Evodevo最新文献

{"title":"Retinoic acid regulates the proliferation, differentiation, and cell death of limb skeletal progenitors, contributing to establish the size and identity of the digits.","authors":"Cristina Duarte-Olivenza, Goretti Moran, Juan M Hurle, Juan A Montero, Carlos I Lorda-Diez","doi":"10.1186/s13227-025-00248-4","DOIUrl":"10.1186/s13227-025-00248-4","url":null,"abstract":"<p><strong>Background: </strong>The development of the digits (fingers/toes) provides an excellent model for analyzing the molecular regulation of skeletal morphogenesis in vertebrates. Digits develop in the autopod as radial chondrogenic condensations separated by interdigital spaces containing undifferentiated skeletal progenitors destined to die by apoptosis. In avian species, leg digits are characterized by a differential size, with the first digit being short and the fourth largest.</p><p><strong>Results: </strong>In vitro experiments using micromass cultures of digit progenitors demonstrated that RA controls the balance between cell death, cell proliferation, and cell differentiation in a dose-dependent fashion. In vivo, qPCR analysis revealed that the RA-synthesizing enzyme Raldh2 and the RA-degrading enzyme Cyp26a1 are expressed in the interdigits in an inverse gradient that correlates with the size of the digit adjacent to each interdigit. RA gain- and loss-of-function experiments via pharmacological approaches confirmed a close correlation between interdigital RA and digit size. A low concentration of RA applied to the first interdigits, when the phalanxes of the first digit are being formed, promoted mesodermal cell proliferation and caused elongation of digit 1, while blocking RA synthesis into the third interdigit inhibited cell proliferation, followed by a reduction in the size of digits 3 and 4.</p><p><strong>Conclusions: </strong>This study reveals a potential role for Retinoic Acid (RA) expressed in the interdigits in the regulation of the differential digit size. The morphological similarity of the digit patterns obtained in our experimental assays with those of other tetrapods suggests an evolutionary role of RA in determining digit morphology.</p>","PeriodicalId":49076,"journal":{"name":"Evodevo","volume":"16 1","pages":"11"},"PeriodicalIF":2.6,"publicationDate":"2025-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12239497/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144601986","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A subset of conserved phagocytic genes are likely used for the intracellular theft of cnidarian stinging organelles in nudibranch gastropods.","authors":"Jessica A Goodheart, Rose Fiorenza, Robin Rio, Rebecca N Lopez-Anido, Noah J Martin, Timothy J Herrlinger, Rebecca D Tarvin, Deirdre C Lyons","doi":"10.1186/s13227-025-00241-x","DOIUrl":"10.1186/s13227-025-00241-x","url":null,"abstract":"<p><strong>Background: </strong>Phagocytosis is a universal physiological process in eukaryotes with many important biological functions. In nudibranch gastropods, a novel form of phagocytosis called nematocyst sequestration is specialized for the uptake of venomous stinging organelles stolen from their cnidarian prey. This process is highly selective. Here we use the emerging model nudibranch species Berghia stephanieae and Hermissenda opalescens to identify genes enriched within the body regions where nematocyst sequestration occurs, and investigate how the expression profile of phagocytosis, immune, and digestive genes differs between nematocyst-sequestering regions relative to those where other phagocytic functions occur.</p><p><strong>Results: </strong>We identified 166 genes with significantly higher expression in sequestering regions in B. stephanieae, including genes associated with development, membrane transport, and metabolism. Of these, at least 31 overlap with transcripts upregulated in H. opalescens sequestering tissues. Using hybridization chain reaction in situs, we show that at least two of these genes were localized to sequestering cells in B. stephanieae, including a putative C-type lectin receptor and a collagen. Genes annotated with phagocytosis, digestion, or immunity GO terms were often expressed in both sequestering and non-sequestering tissues, suggesting that they may also play a role in sequestration processes.</p><p><strong>Conclusion: </strong>Our results suggest that phagocytosis genes likely play a role in the sequestration phenotype, and that a small subset of genes (e.g., collagen) may play unique functions yet to be uncovered. We also show that genes categorized as functioning in endocytosis, immunity, and digestion have lower overall expression in sequestering tissues, supporting the hypothesis that sequestering tissues show a narrowing of function compared to digestive tissues. This study lays the foundation for further inquiry into mechanisms of organelle sequestration in nudibranchs and other organisms.