G3: Genes|Genomes|Genetics最新文献

Temperature fluctuations impose significant physiological challenges on aquatic invertebrates, with far reaching consequences that span from cellular to ecosystem levels. Even low to moderate heat stress can activate molecular responses that reshape development, metabolism, and reproduction. In this study, we investigated the transcriptional response of Daphnia pulex, a common grazer in lentic freshwater systems, to sublethal temperature stress (a temperature below the acute lethal limit, allowing for survival during chronic exposure). D. pulex were exposed to control (20℃) and elevated sublethal (25℃) temperatures to simulate an increased water temperature from a mild heat wave for 168 hours. Our findings indicate a dynamic transcriptional response to elevated temperatures. Notably, differential gene expression between the control and temperature-elevated treatment increased throughout the experiment with a three-fold increase in counts of differentially expressed genes (DEGs) from 247 at 96 hours to 743 at 168 hours. Changes in gene expression were related to development, specifically reproduction, at 96 hours, and a shift towards metabolic processes at 168 hours. D. pulex within the experimental treatment generally had higher mean cumulative offspring produced compared to the control treatment. Given D. pulex's role as a foundational species in aquatic food webs, the observed transcriptional response provides insight into the potential for both plastic and adaptive responses in the face of environmental change.

Circular RNA (circRNA) biogenesis is regulated by RNA-binding proteins (RBPs) that alter back-splicing of exons in protein coding genes. However, few in vivo roles for RBPs in the regulation of circRNA biogenesis have been characterized. We previously showed that many circRNAs increase with age in C. elegans, and that loss of circ-crh-1, an abundant age-accumulated circRNA, extends mean lifespan. Given the established role of the mammalian RBP NOVA2 in promoting circRNA biogenesis, we investigated whether nova-1, the sole C. elegans homolog of NOVA1/2, similarly regulates circRNA expression and function in vivo. RNA-sequencing of nova-1 mutants compared to wild-type identified 686 circRNAs. Of these, 103 were differentially expressed in nova-1 mutants compared to wild-type, with 76 upregulated and 27 downregulated circRNAs, suggesting NOVA-1 acts as a negative regulator of a subset of circRNAs. nova-1 mutants also exhibited linear alternative splicing changes, primarily in alternative 3' splice site usage and exon skipping, and showed minimal overlap with circRNA loci. Notably, circ-crh-1 represented a shared regulatory target, suggesting NOVA-1 may coordinate splicing regulation with the production of crh-1 circRNAs. Motif analysis further revealed that over half of the NOVA-1-regulated splicing events contained YCAY motif sites, with crh-1 harboring a high density of sites, consistent with its alternative 3' splice site usage and circRNA production. Finally, nova-1 mutants exhibited an extended mean lifespan and enhanced heat stress recovery. Together, these findings identify NOVA-1 as a key regulator of circRNA expression and alternative splicing in C. elegans, with likely downstream consequences for organismal lifespan and stress resilience.

Stevia rebaudiana (stevia) is an herbaceous perennial grown to produce sweet tasting non-caloric steviol glycosides produced in the leaves and used as a sugar substitute. While stevia produces more than 60 known steviol glycosides, those with the greatest consumer-desired taste profiles, such as rebaudioside (Reb) D and Reb M, are produced at low concentrations. Efforts to breed stevia with increased concentrations of these minor glycosides have been hampered by limited genetic resources to improve breeding efficiency. We developed the first single nucleotide polymorphism (SNP)-based genetic linkage map for stevia for a highly heterozygous F1 population. The linkage map consists of 1322 SNPs across the 11 stevia chromosomes. The map covered 2991.8 cM, although this was inflated by large gaps on linkage group 8. Excluding linkage group 8, the remaining 10 linkage groups covered 1947.7 cM, with an average density of 1.48 cM per marker. The mapping population was grown in multiple locations in 2020 and 2021 to evaluate steviol glycoside production (stevioside and Reb A, B, C, D, E, M, N, and O). The population exhibited transgressive segregation for production of all evaluated glycosides. QTL were identified for all measured glycosides except Reb M and Reb O. A region of chromosome 1 harbored colocalizing quantitative trait loci (QTL) for stevioside, Reb A, Reb B, Reb D, Reb E, and Reb N. This region contained large-effect QTL explaining up to 38.8% of the observed variation (%VE) for Reb D, and 71.9 and 46.8 %VE, respectively, for the minor glycosides Reb E and Reb N. The linkage map and population described herein will be useful for identifying QTL for other stevia growth and yield traits exhibiting quantitative inheritance and will aid in selection of candidate genes underlying these traits for further evaluation.

