKenna, V. et al. The Aquatic Symbiosis Genomics Project: probing the evolution of symbiosis across the tree of life. Wellcome Open Res. 6, 254 (2021).
Schultz, D. T. et al. A chromosome-scale genome assembly and karyotype of the ctenophore Hormiphora californensis. G3 11, jkab302 (2021).
Johnson, S. B. et al. Speciation of pelagic zooplankton: invisible boundaries can drive isolation of oceanic ctenophores. Front. Genet. 13, 970314 (2022).
Fairclough, S. R. et al. Premetazoan genome evolution and the regulation of cell differentiation in the choanoflagellate Salpingoeca rosetta. Genome Biol. 14, R15 (2013).
Suga, H. et al. The Capsaspora genome reveals a complex unicellular prehistory of animals. Nat. Commun. 4, 2325 (2013).
de Mendoza, A., Suga, H., Permanyer, J., Irimia, M. & Ruiz-Trillo, I. Complex transcriptional regulation and independent evolution of fungal-like traits in a relative of animals. eLife 4, e08904 (2015).
Kenny, N. J. et al. The gene-rich genome of the scallop Pecten maximus. Gigascience 9, giaa037 (2020).
Li, Y. et al. Chromosome-level reference genome of the jellyfish Rhopilema esculentum. Gigascience 9, giaa036 (2020).
Emms, D. M. & Kelly, S. OrthoFinder: phylogenetic orthology inference for comparative genomics. Genome Biol. 20, 238 (2019).
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).
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).
Strassert, J. F. H., Irisarri, I., Williams, T. A. & Burki, F. A molecular timescale for eukaryote evolution with implications for the origin of red algal-derived plastids. Nat. Commun. 12, 1879 (2021).
Schubert, I. & Lysak, M. A. Interpretation of karyotype evolution should consider chromosome structural constraints. Trends Genet. 27, 207–216 (2011).
Ronquist, F. et al. MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Syst. Biol. 61, 539–542 (2012).
Hyman, L. H. The phylogeny of the lower metazoa. Q. Rev. Biol. 51, 344–347 (1976).
Collins, A. G. Evaluating multiple alternative hypotheses for the origin of Bilateria: an analysis of 18S rRNA molecular evidence. Proc. Natl Acad. Sci. USA 95, 15458–15463 (1998).
Laumer, C. E. et al. Revisiting metazoan phylogeny with genomic sampling of all phyla. Proc. Biol. Sci. 286, 20190831 (2019).
Schierwater, B. My favorite animal, Trichoplax adhaerens. Bioessays 27, 1294–1302 (2005).
Simakov, O. et al. Deeply conserved synteny resolves early events in vertebrate evolution. Nat. Ecol. Evol. 4, 820–830 (2020).
Fernández, R. & Gabaldón, T. Gene gain and loss across the metazoan tree of life. Nat. Ecol. Evol. 4, 524–533 (2020).
Moroz, L. L. Multiple origins of neurons from secretory cells. Front. Cell Dev. Biol. 9, 669087 (2021).
Belahbib, H. et al. New genomic data and analyses challenge the traditional vision of animal epithelium evolution. BMC Genom. 19, 393 (2018).
Albalat, R. & Cañestro, C. Evolution by gene loss. Nat. Rev. Genet. 17, 379–391 (2016).
Parker, G. H. The Elementary Nervous System (J.B. Lippincott Company, 1919).
Leys, S. P. Elements of a ‘nervous system’ in sponges. J. Exp. Biol. 218, 581–591 (2015).
Adams, M. et al. One fly-one genome: chromosome-scale genome assembly of a single outbred Drosophila melanogaster. Nucleic Acids Res. 48, e75 (2020).
Putnam, N. H. et al. Chromosome-scale shotgun assembly using an in vitro method for long-range linkage. Genome Res. 26, 342–350 (2016).
Ghurye, J., Pop, M., Koren, S., Bickhart, D. & Chin, C.-S. Scaffolding of long read assemblies using long range contact information. BMC Genom. 18, 527 (2017).
Kerpedjiev, P. et al. HiGlass: web-based visual exploration and analysis of genome interaction maps. Genome Biol. 19, 125 (2018).
Dudchenko, O. et al. The Juicebox Assembly Tools module facilitates de novo assembly of mammalian genomes with chromosome-length scaffolds for under $1000. Preprint at bioRxiv https://doi.org/10.1101/254797 (2018).
Durand, N. C. et al. Juicebox provides a visualization system for Hi-C contact maps with unlimited zoom. Cell Syst. 3, 99–101 (2016).
Denbo, S. et al. Revision of the Capsaspora genome using read mating information adjusts the view on premetazoan genome. Dev. Growth Differ. 61, 34–42 (2019).
Marçais, G. & Kingsford, C. A fast, lock-free approach for efficient parallel counting of occurrences of k-mers. Bioinformatics 27, 764–770 (2011).
Ranallo-Benavidez, T. R., Jaron, K. S. & Schatz, M. C. GenomeScope 2.0 and Smudgeplot for reference-free profiling of polyploid genomes. Nat. Commun. 11, 1432 (2020).
Ruan, J. & Li, H. Fast and accurate long-read assembly with wtdbg2. Nat. Methods 17, 155–158 (2020).
Cheng, H., Concepcion, G. T., Feng, X., Zhang, H. & Li, H. Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm. Nat. Methods 18, 170–175 (2021).
