Erwin, D. H. The origin of animal body plans: a view from fossil evidence and the regulatory genome. Development 147, dev182899 (2020).
Google Scholar
Bone, Q., Kapp, H. & Pierrot-Bults, A. C. The Biology of Chaetognaths (Oxford Univ. Press, 1991).
Rieger, V. et al. Immunohistochemical analysis and 3D reconstruction of the cephalic nervous system in Chaetognatha: insights into the evolution of an early bilaterian brain? Invertebr. Biol. 129, 77–104 (2010).
Müller, C. H. G., Rieger, V., Perez, Y. & Harzsch, S. Immunohistochemical and ultrastructural studies on ciliary sense organs of arrow worms (Chaetognatha). Zoomorphology 133, 167–189 (2014).
Marlétaz, F., Peijnenburg, K. T. C. A., Goto, T., Satoh, N. & Rokhsar, D. S. A new spiralian phylogeny places the enigmatic arrow worms among Gnathiferans. Curr. Biol. 29, 312–318.e3 (2019).
Google Scholar
Laumer, C. E. et al. Revisiting metazoan phylogeny with genomic sampling of all phyla. Proc. Biol. Sci. 286, 20190831 (2019).
Google Scholar
Martín-Zamora, F. M. et al. Annelid functional genomics reveal the origins of bilaterian life cycles. Nature 615, 105–110 (2023).
Google Scholar
Simakov, O. et al. Deeply conserved synteny and the evolution of metazoan chromosomes. Sci. Adv. 8, eabi5884 (2022).
Google Scholar
Telford, M. J. & Holland, P. W. Evolution of 28S ribosomal DNA in chaetognaths: duplicate genes and molecular phylogeny. J. Mol. Evol. 44, 135–144 (1997).
Google Scholar
Marlétaz, F. et al. Chaetognath transcriptome reveals ancestral and unique features among bilaterians. Genome Biol. 9, R94 (2008).
Google Scholar
Park, T.-Y. S. et al. A giant stem-group chaetognath. Sci. Adv. 10, eadi6678 (2024).
Google Scholar
Vinther, J. & Parry, L. A. Bilateral jaw elements in Amiskwia sagittiformis bridge the morphological gap between Gnathiferans and Chaetognaths. Curr. Biol. 29, 881–888.e1 (2019).
Google Scholar
Satoh, N. Chordate Origins and Evolution (Elsevier, 2016).
Budd, G. E. & Telford, M. J. The origin and evolution of arthropods. Nature 457, 812–817 (2009).
Google Scholar
Chen, H. et al. A Cambrian crown annelid reconciles phylogenomics and the fossil record. Nature 583, 249–252 (2020).
Google Scholar
John, C. C. Memoirs: habits, structure, and development of Spadella cephaloptera. Q. J. Microsc. Sci. 75, 625–696 (1933).
Telford, M. J. & Holland, P. W. The phylogenetic affinities of the chaetognaths: a molecular analysis. Mol. Biol. Evol. 10, 660–676 (1993).
Google Scholar
Fröbius, A. C. & Funch, P. Rotiferan Hox genes give new insights into the evolution of metazoan bodyplans. Nat. Commun. 8, 9 (2017).
Google Scholar
Papillon, D., Perez, Y., Fasano, L., Le Parco, Y. & Caubit, X. Hox gene survey in the chaetognath Spadella cephaloptera: evolutionary implications. Dev. Genes Evol. 213, 142–148 (2003).
Google Scholar
Bekkouche, N. & Gąsiorowski, L. Careful amendment of morphological data sets improves phylogenetic frameworks: re-evaluating placement of the fossil Amiskwia sagittiformis. J. Syst. Palaeontol. 20, 1–14 (2022).
Marlétaz, F. et al. Amphioxus functional genomics and the origins of vertebrate gene regulation. Nature 564, 64–70 (2018).
Google Scholar
Parey, E. et al. The brittle star genome illuminates the genetic basis of animal appendage regeneration. Nat. Ecol. Evol. 8, 1505–1521 (2024).
Google Scholar
Simakov, O. et al. Insights into bilaterian evolution from three spiralian genomes. Nature 493, 526–531 (2013).
Google Scholar
Luo, Y.-J. et al. The Lingula genome provides insights into brachiopod evolution and the origin of phosphate biomineralization. Nat. Commun. 6, 8301 (2015).
Google Scholar
Simion, P. et al. Chromosome-level genome assembly reveals homologous chromosomes and recombination in asexual rotifer Adineta vaga. Sci. Adv. 7, eabg4216 (2021).
Google Scholar
Flot, J.-F. et al. Genomic evidence for ameiotic evolution in the bdelloid rotifer Adineta vaga. Nature 500, 453–457 (2013).
