Journal of experimental zoology. Part B, Molecular and developmental evolution最新文献

{"title":"Noncanonical Nucleotides in the Genome Around the Maternal-Zygotic Transition.","authors":"Latifa Kazzazy, Dávid Mező, Kinga K Nagy, Viktória Perey-Simon, Judit Tóth, Angéla Békési, Beáta Vértessy, Máté Varga","doi":"10.1002/jez.b.23292","DOIUrl":"https://doi.org/10.1002/jez.b.23292","url":null,"abstract":"<p><p>From the very moment of fertilization and throughout development, the cells of animal embryos have to continuously orchestrate the dynamic reorganization of their epigenetic landscapes. One of the earliest major events of this reorganization occurs during the time of the maternal-zygotic transition (MZT), when the control of the developmental process gradually shifts from maternal factors (initially present within the oocytes) to the genes of the embryo itself. As maternal transcripts and proteins are degraded, parental epigenetic information is often erased, and pioneer factors will turn on the transcriptional activity of the zygotic genome. This activation also coincides with the decompaction of the chromatin, which is essential for the successful initiation of gene expression in the zygote. Interestingly, in the past decades numerous studies reported findings that supported the role of noncanonical nucleotides in the process of MZT. These nucleobase moieties in these noncanonical nucleotides are covalently modified versions of the canonical bases, and often show a very dynamic presence within the genome. While most of the recent studies have deciphered in great detail the epigenetic role of methylcytosine and its derivates, other Noncanonical bases have received less attention. Here we suggest that the incorporation of nucleotides from deoxyuridine-triphosphate (dUTP) or 6-methyl-deoxyadenine-triphosphate (6m-dATP) into the genome is not mere noise or replication error but serves a well-defined purpose: to aid chromatin decompaction through the timely induction of DNA repair pathways.</p>","PeriodicalId":15682,"journal":{"name":"Journal of experimental zoology. Part B, Molecular and developmental evolution","volume":" ","pages":""},"PeriodicalIF":1.8,"publicationDate":"2025-03-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143710327","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"In the Spotlight-Early Career Researcher.","authors":"Sofía Casasa","doi":"10.1002/jez.b.23291","DOIUrl":"https://doi.org/10.1002/jez.b.23291","url":null,"abstract":"","PeriodicalId":15682,"journal":{"name":"Journal of experimental zoology. Part B, Molecular and developmental evolution","volume":" ","pages":""},"PeriodicalIF":1.8,"publicationDate":"2025-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143573230","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Differential Expression of Hormone-Related Genes in the Heads of Adult and Nymphal Woodroaches (Cryptocercus).","authors":"Takumi Hanada, Hajime Yaguchi, Kokuto Fujiwara, Yoshinobu Hayashi, Christine A Nalepa, Kiyoto Maekawa","doi":"10.1002/jez.b.23290","DOIUrl":"https://doi.org/10.1002/jez.b.23290","url":null,"abstract":"<p><p>Termites are eusocial cockroaches, but the crucial distinctions in gene expression during the evolution of eusociality remain unclear. One reason for the lack of this information is that comparative transcriptome analysis of termites with their sister group, the cockroach genus Cryptocercus, has not been conducted. We identified genes associated with three vital hormones (juvenile hormone [JH], 20-hydoroxyecdysone [20E], and insulin) from the genome sequence of Cryptocercus punctulatus and conducted RNA-seq analysis using the heads of female/male adults and nymphs to elucidate their expression levels. The comprehensive gene expression analysis revealed a multitude of genes exhibiting differences in expression between developmental stages rather than between sexes. Subsequently, we compared the differences in expression patterns of each hormone-related gene by combining the results of a previous RNA-seq study conducted on the heads of castes (reproductives, workers, and soldiers) in the termite Reticulitermes speratus. The results indicated that genes with expression differences among castes in R. speratus, particularly those related to JH and 20E, were significantly more abundant compared to genes with expression differences between adults and nymphs in C. punctulatus. While no significant difference was observed in the number of genes within the insulin signaling pathway, a trend of homologs highly expressed in adult woodroaches but not in adult termites was observed, and the expression patterns of positive and negative regulators in the pathway differed significantly between adults and nymphs. The differences in the expression patterns between Cryptocercus and termites are believed to reflect variations in hormone levels and signaling activities between adults and juveniles, the latter encompassing workers and soldiers in the case of termites.