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

In the Spotlight-Established Researcher. 聚光灯下的知名研究人员。

IF 1.8 3区生物学

Journal of experimental zoology. Part B, Molecular and developmental evolution Pub Date : 2025-05-26 DOI: 10.1002/jez.b.23306

Rodrigo Nunes-da-Fonseca

引用次数: 0

Gene and Genome Duplication in Spiders. 蜘蛛的基因和基因组复制。

IF 1.8 3区生物学

Journal of experimental zoology. Part B, Molecular and developmental evolution Pub Date : 2025-05-25 DOI: 10.1002/jez.b.23304

Chetan Munegowda, Matthias Pechmann, Nikola-Michael Prpic-Schäper, Natascha Turetzek

{"title":"Gene and Genome Duplication in Spiders.","authors":"Chetan Munegowda, Matthias Pechmann, Nikola-Michael Prpic-Schäper, Natascha Turetzek","doi":"10.1002/jez.b.23304","DOIUrl":"https://doi.org/10.1002/jez.b.23304","url":null,"abstract":"Gene and genome duplications are widely observed across various organisms, including plants, yeasts, and animals. Numerous studies link gene duplications to the emergence of novel phenotypes, supporting the hypothesis that duplication events are advantageous for adaptive evolution. Whole-genome duplications (WGD) are especially prevalent in plants and have also occurred ancestrally in vertebrates. However, large-scale duplication events in other animal groups remain understudied, partly due to limited genomic resources. Arthropods, particularly insects, represent one of the most diverse animal clades in terms of both species and phenotypic diversity. With increasing availability of chromosome-level genomes, large-scale duplications appear to be rare in insects but are more frequent in chelicerates (e.g. spiders, scorpions, and horseshoe crabs). This makes chelicerates an intriguing group for comparing the mechanisms, fates, and evolutionary impacts of large-scale duplications with those seen in plants and vertebrates. In this review, we synthesize and discuss current research on WGD in spiders and discuss different scenarios for genes following gene duplication events (conservation, nonfunctionalization, subfunctionalization, specialization, drift, neofunctionalization) in the context of experimental studies. We hypothesize if there might be common trajectories after duplication and how these could be tested.","PeriodicalId":15682,"journal":{"name":"Journal of experimental zoology. Part B, Molecular and developmental evolution","volume":" ","pages":""},"PeriodicalIF":1.8,"publicationDate":"2025-05-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144142241","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}

引用次数: 0

De Novo Whole Genome Assemblies of Unusual Case-Making Caddisflies (Trichoptera) Highlight Genomic Convergence in the Composition of the Major Silk Gene (h-fibroin). 不同寻常的毛翅目制壳虫的全基因组组装突出了主要丝基因（h-丝素）组成的基因组趋同。

IF 1.8 3区生物学

Journal of experimental zoology. Part B, Molecular and developmental evolution Pub Date : 2025-05-19 DOI: 10.1002/jez.b.23301

Xiling Deng, Steffen U Pauls, Ryoichi B Kuranishi, Paul B Frandsen, Jacqueline Heckenhauer