Google Scholar
Arendt, D. et al. The origin and evolution of cell types. Nat. Rev. Genet. 17, 744–757 (2016).
Google Scholar
Goto, T. & Yoshida, M. The mating sequence of the benthic arrowworm Spadella schizoptera. Biol. Bull. 169, 328–333 (1985).
Google Scholar
Ren-feng, W. Analysis of chromosome karyotypes in Chaetognath Sagitta crassa. J. Dalian Fish. Univ. 26, 260–263 (2011).
Lewin, T. D. et al. Fusion, fission, and scrambling of the bilaterian genome in Bryozoa. Genome Res. 35, 78–92 (2025).
Google Scholar
Guijarro-Clarke, C., Holland, P. W. H. & Paps, J. Widespread patterns of gene loss in the evolution of the animal kingdom. Nat. Ecol. Evol. 4, 519–523 (2020).
Google Scholar
Senaratne, A. P. et al. Formation of the CenH3-deficient holocentromere in Lepidoptera avoids active chromatin. Curr. Biol. 31, 173–181.e7 (2021).
Google Scholar
Hofstatter, P. G. et al. Repeat-based holocentromeres influence genome architecture and karyotype evolution. Cell 185, 3153–3168.e18 (2022).
Google Scholar
Lewin, T. D., Liao, I. J.-Y. & Luo, Y.-J. Annelid comparative genomics and the evolution of massive lineage-specific genome rearrangement in bilaterians. Mol. Biol. Evol. 41, msae172 (2024).
Google Scholar
Muller, H., Gil, J. Jr & Drinnenberg, I. A. The impact of centromeres on spatial genome architecture. Trends Genet. 35, 565–578 (2019).
Google Scholar
Houtain, A. et al. Transgenerational chromosome repair in the asexual bdelloid rotifer Adineta vaga. Preprint at bioRxiv https://doi.org/10.1101/2024.01.25.577190 (2024).
Lieberman-Aiden, E. et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326, 289–293 (2009).
Google Scholar
Álvarez-Campos, P. et al. Annelid adult cell type diversity and their pluripotent cellular origins. Nat. Commun. 15, 3194 (2024).
Google Scholar
Piovani, L. et al. Single-cell atlases of two lophotrochozoan larvae highlight their complex evolutionary histories. Sci. Adv. 9, eadg6034 (2023).
Google Scholar
Li, J. et al. Deep learning of cross-species single-cell landscapes identifies conserved regulatory programs underlying cell types. Nat. Genet. 54, 1711–1720 (2022).
Google Scholar
Rieger, V. et al. Development of the nervous system in hatchlings of Spadella cephaloptera (Chaetognatha), and implications for nervous system evolution in Bilateria. Dev. Growth Differ. 53, 740–759 (2011).
Google Scholar
Wollesen, T., Rodriguez Monje, S. V., Oel, A. P. & Arendt, D. Characterization of eyes, photoreceptors, and opsins in developmental stages of the arrow worm Spadella cephaloptera (Chaetognatha). J. Exp. Zool. B 340, 342–353 (2023).
Google Scholar
Wu, L. et al. Genes with spiralian-specific protein motifs are expressed in spiralian ciliary bands. Nat. Commun. 11, 4171 (2020).
Google Scholar
Yasuda, E., Goto, T., Makabe, K. W. & Satoh, N. Expression of actin genes in the arrow worm Paraspadella gotoi (Chaetognatha). Zoolog. Sci. 14, 953–960 (1997).
Google Scholar
Carré, D., Djediat, C. & Sardet, C. Formation of a large Vasa-positive germ granule and its inheritance by germ cells in the enigmatic Chaetognaths. Development 129, 661–670 (2002).
Google Scholar
Piovani, L. & Marlétaz, F. Single-cell transcriptomics refuels the exploration of spiralian biology. Brief. Funct. Genomics 22, 517–524 (2023).
Google Scholar
Sebé-Pedrós, A. et al. Early metazoan cell type diversity and the evolution of multicellular gene regulation. Nat. Ecol. Evol. 2, 1176–1188 (2018).
Google Scholar
Goto, T. & Yoshida, M. in Nervous Systems in Invertebrates (ed. Ali, M. A.) 461–481 (Springer, 1987).
Ahnelt, P. Chaetognatha. in Biology of the Integument: Invertebrates (eds. Bereiter-Hahn, J., Matoltsy, A. G. & Richards, K. S.) 746–755 (Springer, 1984).
Valencia-Montoya, W. A., Pierce, N. E. & Bellono, N. W. Evolution of sensory receptors. Annu. Rev. Cell Dev. Biol. 40, 353–379 (2024).