Understanding the recombination landscape is crucial for revealing the extent of its variation across the tree of life and for uncovering its underlying causes and evolutionary consequences. Among the many factors influencing recombination rates, polymorphic inversions are particularly important modifiers. Increasingly, complex inversion landscapes are being documented across diverse taxa, and detailed recombination rate data are essential for advancing our understanding of variation in inversion-rich genomes. Here, we combined whole-genome sequencing of two two-generation families with cytogenetic karyotyping to reconstruct a linkage map of the inversion-rich spruce bark beetle (Ips typographus) genome. Our results revealed a different chromosome number than previously reported (15AA + Xy) and a recombination landscape strongly shaped by the inversion landscape. The total length of the autosomal, sex-averaged map was 978 cM, with an overall mean recombination rate of 4.9 cM/Mb. Recombination was spatially heterogeneous across the genome and was significantly reduced in parents heterozygous for specific inversion arrangements. We also used the linkage map to upgrade the existing genome assembly to chromosome level, correcting previous misassemblies (often associated with inversions), revising inversion size estimates, identifying new putative inversions, and updating repeat content. Notably, inversions were found to be depleted in transposable elements (TEs). These findings provide a valuable foundation for future research on this important forest pest and offer broader insights into how recombination landscapes are shaped in inversion-rich genomes.

Metazoan eggs are surrounded by a specialized coat of extracellular matrix that mediates sperm-egg interactions. This coat is rapidly remodeled after fertilization to form a barrier that prevents polyspermy, protects against environmental insults, and provides structural support to the developing embryo. In C. elegans, several oocyte surface proteins have been identified that mediate these events. However, whether two of these proteins, EGG-1 and EGG-2, are required for fertilization or downstream events has been unclear. Here, we address this question using more recent advances in genome editing tools through the creation of egg-1 egg-2 deletions of the endogenous loci. We found that egg-1 egg-2 oocytes are fertilization competent and form rudimentary eggshells. While the integrity of the egg-1 egg-2 eggshells are compromised and often rupture within the uterus, some embryos are capable of undergoing several rounds of cell division. Absence of EGG-1 and EGG-2 results in the mislocalization of proteins on the embryo surface and eggshell. CBD-1, CHS-1, and MBK-2, components of the egg activation complex and outermost eggshell layer, were mislocalized, while localization of CPG-1, a component of an inner eggshell layer, was not perturbed. Overall, our findings demonstrate that EGG-1 and EGG-2 are not required for fertilization but rather are involved in the organization of eggshell structural components and oocyte plasma membrane proteins.

CX-5461 (CX) is under investigation for the treatment of late-stage cancers. While CX was first described as an RNA polymerase I inhibitor, it has recently been shown to primarily inhibit the beta isoform of topoisomerase II. This isoform is also inhibited by anthracycline drugs including Doxorubicin (DOX) and mediates the toxic effects of these drugs on the heart. It is unclear whether CX will similarly cause cardiotoxicity. We therefore tested the effects of CX on iPSC-derived cardiomyocytes from six individuals. CX induces cell death in cardiomyocytes at micromolar concentrations. Transcriptome profiling following treatment over time reveals gene expression programs that correspond to the DNA damage response, which are pathways shared with DOX response genes. Micromolar CX concentrations affect heart-specific genes and 14 functionally-validated genes in loci associated with DOX cardiotoxicity. Our data demonstrate the impact of CX on the transcriptome of cardiomyocytes, a potential off-target cell type of the drug.