</p>","PeriodicalId":49076,"journal":{"name":"Evodevo","volume":"16 1","pages":"10"},"PeriodicalIF":4.1,"publicationDate":"2025-06-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12205514/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144530637","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Discoveries and innovations in cnidarian biology at Cnidofest 2024.","authors":"Whitney B Leach, Leslie Babonis, Celina E Juliano, Nagayasu Nakanishi, Christine E Schnitzler, Patrick R H Steinmetz, Michael J Layden","doi":"10.1186/s13227-025-00247-5","DOIUrl":"10.1186/s13227-025-00247-5","url":null,"abstract":"<p><p>The third iteration of the Cnidarian Model Systems Meeting (Cnidofest) was held August 14-17th, 2024 at Lehigh University in Bethlehem, PA. The meeting featured presentations from laboratories representing 11 countries, covering a broad range of topics related to cnidarian species. The research highlighted diverse topics, with sessions focused on regeneration, evo-devo, genomics, symbiosis, cell biology, physiology, neurobiology, and development. A notable shift at this meeting was the extent to which established cnidarian model systems have caught up with the classical laboratory models such as Drosophila and vertebrates, with modern genomic, genetic, and molecular tools now routinely applied. In addition, more cnidarian systems are now being developed for functional studies by the community, enhancing our ability to gain fundamental insights into animal biology that are otherwise difficult in the complex bilaterian model systems. Together, the integration of cnidarian and bilaterian model systems provides researchers with a broader toolkit for selecting animal models best suited to address their specific biological questions.</p>","PeriodicalId":49076,"journal":{"name":"Evodevo","volume":"16 1","pages":"9"},"PeriodicalIF":4.1,"publicationDate":"2025-06-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12172373/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144310712","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The Notch pathway in Metazoa: a comparative analysis across cnidarians and beyond.","authors":"Alena Lövy, Jiří Kyslík, Amparo Picard-Sánchez, Astrid S Holzer, Alena Krejčí, Ivan Fiala","doi":"10.1186/s13227-025-00246-6","DOIUrl":"10.1186/s13227-025-00246-6","url":null,"abstract":"<p><p>The Notch signalling pathway is a conserved regulator of cellular processes, including differentiation, proliferation, and apoptosis, across Metazoa. While its roles in bilaterians are well-characterized, the evolutionary history and functional diversification of Notch signalling in early branching metazoans, including cnidarians and parasitic cnidarians, myxozoans, remain underexplored. This study examines the presence and structural diversity of Notch pathway components across early diverging metazoan lineages, with a particular focus on Myxozoa-parasitic cnidarians characterized by extreme morphological and genomic reduction. Comparative analyses of 58 metazoan species revealed broad conservation of core Notch components, alongside losses in ctenophores, placozoans, poriferans, and cnidarians. Myxozoa retain only 14 of the 28 canonical pathway components, lacking key elements, such as MAML, Hes/Hey, and DVL. Phylogenetic analyses of Notch receptors highlight structural divergence, particularly in extracellular domains, reflecting lineage-specific variations. The phylogeny of Delta and Jagged ligands reveals an evolutionary trajectory, with Delta ligands showing early diversification within metazoans, and their structural variability has been explored, though their functional roles remain unknown. The Notch receptor was detected at the subcellular level in proliferative stages of Sphaerospora molnari through immunolocalization studies, suggesting it is active in these cells. Our findings contribute to understanding the evolution of the Notch signalling pathway, highlighting its conserved role in developmental regulation across early branching Metazoa.</p>","PeriodicalId":49076,"journal":{"name":"Evodevo","volume":"16 1","pages":"8"},"PeriodicalIF":4.1,"publicationDate":"2025-06-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12166595/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144295184","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Antero-posterior patterning in the brittle star Amphipholis squamata and the evolution of echinoderm body plans.","authors":"L Formery, P Peluso, D R Rank, D S Rokhsar, C J Lowe","doi":"10.1186/s13227-025-00244-8","DOIUrl":"10.1186/s13227-025-00244-8","url":null,"abstract":"<p><p>Although the adult pentaradial body plan of echinoderms evolved from a bilateral ancestor, identifying axial homologies between the morphologically divergent echinoderms and their bilaterian relatives has been an enduring problem in zoology. The expression of conserved bilaterian patterning genes in echinoderms provides a molecular framework for resolving this puzzle. Recent studies in juvenile asteroids suggest that the bilaterian antero-posterior axis maps onto the medio-lateral axis of the arms, perpendicular to the proximo-distal axis of each of the five rays of the pentaradial body plan. Here, we test this hypothesis in another echinoderm class, the ophiuroids, using the cosmopolitan brittle star Amphipholis squamata. Our results show that the general principles of axial patterning are similar to those described in asteroids, and comparisons with existing molecular data from other echinoderm taxa support the idea that medio-lateral deployment of the bilaterian AP patterning program across the rays predates the evolution of the asterozoans, and likely the echinoderm crown-group. Our data also reveal expression differences between A. squamata and asteroids, which we attribute to secondary modifications specific to ophiuroids. Together, this work provides important comparative data to reconstruct the evolution of axial properties in echinoderm body plans.