{"title":"De Novo Whole Genome Assemblies of Unusual Case-Making Caddisflies (Trichoptera) Highlight Genomic Convergence in the Composition of the Major Silk Gene (h-fibroin).","authors":"Xiling Deng, Steffen U Pauls, Ryoichi B Kuranishi, Paul B Frandsen, Jacqueline Heckenhauer","doi":"10.1002/jez.b.23301","DOIUrl":"https://doi.org/10.1002/jez.b.23301","url":null,"abstract":"Trichoptera (caddisflies) is one of the most species-rich orders of aquatic insects. Species of caddisflies cover a broad ecological diversity as exemplified by various uses of underwater silk secretions. Diversity of silk use generally aligns with the evolution of major caddisfly lineages, specifically at the subordinal level: Annulipalpia (retreat makers) and Integripalpia (cocoon and tube-case makers). However, silk use within suborders differs for a few exceptional species in these clades. In this study, we provide the first whole genome assemblies and annotations for two unusual Integripalpia species: Limnocentropus insolitus, whose hard tube-case is anchored to boulders by a rigid, elongated silken stalk, and Phryganopsyche brunnea which builds a \"floppy\" cylindrical case that lacks the typical robustness of tube-cases. Its texture rather resembles that of the flexible retreats built by Annulipalpia. Using the two high-quality genome assemblies, we identified and annotated the major silk gene, h-fibroin, and compared its amino acid composition across various groups, including retreat, cocoon, and tube-case makers. Our phylogenetic analysis confirmed the phylogenetic position of the two species in the tube-case-making clade. The major silk gene of L. insolitus shows a similar amino acid composition to other tube-case-making species. In contrast, the amino acid composition of P. brunnea resembles that of retreat-making species, in particular with regard to the high content of proline. This is consistent with the hypothesis that proline could be linked to enhanced extensibility of silk fibers. Taken together, our results underscore the role of silk genes in shaping the evolutionary ecology of retreat- and tube-case-making in caddisflies.","PeriodicalId":15682,"journal":{"name":"Journal of experimental zoology. Part B, Molecular and developmental evolution","volume":" ","pages":""},"PeriodicalIF":1.8,"publicationDate":"2025-05-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144093634","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}

引用次数: 0

Multiomics Reveal Associations Between CpG Methylation, Histone Modifications and Transcription in a Species That has Lost DNMT3, the Colorado Potato Beetle. 多组学揭示了丢失DNMT3的物种科罗拉多马铃薯甲虫CpG甲基化、组蛋白修饰和转录之间的关联。

IF 1.8 3区生物学

Journal of experimental zoology. Part B, Molecular and developmental evolution Pub Date : 2025-05-12 DOI: 10.1002/jez.b.23303

Zoe M Länger, Elisa Israel, Jan Engelhardt, Agata I Kalita, Claudia I Keller Valsecchi, Joachim Kurtz, Sonja J Prohaska

{"title":"Multiomics Reveal Associations Between CpG Methylation, Histone Modifications and Transcription in a Species That has Lost DNMT3, the Colorado Potato Beetle.","authors":"Zoe M Länger, Elisa Israel, Jan Engelhardt, Agata I Kalita, Claudia I Keller Valsecchi, Joachim Kurtz, Sonja J Prohaska","doi":"10.1002/jez.b.23303","DOIUrl":"https://doi.org/10.1002/jez.b.23303","url":null,"abstract":"Insects display exceptional phenotypic plasticity, which can be mediated by epigenetic modifications, including CpG methylation and histone modifications. In vertebrates, both are interlinked and CpG methylation is associated with gene repression. However, little is known about these regulatory systems in invertebrates, where CpG methylation is mainly restricted to gene bodies of transcriptionally active genes. A widely conserved mechanism involves the co-transcriptional deposition of H3K36 trimethylation and the targeted methylation of unmethylated CpGs by the de novo DNA methyltransferase DNMT3. However, DNMT3 has been lost multiple times in invertebrate lineages raising the question of how the links between CpG methylation, histone modifications and gene expression are affected by its loss. Here, we report the epigenetic landscape of Leptinotarsa decemlineata, a beetle species that has lost DNMT3 but retained CpG methylation. We combine RNA-seq, enzymatic methyl-seq and CUT&Tag to study gene expression, CpG methylation and patterns of H3K36me3 and H3K27ac histone modifications on a genome-wide scale. Despite the loss of DNMT3, H3K36me3 mirrors CpG methylation patterns. Together, they give rise to signature profiles for expressed and not expressed genes. H3K27ac patterns show a prominent peak at the transcription start site that is predictive of expressed genes irrespective of their methylation status. Our study provides new insights into the evolutionary flexibility of epigenetic modification systems that urge caution when generalizing across species.","PeriodicalId":15682,"journal":{"name":"Journal of experimental zoology. Part B, Molecular and developmental evolution","volume":" ","pages":""},"PeriodicalIF":1.8,"publicationDate":"2025-05-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143985729","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}