</p>","PeriodicalId":15682,"journal":{"name":"Journal of experimental zoology. Part B, Molecular and developmental evolution","volume":" ","pages":""},"PeriodicalIF":1.8,"publicationDate":"2025-02-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143441068","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Elevated Blood Hemoglobin in Different Cavefish Populations Evolves Through Diverse Hemoglobin Gene Expression Patterns.","authors":"Tyler E Boggs, Joshua B Gross","doi":"10.1002/jez.b.23289","DOIUrl":"https://doi.org/10.1002/jez.b.23289","url":null,"abstract":"<p><p>Cave-dwelling animals thrive in isolated caves despite the pressures of darkness, starvation, and reduced oxygen. Prior work revealed that Astyanax cave-dwelling morphs derived from different cave localities express significantly higher levels of blood hemoglobin compared to surface-dwelling fish. Interestingly, this elevation is maintained in different populations of cavefish, despite captive rearing in normal oxygen conditions. We capitalized on the consistent response of elevated hemoglobin in captive cavefish, which were derived from geographically distinct regions, to determine if this elevation is underpinned by expression of the same Hb genes. Blood hemoglobin proteins are encoded by a large family of hemoglobin (Hb) gene family members, which demonstrate coordinated expression patterns, subject to various organismal (e.g., period of life history) and environmental influences (e.g., oxygen availability). Surprisingly, we found that geographically distinct populations showed mostly divergent patterns of Hb gene expression. Cavefish from two cave localities, Pachón and Tinaja, have a more recent shared origin, and show more similar Hb expression patterns as adults. However, during embryonic phases, Pachón and Tinaja show significant variability in timing of peak expression of Hb family members. In sum, the transcriptomic underpinnings of Hb gene expression represents a complex composite of shared and divergent expression patterns across three captive cavefish populations. We conclude that these differential patterns are likely influenced by life history, and the unique cave conditions in which these animals evolved.</p>","PeriodicalId":15682,"journal":{"name":"Journal of experimental zoology. Part B, Molecular and developmental evolution","volume":" ","pages":""},"PeriodicalIF":1.8,"publicationDate":"2025-02-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143390986","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"In the Spotlight—Graduate Student","authors":"Harsha Sen","doi":"10.1002/jez.b.23288","DOIUrl":"10.1002/jez.b.23288","url":null,"abstract":"&lt;p&gt;Harsha is a recipient of an NIH F31 Fellowship and has been awarded the 2024 SICB price for the best student presentation in the Evolutionary Developmental Biology Division.&lt;/p&gt;&lt;p&gt;Website: https://harsha-sen.weebly.com/&lt;/p&gt;&lt;p&gt;I am from Kolkata, India and have loved nature for as long as I can remember. I was obsessed with Disney's Dinosaur movie as a toddler, and grew up catching bugs, watching tons of Animal Planet, and interacting closely with the urban wildlife around me. When I was in middle school, I remember being amazed by a nature documentary explaining how a population of brown bears that ventured into the Arctic accumulated incrementally beneficial mutations over thousands of generations to evolve into polar bears—I think that was the moment that got me to really understand a bit of how evolution works, and I've enjoyed understanding the processes that lead to natural diversity ever since.&lt;/p&gt;&lt;p&gt;I moved to the United States for college and was lucky to work on two (broadly speaking) evolutionary projects as an undergrad, one with a geneticist and another with a statistician. In my senior year, I took a course in developmental biology since I started recognizing it as the bridge between evolution and genetics. And even when I was a research assistant after college in a lab developing neurogenomic technologies, I found myself drawn to the molecular biology of quirky organisms—I remember reading about the genome of the scaly-foot snail (which can grow iron-mineralized scales!) and would chat with labmates about the molecular basis of temperature-dependent sex determination. I think that it was around then that I realized the type of biologist I want to be is one who can integrate evolutionary, developmental, and genomic lines of inquiry to better understand organisms and their biology.&lt;/p&gt;&lt;p&gt;My graduate program is in Molecular Biology, and I came to Princeton without a specific lab in mind—the program requires students to do three rotations as first years to decide which lab to join for their thesis work. Since I had enjoyed developing a sequencing-based technology during my post-bac, the first two labs I rotated in were CRISPR-based technology development labs. On a whim, I decided to join the Mallarino lab for my last rotation, to be able to study a novel biological system. Pretty soon, I realized that I enjoyed my interactions with labmates, many of whom, like me, were passionate about biodiversity, and were excited to use cutting-edge technologies to better understand it. It is this shared passion and the community in the lab that initially drew me to EvoDevo work for my PhD.