Reduced signatures of gene duplication and non-random gene organization in shaping stage-specific patterns of gene expression across a relatively simple life cycle DOI Creative Commons
James G. DuBose, Levi T. Morran

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Дек. 21, 2024

Abstract Complex eukaryotes generally experience some degree of ecological transition as they develop, which is usually accompanied by the expression different traits across their ontogeny. Theory suggests evolution differentiation between life stages facilitated genes at points throughout ontogeny, alleviates pleiotropic evolutionary constraints. Therefore, ascertaining what contributes to specialized patterns gene ontogeny fundamental understanding ontogenetic complexity. Expression divergence duplicate and organization on chromosomes have been identified important features relatively complex ontogenies. one could predict that link transcriptional specialization may be weaker in simpler cycles. Here, we investigated links duplication, organization, stage-specific simple Caenorhabditis elegans cycle. We found signatures stage-biased chromosomal regions were C. than has previously described organisms with more Furthermore, extent varied pattern was constrained . Overall, our findings add a body evidence duplication

Язык: Английский

Functional innovation through new genes as a general evolutionary process DOI
Shengqian Xia, Jianhai Chen, Deanna Arsala

и другие.

Nature Genetics, Год журнала: 2025, Номер unknown

Опубликована: Янв. 28, 2025

Язык: Английский

Процитировано

1

Network properties constrain natural selection on gene expression in Caenorhabditis elegans DOI Creative Commons
Tyler R. Inskeep, Simon C. Groen

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2025, Номер unknown

Опубликована: Фев. 24, 2025

Gene regulatory networks (GRNs) integrate genetic and environmental signals to coordinate complex phenotypes evolve through a balance of selection drift. Using publicly available datasets from Caenorhabditis elegans , we investigated the extent natural on transcript abundance by linking population-scale variation in gene expression fecundity, key fitness component. While most genes covaried only weakly with fitness, which is typical for polygenic traits, identified seven transcripts under significant directional selection. These included nhr-114 feh-1, implicating nutrient-sensing metabolic pathways as impacting fitness. Stronger tissue-specific older highlighted germline nervous system focal points adaptive change. Network position further constrained expression; high-connectivity faced stronger stabilizing selection, highlighting GRN architecture factor microevolutionary dynamics. The activity transcription factors such zip-3 regulates mitochondrial stress responses, emerged targets revealing potential links between energy homeostasis Our findings demonstrate how GRNs mediate interplay drift, shaping trajectories phenotypic diversity.

Язык: Английский

Процитировано

0

Dimorphic Neural Network Architecture Prioritizes Sexual-related Behaviors in Male C. elegans DOI Open Access
Xuebin Wang, Hanli Liu, Wenjing Yang

и другие.

Опубликована: Фев. 27, 2025

Neural network architecture determines its functional output. However, the detailed mechanisms are not well characterized. In this study, we focused on neural architectures of male and hermaphrodite C. elegans association with sexually dimorphic behaviors. We applied graph theory computational neuroscience methods to systematically discern features these two networks. Our findings revealed that a small percentage sexual-specific neurons exerted dominance throughout entire net-work, suggesting male’s prioritized sexual-related behavior outputs. Based structural dynamical characteristics complete networks, sub-networks containing sex-specific their immediate neighbors, or exclusively comprising sex-shared neurons, predicted behavioral outcomes for males hermaphrodites. To verify prediction, performed calcium imaging experiments dissected circuit is specific increased spontaneous local search in mate-searching. research sheds light circuits underlie behaviors elegans, provides significant insights into inter-connected relationship between at whole-brain level.

Язык: Английский

Процитировано

0

Dimorphic Neural Network Architecture Prioritizes Sexual-related Behaviors in Male C. elegans DOI Open Access
Xuebin Wang, Hanli Liu, Wenjing Yang

и другие.