</p>","PeriodicalId":49076,"journal":{"name":"Evodevo","volume":"16 1","pages":"7"},"PeriodicalIF":4.1,"publicationDate":"2025-05-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12126913/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144192426","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Microinjection, gene knockdown, and CRISPR-mediated gene knock-in in the hard coral, Astrangia poculata.","authors":"Jacob F Warner, Ryan Besemer, Alicia Schickle, Erin Borbee, Isabella V Changsut, Koty Sharp, Leslie S Babonis","doi":"10.1186/s13227-025-00243-9","DOIUrl":"10.1186/s13227-025-00243-9","url":null,"abstract":"<p><p>Cnidarians have become valuable models for understanding many aspects of developmental biology including the evolution of body plan diversity, novel cell type specification, and regeneration. Most of our understanding of gene function during early development in cnidarians comes from a small number of experimental systems including Hydra and the sea anemone, Nematostella vectensis. Few molecular tools have been developed for use in hard corals, limiting our understanding of this diverse and ecologically important clade. Here, we report the development of a suite of tools for manipulating and analyzing gene expression during early development in the northern star coral, Astrangia poculata. We present methods for gene knockdown using short hairpin RNAs, gene overexpression using exogenous mRNAs, and endogenous gene tagging using CRISPR-mediated gene knock-in. Combined with the fact that spawning can be induced in the laboratory, during the reproductive window, these tools make A. poculata a tractable experimental system for investigative studies of coral development. Further application of these tools will enable functional analyses of embryonic patterning and morphogenesis across Anthozoa and open new frontiers in coral biology research.</p>","PeriodicalId":49076,"journal":{"name":"Evodevo","volume":"16 1","pages":"6"},"PeriodicalIF":4.1,"publicationDate":"2025-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12085026/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144086906","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The application of irreversible genomic states to define and trace ancient cell type homologies.","authors":"Oleg Simakov, Günter P Wagner","doi":"10.1186/s13227-025-00242-w","DOIUrl":"10.1186/s13227-025-00242-w","url":null,"abstract":"<p><p>Homology, or relationship among characters by common descent, has been notoriously difficult to assess for many morphological features, and cell types in particular. The ontogenetic origin of morphological traits means that the only physically inherited information is encoded in the genomes. However, the complexity of the underlying gene regulatory network and often miniscule changes that can impact gene expression, make it practically impossible to postulate a clear demarcation line for what molecular signature should \"define\" a homologous cell type between two deeply branching animals. In this Hypothesis article, we propose the use of the recently characterized irreversible genomic states, that occur after chromosomal and sub-chromosomal mixing of genes and regulatory elements, to dissect regulatory signatures of each cell type into irreversible and reversible configurations. While many of such states will be non-functional, some may permanently impact gene expression in a given cell type. Our proposal is that such evolutionarily irreversible, and thus synapomorphic, functional genomic states can constitute a criterion for the timing of the origin of deep evolutionary cell type homologies. Our proposal thus aims to close the gap between the clearly defined homology of the individual genomic characters and their genomic states to the homology at the phenotypic level through the identification of the underlying evolutionarily irreversible and regulatory linked states.</p>","PeriodicalId":49076,"journal":{"name":"Evodevo","volume":"16 1","pages":"5"},"PeriodicalIF":2.6,"publicationDate":"2025-05-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12049793/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143992269","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Early embryonic development in the tick Ixodes scapularis suggests syncytial organization and cellularization before blastoderm formation.","authors":"Isaac A Hinne, Hailee R Ciccotti, Jakub Wudarski, Michael N Pham, Arvind Sharma, Molly M McVicar, Benjamin Faustino, Andrew B Nuss, Prashant P Sharma, Monika Gulia-Nuss","doi":"10.1186/s13227-025-00240-y","DOIUrl":"10.1186/s13227-025-00240-y","url":null,"abstract":"<p><p>Ixodes ticks are the most important vectors of arthropod-borne diseases in the United States, Canada, and Europe. Ixodes scapularis is the major vector that transmits the causative agent of Lyme disease in the eastern United States and can transmit up to six additional pathogens. In recent years, many advances have been made in building the toolkit for I. scapularis research, including genomic resources, transcriptomes, and forward and reverse genetics techniques. However, an understanding of the early embryonic development of this species is still lacking. In this study, we attempted to fill this knowledge gap and to further the efforts of functional genomics tools development. We developed a staging system consisting of 16 (0-15) stages describing unique morphologies and used wheat germ agglutinin staining and fluorescent dye injections to confirm cell membrane formation. These results provide an opportunity to identify an ideal time window for tick transgenics and deepen our understanding of the events during embryo development.