&lt;/p&gt;&lt;p&gt;For me, I think the three are intertwined. I enjoy using novel technologies to better understand biological systems, and information-rich datasets can help generate new questions. I also really enjoy working with understudied organisms, using technology to shed light on their biology and how it differs from more traditional models. It is important to use ","PeriodicalId":15682,"journal":{"name":"Journal of experimental zoology. Part B, Molecular and developmental evolution","volume":"344 3","pages":"117-118"},"PeriodicalIF":1.8,"publicationDate":"2025-02-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jez.b.23288","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143364738","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Fish Evo-Devo: Moving Toward Species-Specific and Knowledge-Based Interactome","authors":"Ehsan Pashay Ahi","doi":"10.1002/jez.b.23287","DOIUrl":"https://doi.org/10.1002/jez.b.23287","url":null,"abstract":"<div>\u0000 \u0000 <p>A knowledge-based interactome maps interactions among proteins and molecules within a cell using experimental data, computational predictions, and literature mining. These interactomes are vital for understanding cellular functions, pathways, and the evolutionary conservation of protein interactions. They reveal how interactions regulate growth, differentiation, and development. Transitioning to functionally validated interactomes is crucial in evolutionary developmental biology (Evo-Devo), especially for non-model species, to uncover unique regulatory networks, evolutionary novelties, and reliable gene interaction models. This enhances our understanding of complex trait evolution across species. The European Evo-Devo 2024 conference in Helsinki hosted the first fish-specific Evo-Devo symposium, highlighting the growing interest in fish models. Advances in genome annotation, genome editing, imaging, and molecular screening are expanding fish Evo-Devo research. High-throughput molecular data have enabled the deduction of gene regulatory networks. The next steps involve creating species-specific interactomes, validating them functionally, and integrating additional molecular data to deepen the understanding of complex regulatory interactions in fish Evo-Devo. This short review aims to address the logical steps for this transition, as well as the necessities and limitations of this journey.</p></div>","PeriodicalId":15682,"journal":{"name":"Journal of experimental zoology. Part B, Molecular and developmental evolution","volume":"344 3","pages":"158-168"},"PeriodicalIF":1.8,"publicationDate":"2025-01-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143749969","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Digestive System Development and Posterior Hox/Parahox Gene Expression During Larval Life and Metamorphosis of the Phoronid Phoronopsis harmeri","authors":"Elena N. Temereva,&nbsp;Roman P. Kostyuchenko","doi":"10.1002/jez.b.23286","DOIUrl":"10.1002/jez.b.23286","url":null,"abstract":"<div>\u0000 \u0000 <p>Phoronida is a small group of marine animals, most of which are characterized by a long larval period and complex metamorphosis. As a result of metamorphosis, their body changes so much that their true anterior and posterior ends are very close to each other, and the intestine becomes long and U-shaped. Using histology and electron microscopy, we have shown that the elongation and change in shape of the digestive tract that occurs during metamorphosis in <i>Phoronopsis harmeri</i> larvae is accompanied by the formation of new parts and changes in ultrastructure. At the same time, our in situ hybridization data suggest that the posterior markers <i>Cdx</i> and <i>Post2</i> are expressed in posterior tissues at larval stages, during metamorphosis, and in juveniles, and that changes in their expression correlate with remodeling of the posterior parts of the digestive tract. Our data may shed light on the evolution of body patterning in animals undergoing complex metamorphosis.</p></div>","PeriodicalId":15682,"journal":{"name":"Journal of experimental zoology. Part B, Molecular and developmental evolution","volume":"344 3","pages":"136-157"},"PeriodicalIF":1.8,"publicationDate":"2025-01-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143006262","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Transcriptomic Landscape of Polypide Development in the Freshwater Bryozoan Cristatella mucedo: From Budding to Degeneration","authors":"A. Yu. Kvach,&nbsp;V. A. Kutyumov,&nbsp;V. V. Starunov,&nbsp;A. N. Ostrovsky","doi":"10.1002/jez.b.23285","DOIUrl":"10.1002/jez.b.23285","url":null,"abstract":"<div>\u0000 \u0000 <p>Colonial invertebrates consist of iterative semi-autonomous modules (usually termed zooids) whose lifespan is significantly shorter than that of the entire colony. Typically, module development begins with budding and ends with degeneration. Most studies on the developmental biology of colonial invertebrates have focused on blastogenesis, whereas the changes occurring throughout the entire zooidal life were examined only for a few tunicates. Here we provide the first description of transcriptomic changes during polypide development in the freshwater bryozoan <i>Cristatella mucedo</i>. For the first time for Bryozoa, we performed bulk RNA sequencing of six polypide stages in <i>C. mucedo</i> (buds, juvenile polypides, three mature stages, and degeneration stage) and generated a high-quality de novo reference transcriptome. Based on these data, we analyzed clusters of differentially expressed genes for enriched pathways and biological processes that may be involved in polypide budding, growth, active functioning, and degradation. Although stem cells have never been described in Bryozoa, our analysis revealed the expression of conservative “stemness” markers in developing buds and juvenile polypides. Our data also indicate that polypide degeneration is a complex regulated process involving autophagy and other types of programmed cell death. We hypothesize that the mTOR signaling pathway plays an important role in regulating the polypide lifespan.