引用次数: 0

Embryogenesis in Myrmicine Ants Combines Features of Short Germ-Band Development With a Progressive Mode of Segmentation. 金蚁的胚胎发育具有短胚带发育特征和渐进式分裂模式。

IF 1.8 3区生物学

Journal of experimental zoology. Part B, Molecular and developmental evolution Pub Date : 2025-05-12 DOI: 10.1002/jez.b.23296

Chi-Chun Fang, Arjuna Rajakumar, Andrew Kenny, Ulrich G Mueller, Ehab Abouheif, David Stein

{"title":"Embryogenesis in Myrmicine Ants Combines Features of Short Germ-Band Development With a Progressive Mode of Segmentation.","authors":"Chi-Chun Fang, Arjuna Rajakumar, Andrew Kenny, Ulrich G Mueller, Ehab Abouheif, David Stein","doi":"10.1002/jez.b.23296","DOIUrl":"https://doi.org/10.1002/jez.b.23296","url":null,"abstract":"Ants exhibit complex social organization, morphologically and functionally distinct castes, and the exploitation of diverse ecological niches. How these features have influenced embryonic development relative to other insects remains unclear. Insect embryogenesis has been classified into three modes: In long germ-band development, exemplified by the fruit fly Drosophila melanogaster, segments along the entire anterior-posterior axis of the embryonic primordium are established almost simultaneously, before gastrulation, with the initial embryonic primordium surrounding almost the entire volume of the egg. In short and intermediate germ-band modes, the embryonic primordium occupies a smaller proportion of the egg surface, with anterior segments initially specified, and remaining segments being added sequentially from a posterior growth zone. Here, we examine embryogenesis in three myrmicine ants, the fungus-gardening ants Atta texana and Mycocepurus smithii, and the red imported fire ant Solenopsis invicta. We find that these ant embryos combine features of short germ-band development with a newly characterized progressive pattern of segmentation that has been associated with some long germ-band-developing insects. Despite similarities in the size of ant and Drosophila eggs, embryogenesis in the three ant species is 10- to 20-fold longer than in Drosophila and is also significantly longer than in two other hymenopteran species that have been studied, the honeybee Apis mellifera and the jewel wasp Nasonia vitripennis. Moreover, the embryos produced by A. texana foundress queens develop to first instar larvae 25% faster than embryos produced by mature queens. We discuss these results in the context of the eusocial lifestyle of ants.","PeriodicalId":15682,"journal":{"name":"Journal of experimental zoology. Part B, Molecular and developmental evolution","volume":" ","pages":""},"PeriodicalIF":1.8,"publicationDate":"2025-05-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143983177","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}

引用次数: 0

CRISPR/Cas9 Knockout of Shell Matrix Protein 1 in the Slipper-Snail Crepidula atrasolea. 滑螺Crepidula atrasolea壳基质蛋白1的CRISPR/Cas9敲除

IF 1.8 3区生物学

Journal of experimental zoology. Part B, Molecular and developmental evolution Pub Date : 2025-05-04 DOI: 10.1002/jez.b.23293

Grant Batzel, Yiqun Wang, Antonia Bock, Elbereth Chen, Stephanie Neal, Rebecca N Lopez-Anido, Yoon Lee, Evan Tjeerdema, Emily Ignatoff, Tejasvi Patil, Gabriela Ramirez, Maryna P Lesoway, Amro Hamdoun, Deirdre C Lyons

