G3: Genes|Genomes|Genetics最新文献

Reduced insulin/IGF signaling (IIS) in Caenorhabditis elegans increases starvation resistance in a daf-16/FoxO-dependent fashion, but it is unclear whether the effects of reduced IIS are entirely dependent on daf-16/FoxO. We used RNA sequencing and phenotypic analysis of L1 starvation resistance to assess epistasis between daf-2/InsR and daf-16/FoxO. We identified 4,653 putative DAF-16/FoxO targets, many of which had not been previously identified, providing a valuable reference data set. Differential gene expression and increased survival caused by disruption of daf-2/InsR during starvation are daf-16-dependent. The effect of daf-2/InsR on growth following starvation is largely but not entirely daf-16-dependent. Notably, daf-16 is dispensable for reproduction following extended starvation, and daf-2 loss preserves reproductive success independent of daf-16. These results show that the effects of reduced IIS during L1 starvation are daf-16/FoxO-dependent but that IIS engages 1 or more additional effectors to buffer larval growth and especially reproduction from persistent effects of early life starvation.

The genus Silene is an important model system for fields as diverse as sex chromosome evolution, speciation and disease ecology. However, genomic resources remain scarce in the genus. Here, we present a near chromosome-scale genome assembly and high-density linkage map for S. uniflora, a hermaphroditic/gynodioecious species which is an important model for rapid adaptation to anthropogenic disturbance and the role of phenotypic plasticity in adaptive evolution. Using a combination of long-read and Hi-C sequencing technologies, we generated a 1,268 Mb genome assembly with a scaffold N50 of 40.72 Mb and 682 Mb assembled into 12 chromosomes. We annotated the genome using evidence from transcriptome and protein mapping in combination with ab initio gene prediction, resulting in 41,603 protein-coding genes and a BUSCO completeness score of 91%. We also present a linkage map which we used to validate the genome assembly and estimate local recombination rate across the genome. Comparison to the only two other Silene species with chromosome-scale genome assemblies reveals widespread genome rearrangements in the genus, suggesting Silene may be a promising study system for the role of genome rearrangement in evolution, particularly in the evolution of sex chromosomes and adaptation.

The Micrapis subgenus, which includes the black dwarf honey bee (Apis andreniformis) and the red dwarf honey bee (Apis florea), remains underrepresented in genomic studies despite its ecological significance. Here, we present high-quality de novo genome assemblies for both species, generated using a hybrid sequencing approach combining Oxford Nanopore Technologies long reads with Illumina short reads. The final assemblies are highly contiguous, with contig N50 values of 5.0 Mb (A. andreniformis) and 4.3 Mb (A. florea), representing a major improvement over the previously published A. florea genome. Genome completeness assessments indicate high quality, with BUSCO scores exceeding 98.5% using the Hymenoptera database and k-mer analyses supporting base-level accuracy. Repeat annotation revealed a relatively low repetitive sequence content (∼6%), consistent with other Apis species. Using RNA sequencing data, we annotated 12,189 genes for A. andreniformis and 12,207 genes for A. florea, with ∼98% completeness in predicted proteomes. These genome assemblies provide a valuable resource for comparative and functional genomic studies, with the potential to offer new insights into the genetic basis of dwarf honey bee adaptations.

This study explored the genetics of cortisol (CL), cortisone (CN), DHEA (DH), and DHEA-S (DS) in hair of 610 pigs that was grown while they were exposed to infectious stressors (IS) from a natural polymicrobial disease challenge. Results were then contrasted with previous results on hair from these same pigs grown while experiencing non-infectious stressors (NIS), such as weaning, castration, transportation, and mixing. All pigs were genotyped for 50K SNPs and imputed to 650K SNPs. Heritability estimates for hormone levels in hair grown under IS ranged from 0.01 for DS to 0.27 for CL. Estimates of genetic correlations between levels of a hormone in hair grown in response to IS versus NIS were not significantly different from zero and was highest, at 0.52, for CL. Genome-wide association studies identified the same major QTL for CL in response to IS that was previously found for response to NIS, near the glucocorticoid receptor gene. The minor allele at the lead SNPs (frequency = 9%) significantly (p < 0.001) reduced CL under IS by 30±4% and CN by 23±6%, had no significant effect on DH or DS, and drove the genetic correlation between CL in hair grown under NIS versus IS. A comparative GSEA approach revealed that genomic windows that were associated with active forms of the stress hormones (CL and DH) tended to explain more variance during response to IS than to NIS, while the opposite was true for their inactive forms (CN and DS). These results may facilitate the selection of pigs that cope better with IS and NIS using hormone levels in hair as a non-invasive sample.

We present G2P Datasets, a novel, open-access repository of publicly available genomic datasets for plants and animals. G2P Datasets currently hosts more than 100 public genomic datasets, meticulously compiled from diverse publications. The repository hosts meta-data (including digital object identifier for the hosted datasets) and scripts that can be used to download and read each dataset hosted into an R-environment. Scientists can submit new datasets by completing an online form. Additionally, many of the curated datasets are accessible through Kaggle and through links that allow rapid download of formatted R-objects. A searchable database of meta-data allows users to search through datasets for more than 60 species of plants and animals in a variety of traits and sample sizes. The repository is accessible via a web app interface with a catalog and clear instructions to contribute by adding new datasets and through GitHub. By unifying genomic and phenotypic meta-data into a navigable platform, we aim to facilitate genome-to-phenotype research in plant and animal genetics. This article provides an overview of the repository's content, organization, and utility.