Selection intensity is expected to influence the magnitude and genetic architecture of adaptive responses, yet it is rarely evaluated as a standalone variable in experimental evolution studies. Here, we evolved outcrossing populations of Saccharomyces cerevisiae for ∼200 generations across a spectrum of environmental stress from zero to moderate to high ethanol exposure, to examine how genomic responses vary with stress intensity. Across treatments, adaptation proceeded through many subtle allele and haplotype frequency shifts rather than large changes at single loci, consistent with a highly polygenic response. At loci associated with ethanol adaptation, the high stress treatment led to larger allele frequency changes compared to the moderate or no ethanol stress treatments, with the genomic architecture of adaptation becoming increasingly polygenic as selection intensity decreased. Moderate and high stress conditions engaged partially distinct biological pathways, indicating that selection intensity shapes both the magnitude and targets of adaptive change. Within this stress continuum, we also observed substantial, ongoing adaptation in control populations despite extensive prior domestication. Many alleles associated with this adaptation showed reduced or absent responses under ethanol stress, consistent with antagonistic pleiotropy. Consequently, laboratory adaptation can represent a major component of evolutionary change and may confound treatment-specific inferences when not explicitly accounted for. Broadly, our results demonstrate that selection intensity structures adaptive responses in experimental evolution and that continued laboratory adaptation remains an important force in these studies. Our findings underscore the importance of clearly-defined controls and careful consideration of selection intensity when interpreting or comparing across experimental evolution studies.

Hedgehog signaling is a conserved developmental pathway that patterns diverse tissues during vertebrate embryogenesis. In zebrafish, disruptions to the hedgehog pathway cause well-characterized defects in specific cell types including neurons and glia derived from the ventral neural tube. We inhibited hedgehog signaling by overexpressing the Gli3 repressor ubiquitously and performed bulk RNA-seq of 30 hours post-fertilization zebrafish embryos. Consistent with known roles of hedgehog signaling, we observed reduced expression of genes marking lateral floor plate, motor neurons, Kolmer-Agduhr cells, dopaminergic neurons, slow muscle cells, and anterior pituitary. Gene set enrichment analysis using marker genes derived from the Daniocell atlas also revealed downregulation of genes marking H+-ATPase-rich ionocytes, which are located in the embryonic skin and are responsible for osmotic homeostasis. Reduced expression of ionocyte-specific transporter genes and the transcription factor foxi3a suggests that Gli activity may play a previously unrecognized role in the specification of this cell type.

Disruption of ribosome biogenesis triggers nucleolar stress, a conserved cellular response that activates p53. We previously demonstrated that depletion of Nucleolar Complex Protein 1 (Noc1) in Drosophila wing imaginal discs impairs rRNA maturation and ribosome assembly, resulting in elevated p53 levels and apoptosis, hallmarks of nucleolar stress. The Drosophila p53 gene produces four mRNA isoforms, yet their individual contributions to nucleolar stress responses remain poorly understood. Using newly designed isoform-specific qPCR primers, we found that although all p53 isoforms exhibit moderate transcriptional changes following Noc1 reduction, the truncated isoform p53E is robustly and preferentially upregulated. Notably, p53E lacks the N-terminal transactivation domain and has been reported to negatively regulate p53-induced apoptosis in specific tissues. Furthermore, our analyses indicate that γ-H2AV accumulation arises from caspase-dependent apoptosis rather than primary genomic lesions, suggesting the activation of a p53-dependent stress pathway distinct from canonical genotoxic pathways. Together, these findings suggest that p53E may be part of a novel mechanism activated during nucleolar stress, providing insight into how cells adapt to defects in ribosome biogenesis.

The Coffee Leaf Miner (Lepidoptera: Lyonetiidae: Leucoptera coffeella) is a specialist herbivore and major global pest of coffee plants. Current pest control strategies primarily rely on chemical pesticides which in turn negatively impact both human health and ecological stability. Additionally, the emergence of insecticide-resistant populations underscores the urgent need for more specific and efficient pest management strategies. The development of novel techniques for controlling this insect pest requires rigorous interrogation of its physiology and interactions with host plants at a molecular/genetic level. To enable future research in this vein, we sequenced and assembled a draft L. coffeella genome using PacBio highly accurate long-reads (HiFi). Our assembly is comprised of 1615 contigs showing fragmentation, yet the majority of gene content is represented (BUSCO complete = 91.7%). We annotated 17467 protein-coding genes within our assembly, seven of which are core components of the small interfering RNA machinery. The expression of these genes was further confirmed via qPCR. This analysis - and the underlying genomic data - highlights potential targets for RNAi-based biopesticide development and will serve as the foundation for important future research aimed at protecting global coffee production from one of its most destructive pests.