{"title":"CRISPR/Cas9 Knockout of Shell Matrix Protein 1 in the Slipper-Snail Crepidula atrasolea.","authors":"Grant Batzel, Yiqun Wang, Antonia Bock, Elbereth Chen, Stephanie Neal, Rebecca N Lopez-Anido, Yoon Lee, Evan Tjeerdema, Emily Ignatoff, Tejasvi Patil, Gabriela Ramirez, Maryna P Lesoway, Amro Hamdoun, Deirdre C Lyons","doi":"10.1002/jez.b.23293","DOIUrl":"https://doi.org/10.1002/jez.b.23293","url":null,"abstract":"Over the course of hundreds of millions of years, biomineralization has evolved independently many times across all kingdoms of life. Among animals, the phylum Mollusca displays a remarkable diversity in biomineral structures, particularly the molluscan shell, which varies greatly in shape, size, pigmentation, and patterning. Shell matrix proteins (SMPs) are key components of these shells, and are thought to drive the precipitation of calcium carbonate minerals and influence shell morphology. However, this structure-function relationship has rarely been studied directly because tools for knocking out genes did not exist in molluscs until recently. In this study, we report the first successful use of CRISPR/Cas9 gene editing to target an SMP in gastropod molluscs. Using the emerging model gastropod Crepidula atrasolea, we generated knockouts of the SMP1 gene. Successful gene editing was confirmed by Sanger and MiSeq sequencing, and loss of SMP1 expression was validated through high-content imaging of crispant embryos. This study establishes C. atrasolea as a valuable model for investigating the genetic basis of shell formation and provides a framework for applying CRISPR/Cas9 technology in other molluscan species. Our approach will enable future studies to thoroughly test the role of SMPs in shaping the diverse array of molluscan shell structures.","PeriodicalId":15682,"journal":{"name":"Journal of experimental zoology. Part B, Molecular and developmental evolution","volume":" ","pages":""},"PeriodicalIF":1.8,"publicationDate":"2025-05-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144022062","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}

引用次数: 0

In the Spotlight-Early Career Researcher. 聚光灯下的早期职业研究者。

IF 1.8 3区生物学

Journal of experimental zoology. Part B, Molecular and developmental evolution Pub Date : 2025-05-02 DOI: 10.1002/jez.b.23302

Leslie S Babonis

引用次数: 0

Comparative Regeneration Dynamics of Platynereis dumerilii and Pygospio elegans (Annelida): Morphological and Cellular Events. 长尾扁柏和长尾扁柏的比较再生动力学：形态学和细胞事件。

IF 1.8 3区生物学

Journal of experimental zoology. Part B, Molecular and developmental evolution Pub Date : 2025-04-29 DOI: 10.1002/jez.b.23298

Elena L Novikova, Zinaida I Starunova, Ksenia V Shunkina, Alexandra I Chava, Valeriia R Khabibulina, Galina A Barmasova, Clementine Z Aster, Viktor V Starunov

引用次数: 0

From Genes to Pathways: A Curated Gene Approach to Accurate Pathway Reconstruction in Teleost Fish Transcriptomics. 从基因到途径：硬骨鱼转录组学中精确途径重建的调控基因方法。

IF 1.8 3区生物学

Journal of experimental zoology. Part B, Molecular and developmental evolution Pub Date : 2025-04-29 DOI: 10.1002/jez.b.23299

Marcela Herrera, Stefano Vianello, Laurie Mitchell, Zoé Chamot, Catherine Lorin-Nebel, Edith Bonnelye, Natacha Roux, Laurence Besseau, Yann Gibert, Vincent Laudet