</p>","PeriodicalId":49076,"journal":{"name":"Evodevo","volume":"16 1","pages":"4"},"PeriodicalIF":3.6,"publicationDate":"2025-04-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12032745/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144041555","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Functional evidence supports the potential role of Tbx4-HLEA in the hindlimb degeneration of cetaceans.","authors":"Zhenhua Zhang, Yao Liu, Na Liang, Zhenpeng Yu, Luoying Deme, Duo Xu, Jia Liu, Wenhua Ren, Shixia Xu, Guang Yang","doi":"10.1186/s13227-025-00239-5","DOIUrl":"10.1186/s13227-025-00239-5","url":null,"abstract":"<p><p>The evolution of limb morphology plays an important role in animal adaptation to different ecological niches. To fully adapt to aquatic life, cetaceans underwent hindlimb degeneration and forelimb transformed into flipper; however, the molecular mechanisms underlying the limb changes in cetaceans remain unclear. We previous study had shown that the Tbx4 hindlimb enhancer A (Tbx4-HLEA) in cetaceans exhibited specific deletions and nucleotide substitutions, with significantly reduced regulatory activity. To further investigate whether cetacean HLEA has a potential impact on hindlimb development in vivo, a knock-in mouse model was generated by knocking in the homologous cetacean HLEA in the present study. Phenotypic analysis showed a significant reduction in hindlimb bud development in homozygous knock-in mice at embryonic day (E)10.5; however, the phenotypic difference was rescued after E11.5. Transcriptomic and epigenetic analyses indicated that the cetacean HLEA acts as an enhancer in the mouse embryos and significantly reduces the transcriptional expression levels of Tbx4 at E10.5, supporting that downregulation of cetaceans HLEA regulatory activity reduces the expression of Tbx4. Additionally, both the number of activated non-coding elements and chromatin accessibility near Tbx4 were increased in homozygous knock-in mice at E11.5. The functional redundancy of enhancers compensated for the functional defect of cetacean HLEA, rescuing the expression level of Tbx4, and may account for the phenotype restoration after E11.5. In conclusion, our study suggested that the evolution of cetacean HLEA may be an important link with relevant molecular mechanism for the hindlimb degeneration.</p>","PeriodicalId":49076,"journal":{"name":"Evodevo","volume":"16 1","pages":"3"},"PeriodicalIF":4.1,"publicationDate":"2025-03-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11929173/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143694198","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Shedding light on the embryogenesis and eye development of the troglophile cave spider Tegenaria pagana C. L. Koch, 1840 (Araneae: Agelenidae).","authors":"Evgenia A Propistsova, Guilherme Gainett, Ariel D Chipman, Prashant P Sharma, Efrat Gavish-Regev","doi":"10.1186/s13227-025-00238-6","DOIUrl":"10.1186/s13227-025-00238-6","url":null,"abstract":"<p><strong>Background: </strong>Relatively little is known about the diversity of embryonic development across lineages of spiders, even though the study of embryonic development is a primary step in evo-devo studies and essential for understanding phenotypic evolution. Practically nothing is known about embryogenesis in cave-dwelling spiders, animals which play an important role in cave ecosystems and may have remarkable adaptations to aphotic habitats such as loss of eyes.</p><p><strong>Results: </strong>Here, we describe embryogenesis and study the expression patterns of several genes of the Retinal Determination Network (RDN) in the troglophile (species that have pre-adaptations to life in caves, and can complete their life cycle in caves, as well as in epigean habitats) eye-bearing funnel-web spider species Tegenaria pagana C. L. Koch, 1840, using fluorescent staining and confocal microscopy. We discuss the characteristic features of T. pagana embryogenesis and key RDN genes. Although in many respects the embryonic development of different species of entelegyne spiders is similar, we found differences in the rate of development, and the details of the opisthosoma, respiratory system, and brain morphogenesis in comparison with established spider model species. Our data supports the hypothesis of a conserved role of sine oculis gene in the eye formation of arachnids.</p><p><strong>Conclusions: </strong>Given the recent discovery of congeneric cave species with different degrees of eye reduction throughout Israel, these data sets provide a foundational point of comparison for studying eye reduction and eye loss events in the spider genus Tegenaria.</p>","PeriodicalId":49076,"journal":{"name":"Evodevo","volume":"16 1","pages":"2"},"PeriodicalIF":4.1,"publicationDate":"2025-03-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11889846/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143587645","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}