The emergence of new structures can often be linked to the evolution of novel cell types that follows the rewiring of developmental gene regulatory subnetworks. Vertebrates are characterized by a complex body plan compared to the other chordate clades and the question remains of whether and how the emergence of vertebrate morphological innovations can be related to the appearance of new embryonic cell populations. We previously proposed, by studying mesoderm development in the cephalochordate amphioxus, a scenario for the evolution of the vertebrate head mesoderm. To further test this scenario at the cell population level, we used scRNA-seq to construct a cell atlas of the amphioxus neurula, stage at which the main mesodermal compartments are specified. Our data allowed us to validate the presence of a prechordal-plate like territory in amphioxus. Additionally, the transcriptomic profile of somite cell populations supports the homology between specific territories of amphioxus somites and vertebrate cranial/pharyngeal and lateral plate mesoderm. Finally, our work provides evidence that the appearance of the specific mesodermal structures of the vertebrate head was associated to both segregation of pre-existing cell populations, and co-option of new genes for the control of myogenesis., We would like to thank Jose Luis Ferran for advices on the revision. This work benefited from access to the Observatoire Océanologique de Banyuls-sur-Mer, an EMBRC-France and EMBRC-ERIC site. Embryo imaging experiments were undertaken using the material of the BIOPIC platform. The laboratory of H.E. and S.B. was supported by the CNRS, and by the “Agence Nationale de la Recheche” under the grants ANR-19-CE13-0011 to H.E. and ANR-21-CE13-0034 to S.B. Research in A.S-P. group was supported by the European Research Council (ERC-StG 851647 to A.S-P.) and the Spanish Ministry of Science and Innovation (PID2021-124757NB-I00 to A.S-P.). X.G-B. is supported by the European Union’s H2020 research and innovation program under Marie Sklodowska-Curie grant agreement 101031767 to X.G-B. A.E. was supported by FPI PhD fellowships from the Spanish Ministry of Science and Innovation. J.J.T. was supported by the Spanish Ministerio de Economía y Competitividad (grant PID2019-103921GB-I00 and PID2022-141288NB-I00 to J.T.). M.I. laboratory research has been funded by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (ERCCoG-LS2-101002275 to M.I.), by the Spanish Ministry of Economy and Competitiveness (PID2020-115040GB-I00 to M.I.) and by the ‘Centro de Excelencia Severo Ochoa 2013-2017’(SEV-2012-0208 to M. I.).

The emergence of new structures can often be linked to the evolution of novel
cell types that follows the rewiring of developmental gene regulatory subnetworks. Vertebrates are characterized by a complex body plan compared to
the other chordate clades and the question remains of whether and how the
emergence of vertebrate morphological innovations can be related to the
appearance of new embryonic cell populations. We previously proposed, by
studying mesoderm development in the cephalochordate amphioxus, a scenario for the evolution of the vertebrate head mesoderm. To further test this
scenario at the cell population level, we used scRNA-seq to construct a cell
atlas of the amphioxus neurula, stage at which the main mesodermal compartments are specified. Our data allowed us to validate the presence of a
prechordal-plate like territory in amphioxus. Additionally, the transcriptomic
profile of somite cell populations supports the homology between specific
territories of amphioxus somites and vertebrate cranial/pharyngeal and lateral
plate mesoderm. Finally, our work provides evidence that the appearance of
the specific mesodermal structures of the vertebrate head was associated to
both segregation of pre-existing cell populations, and co-option of new genes
for the control of myogenesis., The laboratory of H.E. and S.B. was supported by the CNRS, and by the “Agence Nationale de la Recheche” under the grants ANR-19-CE13-0011 to H.E. and ANR-21-CE13-0034 to S.B. Research in A.S-P. group was supported by the European Research Council (ERC-StG 851647 to A.S-P.) and the Spanish Ministry of Science and Innovation (PID2021-124757NB-I00 to A.S-P.). X.G-B. is supported by the European Union’s H2020 research and innovation program under Marie Sklodowska-Curie grant agreement 101031767 to X.G-B. A.E. was supported by FPI PhD fellowships from the Spanish Ministry of Science and Innovation. J.J.T. was supported by the Spanish Ministerio de Economía y Competitividad (grant PID2019-103921GB-I00 and PID2022-141288NB-I00 to J.T.). M.I. laboratory research has been funded by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (ERCCoG-LS2-101002275 to M.I.), by the Spanish Ministry of Economy and Competitiveness (PID2020-115040GB-I00 to M.I.) and by the ‘Centro de Excelencia Severo Ochoa 2013-2017’(SEV-2012-0208 to M. I.)., Peer reviewed

