Northcutt, R. G. & Gans, C. The genesis of neural crest and epidermal placodes: a reinterpretation of vertebrate origins. Q. Rev. Biol. 58, 1–28 (1983).
Google Scholar
Horie, R. et al. Shared evolutionary origin of vertebrate neural crest and cranial placodes. Nature 560, 228–232 (2018).
Google Scholar
Stolfi, A., Ryan, Okay., Meinertzhagen, I. A. & Christiaen, L. Migratory neuronal progenitors come up from the neural plate borders in tunicates. Nature 527, 371–374 (2015).
Google Scholar
Shimeld, S. M. & Holland, P. W. Vertebrate improvements. Proc. Natl Acad. Sci. USA 97, 4449–4452 (2000).
Google Scholar
Patthey, C. et al. Identification of molecular signatures particular for distinct cranial sensory ganglia within the creating chick. Neural Dev. 11, 3 (2016).
Google Scholar
Adamska, M. et al. 5 Nkx5 genes present differential expression patterns in anlagen of sensory organs in medaka: perception into the evolution of the gene household. Dev. Genes Evol. 211, 338–349 (2001).
Google Scholar
Wang, W., Lo, P., Frasch, M. & Lufkin, T. Hmx: an evolutionary conserved homeobox gene household expressed within the creating nervous system in mice and Drosophila. Mech. Dev. 99, 123–137 (2000).
Google Scholar
Feng, Y. & Xu, Q. Pivotal position of hmx2 and hmx3 in zebrafish interior ear and lateral line growth. Dev. Biol. 339, 507–518 (2010).
Google Scholar
Kelly, L. E. & El-Hodiri, H. M. Xenopus laevis Nkx5.3 and sensory organ homeobox (SOHo) are expressed in creating sensory organs and ganglia of the top and anterior trunk. Dev. Genes Evol. 226, 423–428 (2016).
Google Scholar
Kiernan, A. E., Nunes, F., Wu, D. Okay. & Fekete, D. M. The expression area of two associated homeobox genes defines a compartment within the rooster interior ear which may be concerned in semicircular canal formation. Dev. Biol. 191, 215–229 (1997).
Google Scholar
Quina, L. A., Tempest, L., Hsu, Y. W., Cox, T. C. & Turner, E. E. Hmx1 is required for the conventional growth of somatosensory neurons within the geniculate ganglion. Dev. Biol. 365, 152–163 (2012).
Google Scholar
Takahashi, H., Shintani, T., Sakuta, H. & Noda, M. CBF1 controls the retinotectal topographical map alongside the anteroposterior axis by means of a number of mechanisms. Growth 130, 5203–5215 (2003).
Google Scholar
Bayramov, A. V., Martynova, N. Y., Eroshkin, F. M., Ermakova, G. V. & Zaraisky, A. G. The homeodomain-containing transcription issue X-nkx-5.1 inhibits expression of the homeobox gene Xanf-1 throughout the Xenopus laevis forebrain growth. Mech. Dev. 121, 1425–1441 (2004).
Google Scholar
Takatori, N. et al. Complete survey and classification of homeobox genes within the genome of amphioxus, Branchiostoma floridae. Dev. Genes Evol. 218, 579–590 (2008).
Google Scholar
Wada, S. et al. A genomewide survey of developmentally related genes in Ciona intestinalis. II. Genes for homeobox transcription components. Dev. Genes Evol. 213, 222–234 (2003).
Google Scholar
Ryan, Okay., Lu, Z. & Meinertzhagen, I. A. The CNS connectome of a tadpole larva of Ciona intestinalis (L.) highlights sidedness within the mind of a chordate sibling. eLife 5, e16962 (2016).
Google Scholar
Wang, W., Chan, E. Okay., Baron, S., Van de Water, T. & Lufkin, T. Hmx2 homeobox gene management of murine vestibular morphogenesis. Growth 128, 5017–5029 (2001).
Google Scholar
Wang, W., Grimmer, J. F., Van De Water, T. R. & Lufkin, T. Hmx2 and Hmx3 homeobox genes direct growth of the murine interior ear and hypothalamus and will be functionally changed by Drosophila Hmx. Dev. Cell 7, 439–453 (2004).
Google Scholar
Wang, W., Van De Water, T. & Lufkin, T. Inside ear and maternal reproductive defects in mice missing the Hmx3 homeobox gene. Growth 125, 621–634 (1998).
Google Scholar
Tang, W. J., Chen, J. S. & Zeller, R. W. Transcriptional regulation of the peripheral nervous system in Ciona intestinalis. Dev. Biol. 378, 183–193 (2013).
Google Scholar
Sharma, S., Wang, W. & Stolfi, A. Single-cell transcriptome profiling of the Ciona larval mind. Dev. Biol. 448, 226–236 (2019).