{"title":"From Genes to Pathways: A Curated Gene Approach to Accurate Pathway Reconstruction in Teleost Fish Transcriptomics.","authors":"Marcela Herrera, Stefano Vianello, Laurie Mitchell, Zoé Chamot, Catherine Lorin-Nebel, Edith Bonnelye, Natacha Roux, Laurence Besseau, Yann Gibert, Vincent Laudet","doi":"10.1002/jez.b.23299","DOIUrl":"https://doi.org/10.1002/jez.b.23299","url":null,"abstract":"Interpreting the vast amounts of data generated by high-throughput sequencing technologies can often present a significant challenge, particularly for non-model organisms. While automated approaches like GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) enrichment analyses are widely used, they often lack specificity for non-model organisms. To bridge this gap, we present a manually curated gene list tailored for teleost fish transcriptomics. This resource focuses on key biological processes crucial for understanding teleost fish physiology, development, and adaptation, including hormone signaling, various metabolic pathways, appetite regulation, digestion, gastrointestinal function, vision, ossification, osmoregulation, and pigmentation. Developed through collaborative efforts of specialists in diverse fields, the list prioritizes genes with established roles in teleost physiology, experimental evidence, and conservation across species. This curated list aims to provide researchers with a reliable starting point for transcriptomic analyses, offering a carefully evaluated set of genes relevant to current research priorities. By streamlining the process of gene selection and interpretation, this resource supports the broader teleost fish research community in designing and analyzing studies that investigate molecular responses to developmental and environmental changes. We encourage the scientific community to collaboratively expand and refine this list, ensuring its continued relevance and utility for teleost fish research.","PeriodicalId":15682,"journal":{"name":"Journal of experimental zoology. Part B, Molecular and developmental evolution","volume":" ","pages":""},"PeriodicalIF":1.8,"publicationDate":"2025-04-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144002570","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}

引用次数: 0

Fractal Dimension and Suture Complexity During Postnatal Ontogeny in Neotropical Deer in Relation to Sexual Dimorphism and Other Biological Features. 新生热带鹿出生后个体发育的分形维数和缝线复杂性与两性二态性和其他生物学特征的关系。

IF 1.8 3区生物学

Journal of experimental zoology. Part B, Molecular and developmental evolution Pub Date : 2025-04-29 DOI: 10.1002/jez.b.23300

Nuria S Di Guida, Guillermo H Cassini

{"title":"Fractal Dimension and Suture Complexity During Postnatal Ontogeny in Neotropical Deer in Relation to Sexual Dimorphism and Other Biological Features.","authors":"Nuria S Di Guida, Guillermo H Cassini","doi":"10.1002/jez.b.23300","DOIUrl":"https://doi.org/10.1002/jez.b.23300","url":null,"abstract":"In mammals, the increase in cranial suture complexity throughout postnatal ontogeny has been linked to mechanical forces that load on the skull, including compression forces from mastication and the presence and use of cranial appendages in ungulates. Suture complexity, or interdigitation, provides a large absorptive capacity for mechanical stress. Deer are unique among ungulates by the presence of antlers only in males. In particular, Neotropical species exhibit a great diversity in terms of morphology, weight, sexual size dimorphism (absence or presence), and ecology. To evaluate the relationship of suture interdigitation with the mechanical stress produced by antlers, we quantified the complexity of the interfrontal and coronal sutures using fractal dimension (D) in six Neotropical deer species. Utilizing the occlusal tooth area (OTA) of the first upper molar as a proxy of age, we analyze changes of D throughout postnatal ontogeny and test for sexual dimorphism. In all species, ontogenetic series indicate an increase of complexity of both sutures with OTA. Overall, the species with a significant sexual dimorphism in body size and antlers with more than one tine show the more complex sutures, with the presence of greater interdigitation in adult males than in females, regardless of the existence of intraspecific fights during the rut. This is the first study where sexual dimorphism in cranial suture complexity in relation to the presence of antlers in deer is reported, suggesting the role of the interfrontal and coronal sutures on the dissipation of mechanical stress forces produced by the presence of antlers.","PeriodicalId":15682,"journal":{"name":"Journal of experimental zoology. Part B, Molecular and developmental evolution","volume":" ","pages":""},"PeriodicalIF":1.8,"publicationDate":"2025-04-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143985665","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}

引用次数: 0