Google Scholar
Vakirlis, N., Carvunis, A.-R. & McLysaght, A. Synteny-based analyses indicate that sequence divergence is not the main source of orphan genes. eLife 9, e53500 (2020).
Google Scholar
Maeso, I., Acemel, R. D. & Gómez-Skarmeta, J. L. Cis-regulatory landscapes in development and evolution. Curr. Opin. Genet. Dev. 43, 17–22 (2017).
Google Scholar
de Mendoza, A. et al. Convergent evolution of a vertebrate-like methylome in a marine sponge. Nat. Ecol. Evol. 3, 1464–1473 (2019).
Google Scholar
Rošić, S. et al. Evolutionary analysis indicates that DNA alkylation damage is a byproduct of cytosine DNA methyltransferase activity. Nat. Genet. 50, 452–459 (2018).
Google Scholar
Kim, I. V. et al. Chromatin loops are an ancestral hallmark of the animal regulatory genome. Nature 642, 1097–1105 (2025).
Google Scholar
Guynes, K. et al. Annelid methylomes reveal ancestral developmental and aging-associated epigenetic erosion across Bilateria. Genome Biol. 25, 204 (2024)
Schwaiger, M. et al. Evolutionary conservation of the eumetazoan gene regulatory landscape. Genome Res. 24, 639–650 (2014).
Google Scholar
Barau, J. et al. The DNA methyltransferase DNMT3C protects male germ cells from transposon activity. Science 354, 909–912 (2016).
Google Scholar
Zaslaver, A., Baugh, L. R. & Sternberg, P. W. Metazoan operons accelerate recovery from growth-arrested states. Cell 145, 981–992 (2011).
Google Scholar
Douris, V., Telford, M. J. & Averof, M. Evidence for multiple independent origins of trans-splicing in Metazoa. Mol. Biol. Evol. 27, 684–693 (2010).
Google Scholar
Danks, G. B. et al. Trans-splicing and operons in metazoans: translational control in maternally regulated development and recovery from growth arrest. Mol. Biol. Evol. 32, 585–599 (2015).
Google Scholar
Wilson, C. G., Pieszko, T., Nowell, R. W. & Barraclough, T. G. Recombination in bdelloid rotifer genomes: asexuality, transfer and stress. Trends Genet. 40, 422–436 (2024).
Google Scholar
Morel, B., Kozlov, A. M., Stamatakis, A. & Szöllősi, G. J. GeneRax: a tool for species-tree-aware maximum likelihood-based gene family tree inference under gene duplication, transfer, and loss. Mol. Biol. Evol. 37, 2763–2774 (2020).
Google Scholar
Goto, T. & Yoshida, M. Growth and reproduction of the benthic arrowworm Paraspadella gotoi (Chaetognatha) in laboratory culture. Invertebr. Reprod. Dev. 32, 201–207 (1997).
Green, M. R. & Sambrook, J. Molecular Cloning. A Laboratory Manual 4th edn (2012).
Rao, S. S. P. et al. A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell 159, 1665–1680 (2014).
Google Scholar
Chapman, J. A. et al. Meraculous: de novo genome assembly with short paired-end reads. PLoS ONE 6, e23501 (2011).
Google Scholar
Putnam, N. H. et al. Chromosome-scale shotgun assembly using an in vitro method for long-range linkage. Genome Res. 26, 342–350 (2016).
Google Scholar
Simakov, O. et al. Deeply conserved synteny resolves early events in vertebrate evolution. Nat. Ecol. Evol. 4, 820–830 (2020).
Google Scholar
Rhie, A., Walenz, B. P., Koren, S. & Phillippy, A. M. Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies. Genome Biol. 21, 245 (2020).
Google Scholar
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).
Google Scholar
Grabherr, M. G. et al. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat. Biotechnol. 29, 644–652 (2011).
Google Scholar
Haas, B. J. et al. Automated eukaryotic gene structure annotation using EVidenceModeler and the program to assemble spliced alignments. Genome Biol. 9, R7 (2008).
Google Scholar
Stanke, M. et al. AUGUSTUS: ab initio prediction of alternative transcripts. Nucleic Acids Res. 34, W435–W439 (2006).
Google Scholar
Huerta-Cepas, J. et al. eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses. Nucleic Acids Res. 47, D309–D314 (2019).
Google Scholar
Klopfenstein, D. V. et al. GOATOOLS: a Python library for Gene Ontology analyses. Sci Rep. 8, 10872 (2018).
Google Scholar
Derelle, R., Philippe, H. & Colbourne, J. K. Broccoli: combining phylogenetic and network analyses for orthology assignment. Mol. Biol. Evol. 37, 3389–3396 (2020).
Google Scholar
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).