Deuterostomes are one major group of bilaterians composed by hemichordates and echinoderms (collectively called Ambulacraria) and chordates. Comparative studies between these groups can provide valuable insights into the nature of the last common ancestor of deuterostomes and that of bilaterians. Indirect development of hemichordates, with larval phases similar to echinoderms and an adult body plan with an anteroposterior polarity like chordates and other bilaterians, makes them a suitable model for studying the molecular basis of development among deuterostomes. However, a comprehensive, quantitative catalogue of gene expression and chromatin dynamics in hemichordates is still lacking. In this study, we analysed the transcriptomes and chromatin accessibility of multiple developmental stages of the indirect-developing hemichordate Ptychodera flava. We observed that P. flava development is underpinned by a biphasic transcriptional program probably controlled by distinct genetic networks. Comparisons with other bilaterian species revealed similar transcriptional and regulatory dynamics during hemichordate gastrulation, cephalochordate neurulation and elongation stages of annelids. By means of regulatory networks analysis and functional validations by transgenesis experiments in echinoderms, we propose that gastrulation is the stage of highest molecular resemblance in deuterostomes and that much of the molecular basis of deuterostome development was probably present in the bilaterian last common ancestor., This study was supported by the Ministry of Science and Technology, Taiwan (grant no. MOST-110-2326-B-001-006 to Y.-H.S. and grant no. MOST-110-2621-B-001-001-MY3 to J.-K.Y.) and Academia Sinica (AS-GC-111-L01 to Y.-H.S. and J.-K.Y.). J.J.T. and J.L.G.S. were supported by the European Research Council (grant agreement no. 740041) and the Spanish Ministerio de Economía y Competitividad (grant no. PID2019-103921GB-I00). J.J.T. was also funded by the Spanish Ministerio de Ciencia e Innovación (grant no. PID2022-141288NB-I00). We thank A. G. Galvez and P. Firbas for advice with the analyses and M. Van der Sande, S. Frolich and S. Van Heeringen, for their advice with ANANSE. A.P.-P. thanks the rest of the authors and all the members of the Skarmeta/Tena laboratory, as well as J. Solana, D. Salamanca-Diaz and M. Rosselló, for their support during the difficult times of this project., Peer reviewed

Cis-regulatory elements (CREs) orchestrate the spatiotemporal regulation of key transcriptional programs. These genomic regions-including promoters, enhancers, and insulators-play a crucial role during embryonic development, and their functional diversification is thought to contribute significantly to the morphological evolution of animal body plans. We performed chromatin immunoprecipitation for various histone modifications (H3K4me3, H3K27ac, and H3K4me1) from equivalent developmental stages of mouse (E11.5) and pig (day 23; D23) to identify active regulatory regions during forelimb development in both species. The overlap of these epigenomic signatures with the pattern of open chromatin allowed us to classify these putative regulatory regions into different chromatin states in mouse and pig limb primordia. Our profiling of the regulatory genome in mouse and pig limb buds offers a valuable resource in the evo-devo field for exploring mechanisms underlying the morphological evolution of the tetrapod limb., This work was funded by MICIU/AEI/10.13039/501100011033 (Grants PID2020-113497GB-I00 to JL-R, PID2022-141288NB-I00 to JJT, and María de Maeztu Institutional Grant CEX2020-001088-M to JL-R and JJT)., With funding from the Spanish government through the "Maria de Maeztu Centre of Excellence" accreditation (CEX2020-001088-M)., Peer reviewed

