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

Understanding how genomic information is selectively utilized across different life stages is essential for deciphering the developmental and evolutionary strategies of metazoans. In holometabolous insects, the dynamic expression of genes enables distinct functional adaptations at embryonic, larval, pupal, and adult stages, likely contributing to their evolutionary success. While Drosophila melanogaster (D. melanogaster) has been extensively studied, less is known about the evolutionary dynamics that could govern stage-specific gene expression. To address this question, we compared the distribution of stage-specific genes, that is, genes expressed in temporally restricted developmental stages, across the development of D. melanogaster and Aedes aegypti (A. aegypti). Using tau-scoring, a computational method to determine gene expression specificity, we found that, on average, a large proportion of genes (20%–30% of all protein-coding genes) in both species exhibit restricted expression to specific developmental stages. Phylostratigraphy analysis, a method to date the age of genes, further revealed that stage-specific genes fall into two major categories: highly conserved and recently evolved. Notably, many of the recently evolved and stage-specific genes identified in A. aegypti and D. melanogaster are restricted to Diptera order (20%–35% of all stage-specific genes), highlighting ongoing evolutionary processes that continue to shape life-stage transitions. Overall, our findings underscore the complex interplay between gene evolutionary age, expression specificity, and morphological transformations in development. These results suggest that the attraction of genes to critical life-stage transitions is an ongoing process that may not be constant across evolutionary time or uniform between different lineages, offering new insights into the adaptability and diversification of dipteran genomes.

Aedes aegypti, a critical vector for tropical diseases, poses significant challenges for studying its embryogenesis due to difficulties in removing its rigid chorion and achieving effective fixation for in situ hybridization. Here, we present novel methodologies for fixation, dechorionation, DAPI staining, and in situ hybridization, enabling the detailed analysis of gene expression throughout Ae. aegypti embryogenesis. By synchronizing eggs at various developmental stages (0-72 h), we localized the transcripts of the gap gene mille-pattes (mlpt), the dorsoventral gene cactus (cact), and the pioneer transcription factor (pTF) zelda (zld). In situ hybridization and RT-qPCR analyses revealed that mlpt and cact are maternally expressed, while zld expression begins zygotically during cellularization and later becomes prominent in neuroblasts. Analysis of previously published transcriptomes suggests that three other pTFs, CLAMP, grainyhead, and GAF, are also maternally expressed and may function as pioneer transcription factors during Ae. aegypti embryogenesis. These findings suggest that the transcription factors responsible for genome activation in mosquitoes differ from those in fruit flies, highlighting significant divergence in the genetic regulation of early Dipteran embryogenesis.

The V Argentine Workshop on Vertebrate Morphology (Taller Argentino de Morfología de Vertebrados-TAMV) was held in the CICyTTP-CONICET, city of Diamante, Entre Ríos, Argentina, from September 4th to 6th, 2024. Over the course of 3 days, 32 Argentine morphologists congregated to share the progress of their research, discuss emerging trends in morphology, and particularly, to delve into the utilization of new methodologies as indispensable tools for advancing their work. The workshop was based on a dynamic format featuring the presentation of manuscripts or expanded abstracts, along with three hands-on workshops on current methodologies implemented in the participants' research lines.

The 2024 Latin American Developmental Biology Conference, held in Valparaíso, Chile, brought together a dynamic and diverse community of researchers to discuss current advances and prospectives in embryology. With participants from across the Americas and beyond, this extraordinary meeting highlighted the region's growing role in the field. A central theme throughout was the growing need for integrative approaches that connect multiple layers of biological phenomena to explain how form and function emerge during development: in Latin America, applications of genomics, imaging, genetics, and computational modelling to unique biological resource are transforming our understanding of developmental systems. The conference also fostered a highly inclusive and interactive environment with enthusiastic participation from trainees and early-career scientists. Poster sessions, lightning talks, and workshops offered platforms for critical reflection on issues such as challenges in funding, inclusion, and research ethics. Despite political and institutional challenges in the region, the conference showcased the creativity, resilience, and momentum of Latin American scientists, affirming their critical role in directing developmental biology towards the new horizon.

The Assay for Transposase-Accessible Chromatin with sequencing (ATAC-seq) is a versatile and widely utilized method for identifying potential regulatory regions, such as promoters and enhancers, within a genome. ATAC-seq has been successfully applied to a wide range of established and emerging model organisms. However, implementing this method in emerging model systems, such as arthropods, can be challenging due to several factors that influence data quality. These factors include the availability of a sufficient amount and quality of tissue or cells, the need for species- and tissue-specific protocol optimization, the completeness and accuracy of the reference genome, and the quality of the genome annotation. In this article, we emphasize the key steps in the ATAC-seq protocol that, based on our experience, have the greatest impact on data quality when adapting this method for emerging model organisms. Specifically, we discuss the importance of nuclei isolation, the incubation conditions of the Tn5 transposase, and PCR amplification of the library. Furthermore, we outline essential quality checkpoints during the bioinformatic analysis of ATAC-seq data to assist in assessing data integrity and consistency. Given that many emerging model organisms may not be readily available in laboratory cultures, we also emphasize the importance of evaluating how different preservation methods affect ATAC-seq data quality. Based on examples in one spider and one ant species, we demonstrate that replication and thorough quality controls at all steps of the protocol and data analysis are essential to assess the usability of ATAC-seq data. Our data highlights the importance of isolating the right number of intact nuclei, as well as ensuring optimal amplification conditions during library preparation to obtain good-quality sequence data for downstream analyses. We recommend using fresh tissue samples if possible because we show that direct cryopreservation of the tissue may affect chromatin integrity. This effect could be avoided or reduced by preserving the homogenate in cell culture medium. Overall, we explain the ATAC-seq protocol and downstream analyses in detail and give step-by-step advice to researchers who are new to the field and want to implement this method. With careful planning and validation, ATAC-seq can reveal the regulatory landscape of a genome and aid in identifying elements that govern gene expression.

Early embryogenesis relies on a series of maternal factors to coordinate cell division and axial patterning. In insects, maternal Toll receptor and Bone Morphogenetic Protein (BMP) pathway activities drive the spatial allocation of zygotic gene expression territories along the dorsal-ventral (DV) axis. The respective contribution of each pathway varies among insect orders and suggests that Toll was co-opted from an ancestral immune function for insect DV patterning. The Ca⁺² dependent modulatory Calpain proteases also influence insect DV patterning, in addition to their role in regulating mitosis. Calpains alter gene expression patterns in insect species that depend on either Toll or BMPs for the establishment of DV territories, raising the question of when calpains acquired this crucial role. Here we review the function of calpains in early embryogenesis within the context of an evolving insect DV patterning landscape. We discuss the essential components for the transition from BMP-driven to Toll-centered axial patterning and how insect Calpains may have adapted to this changing regulatory network.

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.