Google Scholar
Kim, Okay. et al. Regulation of neurogenesis by FGF signaling and neurogenin within the invertebrate chordate ciona. Entrance. Cell Dev. Biol. 8, 477 (2020).
Google Scholar
Chacha, P. P. et al. Neuronal identities derived by misexpression of the POU IV sensory determinant in a protovertebrate. Proc. Natl Acad. Sci. USA 119, e2118817119 (2022).
Google Scholar
Brozovic, M. et al. ANISEED 2017: extending the built-in ascidian database to the exploration and evolutionary comparability of genome-scale datasets. Nucleic Acids Res. 46, D718–D725 (2018).
Google Scholar
Doglio, L. et al. Parallel evolution of chordate cis-regulatory code for growth. PLoS Genet. 9, e1003904 (2013).
Google Scholar
McEwen, G. Okay. et al. Early evolution of conserved regulatory sequences related to growth in vertebrates. PLoS Genet. 5, e1000762 (2009).
Google Scholar
Shimeld, S. M. & Donoghue, P. C. Evolutionary crossroads in developmental biology: cyclostomes (lamprey and hagfish). Growth 139, 2091–2099 (2012).
Google Scholar
Parker, H. J., Bronner, M. E. & Krumlauf, R. A Hox regulatory community of hindbrain segmentation is conserved to the bottom of vertebrates. Nature 514, 490–493 (2014).
Google Scholar
Scerbo, P. & Monsoro-Burq, A. H. The vertebrate-specific VENTX/NANOG gene empowers neural crest with ectomesenchyme potential. Sci. Adv. 6, eaaz1469 (2020).
Google Scholar
Zalc, A. et al. Reactivation of the pluripotency program precedes formation of the cranial neural crest. Science 371, eabb4776 (2021).
Google Scholar
Mazet, F. et al. Molecular proof from Ciona intestinalis for the evolutionary origin of vertebrate sensory placodes. Dev. Biol. 282, 494–508 (2005).
Google Scholar
Roure, A., Lemaire, P. & Darras, S. An otx/nodal regulatory signature for posterior neural growth in ascidians. PLoS Genet. 10, e1004548 (2014).
Google Scholar
Holland, L. Z. Tunicates. Curr. Biol. 26, R146–R152 (2016).
Google Scholar
Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq information with DESeq2. Genome Biol. 15, 550 (2014).
Google Scholar
Brunetti, R. et al. Morphological proof that the molecularly decided Ciona intestinalis sort A and kind B are totally different species: Ciona robusta and Ciona intestinalis. J. Zool. Syst. Evol. Res. 53, 186–193 (2015).
Google Scholar
Adameyko, I. et al. Schwann cell precursors from nerve innervation are a mobile origin of melanocytes in pores and skin. Cell 139, 366–379 (2009).
Google Scholar
Adamska, M. et al. Inside ear and lateral line expression of a zebrafish Nkx5-1 gene and its downregulation within the ears of FGF8 mutant, ace. Mech. Dev. 97, 161–165 (2000).
Google Scholar
Apostolova, G. et al. Neurotransmitter phenotype-specific expression modifications in creating sympathetic neurons. Mol. Cell. Neurosci. 35, 397–408 (2007).
Google Scholar
Bober, E., Baum, C., Braun, T. & Arnold, H. H. A novel NK-related mouse homeobox gene: expression in central and peripheral nervous constructions throughout embryonic growth. Dev. Biol. 162, 288–303 (1994).
Google Scholar
Boisset, G. & Schorderet, D. F. Zebrafish hmx1 promotes retinogenesis. Exp. Eye Res. 105, 34–42 (2012).
Google Scholar
Herbrand, H. et al. Two regulatory genes, cNkx5-1 and cPax2, present totally different responses to native alerts throughout otic placode and vesicle formation within the chick embryo. Growth 125, 645–654 (1998).
Google Scholar
Munroe, R. J. et al. Mouse H6 homeobox 1 (Hmx1) mutations trigger cranial abnormalities and lowered physique mass. BMC Dev. Biol 9, 27 (2009).
Google Scholar
Quina, L. A. et al. Deletion of a conserved regulatory component required for Hmx1 expression in craniofacial mesenchyme within the dumbo rat: a newly recognized reason behind congenital ear malformation. Dis. Mannequin Mech. 5, 812–822 (2012).
Google Scholar
Hartwell, R. D. et al. Anteroposterior patterning of the zebrafish ear by means of Fgf- and Hh-dependent regulation of hmx3a expression. PLoS Genet. 15, e1008051 (2019).
Google Scholar
Liu, J. et al. Evolutionarily conserved regulation of hypocretin neuron specification by Lhx9. Growth 142, 1113–1124 (2015).