</p></div>","PeriodicalId":15682,"journal":{"name":"Journal of experimental zoology. Part B, Molecular and developmental evolution","volume":"344 3","pages":"119-135"},"PeriodicalIF":1.8,"publicationDate":"2025-01-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143006266","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"High Nutritional Conditions Influence Feeding Plasticity in Pristionchus pacificus and Render Worms Non-Predatory","authors":"Veysi Piskobulu,&nbsp;Marina Athanasouli,&nbsp;Hanh Witte,&nbsp;Christian Feldhaus,&nbsp;Adrian Streit,&nbsp;Ralf J. Sommer","doi":"10.1002/jez.b.23284","DOIUrl":"10.1002/jez.b.23284","url":null,"abstract":"<p>Developmental plasticity, the ability of a genotype to produce different phenotypes in response to environmental conditions, has been subject to intense studies in the last four decades. The self-fertilising nematode <i>Pristionchus pacificus</i> has been developed as a genetic model system for studying developmental plasticity due to its mouth-form polyphenism that results in alternative feeding strategies with a facultative predatory and non-predatory mouth form. Many studies linked molecular aspects of the regulation of mouth-form polyphenism with investigations of its evolutionary and ecological significance. Also, several environmental factors influencing <i>P. pacificus</i> feeding structure expression were identified including temperature, culture condition and population density. However, the nutritional plasticity of the mouth form has never been properly investigated although polyphenisms are known to be influenced by changes in nutritional conditions. For instance, studies in eusocial insects and scarab beetles have provided significant mechanistic insights into the nutritional regulation of polyphenisms but also other forms of plasticity. Here, we study the influence of nutrition on mouth-form polyphenism in <i>P. pacificus</i> through experiments with monosaccharide and fatty acid supplementation. We show that in particular glucose supplementation renders worms non-predatory. Subsequent transcriptomic and mutant analyses indicate that <i>de novo</i> fatty acid synthesis and peroxisomal beta-oxidation pathways play an important role in the mediation of this plastic response. Finally, the analysis of fitness consequences through fecundity counts suggests that non-predatory animals have an advantage over predatory animals grown in the glucose-supplemented condition.</p>","PeriodicalId":15682,"journal":{"name":"Journal of experimental zoology. Part B, Molecular and developmental evolution","volume":"344 2","pages":"94-111"},"PeriodicalIF":1.8,"publicationDate":"2025-01-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jez.b.23284","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143006264","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Developmental Plasticity in Growth and Performance Blur Taxonomic Boundaries in South American True Toads (Rhinella)","authors":"Lucas Ferriolli Mariotto,&nbsp;Leandro Lofeu,&nbsp;Tiana Kohlsdorf","doi":"10.1002/jez.b.23283","DOIUrl":"10.1002/jez.b.23283","url":null,"abstract":"<div>\u0000 \u0000 <p>Developmental plasticity can affect traits directly related to survival, and some changes may promote or impair population persistence in changing environments. At the same time, it can also originate new complex phenotypes, surpassing species-specific boundaries. Therefore, plastic responses have the potential to participate in processes of micro and macroevolution. In this study, we evaluate plastic responses to different thermal regimes during development in traits related to survival and also used for taxonomic classification of two true-toad species, <i>Rhinella icterica</i> and <i>Rhinella ornata</i>. We raised tadpoles representing distinct operational taxonomic units (OTUs) at different temperatures, and the resulting phenotypic patterns suggest canalization in <i>R. icterica</i> and complex variation revealed by plasticity among <i>R. ornata</i> OTUs. Plastic responses to thermal regimes produced differences among the OTUs in traits associated with specific survival strategies of <i>Rhinella</i> species. Some changes surpassed taxonomic boundaries and rescued lineage-specific phenotypic patterns, establishing unusual phenotypic combinations for these species. Our results illustrate the contribution of developmental plasticity for processes involving phenotypic differentiation among species in traits directly related to survival.</p></div>","PeriodicalId":15682,"journal":{"name":"Journal of experimental zoology. Part B, Molecular and developmental evolution","volume":"344 2","pages":"80-93"},"PeriodicalIF":1.8,"publicationDate":"2024-12-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142881839","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}