Li, H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. Preprint at https://arxiv.org/abs/1303.3997 (2013).
Open2C et al. Pairtools: from sequencing data to chromosome contacts. Preprint at bioRxiv https://doi.org/10.1101/2023.02.13.528389 (2023).
Abdennur, N. & Mirny, L. A. Cooler: scalable storage for Hi-C data and other genomically labeled arrays. Bioinformatics 36, 311–316 (2020).
Xu, M. et al. TGS-GapCloser: a fast and accurate gap closer for large genomes with low coverage of error-prone long reads. Gigascience 9, giaa094 (2020).
Roach, M. J., Schmidt, S. A. & Borneman, A. R. Purge Haplotigs: allelic contig reassignment for third-gen diploid genome assemblies. BMC Bioinform. 19, 460 (2018).
Walker, B. J. et al. Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS ONE 9, e112963 (2014).
Buchfink, B., Reuter, K. & Drost, H.-G. Sensitive protein alignments at tree-of-life scale using DIAMOND. Nat. Methods 18, 366–368 (2021).
Laetsch, D. R. & Blaxter, M. L. BlobTools: interrogation of genome assemblies. F1000Res. 6, 1287 (2017).
Cabanettes, F. & Klopp, C. D-GENIES: dot plot large genomes in an interactive, efficient and simple way. PeerJ 6, e4958 (2018).
Li, H. Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics 34, 3094–3100 (2018).
Gertz, E. M., Yu, Y.-K., Agarwala, R., Schäffer, A. A. & Altschul, S. F. Composition-based statistics and translated nucleotide searches: improving the TBLASTN module of BLAST. BMC Biol. 4, 41 (2006).
Santini, S. et al. The compact genome of the sponge Oopsacas minuta (Hexactinellida) is lacking key metazoan core genes. Preprint at bioRxiv https://doi.org/10.1101/2022.07.26.501511 (2022).
Whelan, N. V., Kocot, K. M., Moroz, L. L. & Halanych, K. M. Error, signal, and the placement of Ctenophora sister to all other animals. Proc. Natl Acad. Sci. USA 112, 5773–5778 (2015).
Li, H. Protein-to-genome alignment with miniprot. Bioinformatics 39, btad014 (2023).
Hoff, K. J., Lomsadze, A., Borodovsky, M. & Stanke, M. Whole-genome annotation with BRAKER. Methods Mol. Biol. 1962, 65–95 (2019).
Dobin, A. et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29, 15–21 (2013).
Brůna, T., Lomsadze, A. & Borodovsky, M. GeneMark-EP+: eukaryotic gene prediction with self-training in the space of genes and proteins. NAR Genom. Bioinform. 2, lqaa026 (2020).
Francis, W. R., Shaner, N. C., Christianson, L. M., Powers, M. L. & Haddock, S. H. D. Occurrence of isopenicillin-N-synthase homologs in bioluminescent ctenophores and implications for coelenterazine biosynthesis. PLoS ONE 10, e0128742 (2015).
Townsend, J. P. et al. A mesopelagic ctenophore representing a new family, with notes on family-level taxonomy in Ctenophora: Vampyroctena delmarvensis gen. nov. sp. nov. (Vampyroctenidae, fam. nov.). Mar. Biodivers. 50, 34 (2020).
Babonis, L. S. et al. Integrating embryonic development and evolutionary history to characterize tentacle-specific cell types in a ctenophore. Mol. Biol. Evol. 35, 2940–2956 (2018).
Grabherr, M. G. et al. Full-length transcriptome assembly from RNA-seq data without a reference genome. Nat. Biotechnol. 29, 644–652 (2011).
Simão, F. A., Waterhouse, R. M., Ioannidis, P., Kriventseva, E. V. & Zdobnov, E. M. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics 31, 3210–3212 (2015).
Altschul, S. F. et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389–3402 (1997).
Emms, D. M. & Kelly, S. OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy. Genome Biol. 16, 157 (2015).
The Darwin Tree of Life Project. Sequence locally, think globally: The Darwin Tree of Life Project. Proc. Natl Acad. Sci. USA 119, e2115642118 (2022).
Katoh, K., Misawa, K., Kuma, K.-I. & Miyata, T. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res. 30, 3059–3066 (2002).
Potter, S. C. et al. HMMER web server: 2018 update. Nucleic Acids Res. 46, W200–W204 (2018).
Srivastava, M. et al. The Trichoplax genome and the nature of placozoans. Nature 454, 955–960 (2008).
Zimmermann, B. et al. Sea anemone genomes reveal ancestral metazoan chromosomal macrosynteny. Preprint at bioRxiv https://doi.org/10.1101/2020.10.30.359448 (2020).
Mi, H., Muruganujan, A., Casagrande, J. T. & Thomas, P. D. Large-scale gene function analysis with the PANTHER classification system. Nat. Protoc. 8, 1551–1566 (2013).
Lander, E. S. et al. Initial sequencing and analysis of the human genome. Nature 409, 860–921 (2001).
Höhna, S. et al. RevBayes: Bayesian phylogenetic inference using graphical models and an interactive model-specification language. Syst. Biol. 65, 726–736 (2016).
Köster, J. & Rahmann, S. Snakemake—a scalable bioinformatics workflow engine. Bioinformatics 28, 2520–2522 (2012).
More News
Author Correction: Stepwise activation of a metabotropic glutamate receptor – Nature
Changing rainforest to plantations shifts tropical food webs
Streamlined skull helps foxes take a nosedive