Google Scholar
Lara-Ramirez, R., Poncelet, G., Patthey, C. & Shimeld, S. M. The construction, splicing, synteny and expression of lamprey COE genes and the evolution of the COE gene household in chordates. Dev. Genes Evol. 227, 319–338 (2017).
Google Scholar
Smith, J. J. et al. Sequencing of the ocean lamprey (Petromyzon marinus) genome gives insights into vertebrate evolution. Nat. Genet. 45, 415–421 (2013).
Google Scholar
Smith, J. J. et al. The ocean lamprey germline genome gives insights into programmed genome rearrangement and vertebrate evolution. Nat. Genet. 50, 270–277 (2018).
Google Scholar
Mehta, T. Okay. et al. Proof for a minimum of six Hox clusters within the Japanese lamprey (Lethenteron japonicum). Proc. Natl Acad. Sci. USA 110, 16044–16049 (2013).
Google Scholar
Woolfe, A. et al. CONDOR: a database useful resource of developmentally related conserved non-coding parts. BMC Dev. Biol. 7, 100 (2007).
Google Scholar
Edgar, R. C. MUSCLE: a number of sequence alignment with excessive accuracy and excessive throughput. Nucleic Acids Res. 32, 1792–1797 (2004).
Google Scholar
Stamatakis, A. RAxML model 8: a instrument for phylogenetic evaluation and post-analysis of huge phylogenies. Bioinformatics 30, 1312–1313 (2014).
Google Scholar
Marletaz, F. et al. Amphioxus useful genomics and the origins of vertebrate gene regulation. Nature 564, 64–70 (2018).
Google Scholar
Lara-Ramirez, R., Patthey, C. & Shimeld, S. M. Characterization of two neurogenin genes from the brook lamprey Lampetra planeri and their expression within the lamprey nervous system. Dev. Dyn. 244, 1096–1108 (2015).
Google Scholar
Boorman, C. J. & Shimeld, S. M. Pitx homeobox genes in Ciona and amphioxus present left–proper asymmetry is a conserved chordate character and outline the ascidian adenohypophysis. Evol. Dev. 4, 354–365 (2002).
Google Scholar
Fuentes, M. et al. Insights into spawning habits and growth of the European amphioxus (Branchiostoma lanceolatum). J. Exp. Zool. B 308, 484–493 (2007).
Google Scholar
Fuentes, M. et al. Preliminary observations on the spawning circumstances of the European amphioxus (Branchiostoma lanceolatum) in captivity. J. Exp. Zool. B 302, 384–391 (2004).
Google Scholar
Holland, P. W. H. Wholemount in situ hybridization to amphioxus embryos. Strategies Mol. Biol. 97, 641–644 (1999).
Google Scholar
Parker, H. J., Sauka-Spengler, T., Bronner, M. & Elgar, G. A reporter assay in lamprey embryos reveals each useful conservation and elaboration of vertebrate enhancers. PLoS ONE 9, e85492 (2014).
Google Scholar
Schindelin, J. et al. Fiji: an open-source platform for biological-image evaluation. Nat. Strategies 9, 676–682 (2012).
Google Scholar
Corbo, J. C., Levine, M. & Zeller, R. W. Characterization of a notochord-specific enhancer from the Brachyury promoter area of the ascidian, Ciona intestinalis. Growth 124, 589–602 (1997).
Google Scholar
Nakamura, M. J., Terai, J., Okubo, R., Hotta, Okay. & Oka, Okay. Three-dimensional anatomy of the Ciona intestinalis tailbud embryo at single-cell decision. Dev. Biol. 372, 274–284 (2012).
Google Scholar
Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: a versatile trimmer for Illumina sequence information. Bioinformatics 30, 2114–2120 (2014).
Google Scholar
Dobin, A. et al. STAR: ultrafast common RNA-seq aligner. Bioinformatics 29, 15–21 (2013).
Google Scholar
Harafuji, N., Keys, D. N. & Levine, M. Genome-wide identification of tissue-specific enhancers within the Ciona tadpole. Proc. Natl Acad. Sci. USA 99, 6802–6805 (2002).
Google Scholar
Chen, W. C. et al. Dissection of a Ciona regulatory component reveals complexity of cross-species enhancer exercise. Dev. Biol. 390, 261–272 (2014).
Google Scholar
Kari, W., Zeng, F., Zitzelsberger, L., Will, J. & Rothbacher, U. Embryo microinjection and electroporation within the chordate Ciona intestinalis. J. Vis. Exp. 16, 54313 (2016).
Stolfi, A., Gandhi, S., Salek, F. & Christiaen, L. Tissue-specific genome modifying in Ciona embryos by CRISPR–Cas9. Growth 141, 4115–4120 (2014).
Google Scholar