Опубликована: Фев. 27, 2025

Neural network architecture determines its functional output. However, the detailed mechanisms are not well characterized. In this study, we focused on neural architectures of male and hermaphrodite C. elegans association with sexually dimorphic behaviors. We applied graph theory computational neuroscience methods to systematically discern features these two networks. Our findings revealed that a small percentage sexual-specific neurons exerted dominance throughout entire net-work, suggesting male’s prioritized sexual-related behavior outputs. Based structural dynamical characteristics complete networks, sub-networks containing sex-specific their immediate neighbors, or exclusively comprising sex-shared neurons, predicted behavioral outcomes for males hermaphrodites. To verify prediction, performed calcium imaging experiments dissected circuit is specific increased spontaneous local search in mate-searching. research sheds light circuits underlie behaviors elegans, provides significant insights into inter-connected relationship between at whole-brain level.

Язык: Английский

Процитировано

0

Recently evolved, stage-specific genes are enriched at life stage transitions in flies DOI

Andreas Remmel,

Karl K. Käther,

Peter F. Stadler

и другие.

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2025, Номер unknown

Опубликована: Апрель 29, 2025

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

Язык: Английский

Процитировано

0

Divergence in neuronal signaling pathways despite conserved neuronal identity among Caenorhabditis species DOI Creative Commons
Itai Antoine Toker, Lidia Ripoll-Sánchez, Luke T. Geiger

и другие.

Current Biology, Год журнала: 2025, Номер unknown

Опубликована: Май 1, 2025

One avenue to better understand brain evolution is map molecular patterns of evolutionary changes in neuronal cell types across entire nervous systems distantly related species. Generating whole-animal single-cell transcriptomes three nematode species from the Caenorhabditis genus, we observed a remarkable stability neuronal-cell-type identities over more than 45 million years evolution. Conserved combinatorial expression homeodomain transcription factors are among best classifiers homologous neuron classes. Unexpectedly, discover an extensive divergence signaling pathways. Although neurotransmitter-producing neurons (glutamate, acetylcholine, γ-aminobutyric acid [GABA], and several monoamines) remain stable, ionotropic metabotropic receptors for all these neurotransmitter shows substantial divergence, resulting half classes changing their capacity be receptive specific neurotransmitters. Neuropeptidergic also remarkably divergent, both at level neuropeptide receptor expression, yet overall dense network topology wireless neuropeptidergic connectome remains stable. Novel pathways suggested by our discovery small secreted proteins that show no obvious hallmarks conventional neuropeptides but similar highly neuron-type-specific evolvable profiles. In conclusion, investigating resolution single-neuron classes, uncover may reflect basic principles governing novelty circuits.

Язык: Английский

Процитировано

0

Molecular patterns of evolutionary changes throughout the whole nervous system of multiple nematode species DOI Creative Commons
Itai Antoine Toker, Lidia Ripoll-Sánchez, Luke T. Geiger

и другие.

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Ноя. 25, 2024

One avenue to better understand brain evolution is map molecular patterns of evolutionary changes in neuronal cell types across entire nervous systems distantly related species. Generating whole-animal single-cell transcriptomes three nematode species from the

Язык: Английский

Процитировано

3

Single-cell phylotranscriptomics of developmental and cell type evolution DOI
Fuqiang Ma, Chaogu Zheng

Trends in Genetics, Год журнала: 2024, Номер 40(6), С. 495 - 510

Опубликована: Март 14, 2024

Язык: Английский

Процитировано

1

Pervasive conservation of intron number and other genetic elements revealed by a chromosome-level genomic assembly of the hyper-polymorphic nematode Caenorhabditis brenneri DOI
Anastasia Teterina, John H. Willis, Charles F. Baer

и другие.

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Июнь 28, 2024

With within-species genetic diversity estimates that span the gambit of seen across entirety animals,

Язык: Английский

Процитировано

0

Visualizing genomic evolution in Caenorhabditis through WormSynteny DOI Creative Commons

Lilly Bouvarel,

Dongyao Liu, Chaogu Zheng

и другие.

BMC Genomics, Год журнала: 2024, Номер 25(1)

Опубликована: Окт. 28, 2024

Язык: Английский

Процитировано

0