Google Scholar
Steenwyk, J. L., Buida, T. J. 3rd, Li, Y., Shen, X.-X. & Rokas, A. ClipKIT: a multiple sequence alignment trimming software for accurate phylogenomic inference. PLoS Biol. 18, e3001007 (2020).
Google Scholar
Nguyen, L.-T., Schmidt, H. A., von Haeseler, A. & Minh, B. Q. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol. Biol. Evol. 32, 268–274 (2015).
Google Scholar
Barrera-Redondo, J., Lotharukpong, J. S., Drost, H.-G. & Coelho, S. M. Uncovering gene-family founder events during major evolutionary transitions in animals, plants and fungi using GenEra. Genome Biol. 24, 54 (2023).
Google Scholar
Steinegger, M. & Söding, J. MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets. Nat. Biotechnol. 35, 1026–1028 (2017).
Google Scholar
Benton M. J., Donoghue P. C. J. & Asher R. J. in The Timetree Of Life (ed. Kumar, S. B. H.) 35–86 (Oxford Univ. Press, 2009).
Rota-Stabelli, O., Daley, A. C. & Pisani, D. Molecular timetrees reveal a Cambrian colonization of land and a new scenario for ecdysozoan evolution. Curr. Biol. 23, 392–398 (2013).
Google Scholar
Vannier, J., Steiner, M., Renvoisé, E., Hu, S.-X. & Casanova, J.-P. Early Cambrian origin of modern food webs: evidence from predator arrow worms. Proc. Biol. Sci. 274, 627–633 (2007).
Google Scholar
Mendes, F. K., Vanderpool, D., Fulton, B. & Hahn, M. W. CAFE 5 models variation in evolutionary rates among gene families. Bioinformatics 36, 5516–5518 (2021).
Google Scholar
Matus, D. Q., Halanych, K. M. & Martindale, M. Q. The Hox gene complement of a pelagic chaetognath, Flaccisagitta enflata. Integr. Comp. Biol. 47, 854 (2007).
Google Scholar
Open2C, et al. Pairtools: from sequencing data to chromosome contacts. PLoS Comput. Biol. 20, e1012164 (2024).
Durand, N. C. et al. Juicer provides a one-click system for analyzing loop-resolution Hi-C experiments. Cell Syst. 3, 95–98 (2016).
Google Scholar
Knight, P. A. & Ruiz, D. A fast algorithm for matrix balancing. IMA J. Numer. Anal. 33, 1029–1047 (2013).
Google Scholar
Kruse, K., Hug, C. B. & Vaquerizas, J. M. FAN-C: a feature-rich framework for the analysis and visualisation of chromosome conformation capture data. Genome Biol. 21, 303 (2020).
Google Scholar
Marlétaz, F. et al. Analysis of the P. lividus sea urchin genome highlights contrasting trends of genomic and regulatory evolution in deuterostomes. Cell Genomics 3, 100295 (2023).
Google Scholar
Corces, M. R. et al. An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues. Nat. Methods 14, 959–962 (2017).
Google Scholar
Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357–359 (2012).
Google Scholar
Heinz, S. et al. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol. Cell 38, 576–589 (2010).
Google Scholar
Wenzel, M. A., Müller, B. & Pettitt, J. SLIDR and SLOPPR: flexible identification of spliced leader trans-splicing and prediction of eukaryotic operons from RNA-seq data. BMC Bioinformatics 22, 140 (2021).
Google Scholar
Liao, Y., Smyth, G. K. & Shi, W. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics 30, 923–930 (2014).
Google Scholar
Hao, Y. et al. Dictionary learning for integrative, multimodal and scalable single-cell analysis. Nat. Biotechnol. 42, 293–304 (2024).
Google Scholar
Kryuchkova-Mostacci, N. & Robinson-Rechavi, M. A benchmark of gene expression tissue-specificity metrics. Brief. Bioinformatics 18, 205–214 (2016).
García-Castro, H. et al. ACME dissociation: a versatile cell fixation-dissociation method for single-cell transcriptomics. Genome Biol. 22, 89 (2021).
Google Scholar
Hejnol, A. & Martindale, M. Q. Acoel development indicates the independent evolution of the bilaterian mouth and anus. Nature 456, 382–386 (2008).
Google Scholar
Hejnol, A. In situ protocol for embryos and juveniles of Convolutriloba longifissura. Protoc. Exch. https://doi.org/10.1038/nprot.2008.201 (2008).
Marlétaz, F. et al. The genomic origin of the unique chaetognath body plan [Data set]. Zenodo https://doi.org/10.5281/zenodo.13936459 (2024).
Gąsiorowski, L., Martín-Durán, J. M. & Hejnolin, A. in Hox Modules in Evolution and Development (ed. Ferrier, D. E. K.) 177–194 (CRC, 2023).