The analysis of gene function frequently requires the generation of mutants. Deep-mutational scanning (DMS) has emerged as a powerful tool to decipher important functional residues within genes and proteins. However, methods for performing DMS tend to be complex or laborious. Here, we introduce Tiled-Region Exchange (T-REx) Mutagenesis, which is a multiplexed modification of the EMPIRIC mutagenesis approach. Self-encoded removal fragments are cloned in parallel in non-overlapping gene locations and pooled. In a one-pot reaction, oligonucleotides are then swapped with their corresponding self-encoded removal fragments in bulk using a single Golden Gate reaction. To aid in downstream phenotyping, the library is then fused with unique DNA barcodes using the Bxb1 recombinase. We demonstrate this approach and its optimizations, to show that it is both easy to perform and efficient. This method offers simple and expedient means to create comprehensive mutagenesis libraries.

Human Lyme disease is a frequent tick-borne human disease that is caused by several species in the Borrelia burgdorferi sensu lato (BBSL) clade of the bacterial spirochete genus Borrelia. Although Borrelia lusitaniae does not appear to be a major cause of this disease, it has been isolated from human patients. This Borrelia species is unusual in that its vertebrate reservoir includes reptiles in Europe and North Africa. We describe here the complete genome sequences of three B. lusitaniae isolates, PotiB2T (the species type strain) and PotiB3 that represent a Southern Portugal-North African lineage and PoHL1 that represents a Northern Portugal-Central Europe lineage. Like other members of this genus, their genomes include linear chromosomes as well as numerous circular and linear plasmids. Their total genomes contain 1,202,579 bp (PotiB2T), 1,171,499 bp (PotiB3), 1,155,617 bp (PoHL1), and they carry eight (PotiB2T and PotiB3) or six (PoHL1) plasmids. We discuss the differences and similarities of these genomes with other members of the BBSL species group. A most unusual feature of the B. lusitaniae genomes is that their important cp26 plasmids are partially degraded dimers of the cp26 plasmid that is present in all other BBSL isolates analyzed to date. The cp26 plasmid has been shown to be essential for growth of B. burgdorferi sensu stricto B31T. The B. lusitaniae dimer cp26 plasmids carry multiple ospC genes of different types, which is unique to this species. OspC is an important protein that is required for the establishment of mammalian infection by B. burgdorferi B31T and tick salivary gland infection in B. afzelii. It remains unclear how genes of more than one OspC type in one strain might affect the infection process.

Amphibians of the Afrobatrachia clade represent a major component of sub-Saharan Africa's biodiversity, yet they remain underrepresented in genomic databases. Here, we present the first whole-genome assembly of the Common Reed Frog, Hyperolius viridiflavus viridiflavus Ahl, 1931 from Ethiopia, a member of the H. viridiflavus superspecies complex. The genome was sequenced using PacBio HiFi long-read technology and assembled de novo with HiFiasm, resulting in a 4.4 Gb assembly across 10,009 contigs with an N50 of 1.09 Mb. Genome completeness had a BUSCO score of 84.2%, with 29,809 annotated genes, including 27,983 protein-coding genes and 942 long non-coding RNAs. Despite a similar estimated size, scaffolding against the chromosome-level genome of Hyperolius riggenbachi Nieden, 1910 revealed low mapping coverage (0.0654 per base across 1 Mb windows), likely due to phylogenetic divergence (∼14 Mya) and high repeat content. The complete mitochondrial genome (23,453 bp) was also assembled and annotated, revealing structural differences from closely related species. Phylogenomic analyses using 416 single-copy BUSCO genes and mitochondrial 16S sequences confirmed the distinctiveness of H. v. viridiflavus within the Hyperoliidae. As only one other Afrobatrachian genome exceeds 50% completeness in public databases (H. riggenbachi), this genome expands the resources available for African frogs and supports future research in systematics and conservation. Further, when considering the complex taxonomy and evolutionary history of the H. viridiflavus superspecies complex, this genome can serve as a tool for species delimitation and conservation when compared to other species and subspecies within the clade.

Meiotic recombination ensures the fidelity of chromosome segregation in most organisms with sexual reproduction. The distribution of crossovers along chromosomes is governed in part by interference, which prevents multiple crossovers from occurring in close proximity, though not all crossovers are subject to interference. Neither the factors that control the strength of interference, nor the extent to which they vary within and between species, are well understood. Here, I confirm that crossover interference is stronger in male than in female meiosis in house mice (Mus musculus), provide the first estimate of the proportion of non-interfering crossovers in female mice, and show that this proportion is lower than in males. Interference is stronger on shorter chromosomes in both sexes, but the frequency of non-interfering crossovers is similar across the range of chromosome size. Together with evidence that interference varies across strains and subspecies, my results provide a foundation for studying the evolution and sexual dimorphism in this important feature of meiosis in mice.

CRISPR/Cas9 is a powerful tool for targeted genome editing experiments. Using CRISPR/Cas9, genes can be deleted or modified by inserting specific DNA sequences, encoding for fluorescent proteins, small peptide tags, or other modifications. Such experiments are essential for detailed gene and protein characterization. However, designing and cloning the corresponding constructs can be repetitive, time-consuming, and laborious. To assist users in CRISPR/Cas9-based genome engineering, we developed CrisprBuildr, an open-source, web-based application for designing modifications to their target genes. CrisprBuildr guides users through creating guide RNAs and repair template vectors to generate cloning maps. The application is designed for the Drosophila melanogaster genome but can serve as a template for other available genomes. We also created new tagging vectors using EGFP and mCherry combined with the small peptide SspB-Q73R for use in iLID-based optogenetic experiments.