Spermatogenesis is the biological process by which male sperm cells (spermatozoa) are produced in the testes. Beyond facilitating the transmission of genetic information, spermatogenesis also provides a potential framework for inter- and transgenerational inheritance of gene-regulatory states. While extensively studied in mammals, our understanding of spermatogenesis in anamniotes remains limited. Here we present a comprehensive single-cell multiomics resource, combining single-cell RNA sequencing (scRNA-seq) and single-cell chromatin accessibility (scATAC-seq) profiling, with base-resolution DNA methylome (WGBS) analysis of sorted germ cell populations from zebrafish (Danio rerio) testes. We identify the major germ cell types involved in zebrafish spermatogenesis as well as key drivers associated with these transcriptional states. Moreover, we describe localised DNA methylation changes associated with spermatocyte populations, as well as local and global changes in chromatin accessibility leading to chromatin compaction in spermatids. Notably, we identify loci that evade global chromatin compaction, and which remain accessible, suggesting a potential mechanism for the intergenerational transmission of gene-regulatory states. In summary, this high-resolution atlas of zebrafish spermatogenesis provides a valuable resource for studying vertebrate germ cell development and epigenetic inheritance, while offering a robust framework for comparative analyses across diverse models of germ cell biology.

The emergence of new structures can often be linked to the evolution of novel cell types that follows the rewiring of developmental gene regulatory subnetworks. Vertebrates are characterized by a complex body plan compared to the other chordate clades and the question remains of whether and how the emergence of vertebrate morphological innovations can be related to the appearance of new embryonic cell populations. We previously proposed, by studying mesoderm development in the cephalochordate amphioxus, a scenario for the evolution of the vertebrate head mesoderm. To further test this scenario at the cell population level, we used scRNA-seq to construct a cell atlas of the amphioxus neurula, stage at which the main mesodermal compartments are specified. Our data allowed us to validate the presence of a prechordal-plate like territory in amphioxus. Additionally, the transcriptomic profile of somite cell populations supports the homology between specific territories of amphioxus somites and vertebrate cranial/pharyngeal and lateral plate mesoderm. Finally, our work provides evidence that the appearance of the specific mesodermal structures of the vertebrate head was associated to both segregation of pre-existing cell populations, and co-option of new genes for the control of myogenesis., We would like to thank Jose Luis Ferran for advices on the revision. This work benefited from access to the Observatoire Océanologique de Banyuls-sur-Mer, an EMBRC-France and EMBRC-ERIC site. Embryo imaging experiments were undertaken using the material of the BIOPIC platform. The laboratory of H.E. and S.B. was supported by the CNRS, and by the “Agence Nationale de la Recheche” under the grants ANR-19-CE13-0011 to H.E. and ANR-21-CE13-0034 to S.B. Research in A.S-P. group was supported by the European Research Council (ERC-StG 851647 to A.S-P.) and the Spanish Ministry of Science and Innovation (PID2021-124757NB-I00 to A.S-P.). X.G-B. is supported by the European Union’s H2020 research and innovation program under Marie Sklodowska-Curie grant agreement 101031767 to X.G-B. A.E. was supported by FPI PhD fellowships from the Spanish Ministry of Science and Innovation. J.J.T. was supported by the Spanish Ministerio de Economía y Competitividad (grant PID2019-103921GB-I00 and PID2022-141288NB-I00 to J.T.). M.I. laboratory research has been funded by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (ERCCoG-LS2-101002275 to M.I.), by the Spanish Ministry of Economy and Competitiveness (PID2020-115040GB-I00 to M.I.) and by the ‘Centro de Excelencia Severo Ochoa 2013-2017’(SEV-2012-0208 to M. I.).