G3: Genes|Genomes|Genetics最新文献

Foraging to acquire nutrients is an essential and sometimes risky behavior displayed by nearly all animals. Appropriately balancing foraging risks with nutrient requirements is pivotal for peak survival and reproduction, and metabolic state (i.e., how urgently the animal requires nutrients) is a strong modulator of risky foraging behavior. In this study, we asked what molecular signal allows C. elegans to change its foraging behavior in response to changes in its metabolic state. We used an assay of risky foraging behavior, where wild type worms increase risky foraging behavior after food deprivation, to screen for candidate genes. We found that DAF-2, the singular receptor in the C. elegans insulin/IGF-1 signaling (IIS) pathway, is necessary for worms to modulate risky foraging behavior in response to short-term food deprivation. Worms with mutations in genes upstream and downstream of daf-2 in the IIS pathway also exhibited a reduction in the effect of food deprivation. While a canonical understanding of the IIS pathway would suggest that the FOXO transcription factor DAF-16 is the primary downstream IIS pathway target, we found that DAF-16 was not required for worms to exhibit food-deprivation-driven changes in foraging behavior. Furthermore, we determined that the calsyntenin ortholog CASY-1, which allows DAF-2c to traffic to axons, is required for food deprivation to modulate risky foraging behavior. These results both validate the IIS receptor as a pivotal regulator of risky foraging behavior and suggest a multi-pronged downstream pathway. Overall, these data enrich our understanding of how organisms transduce metabolic state information to make vital decisions about when to engage in risky foraging behaviors.

The phagocytic receptor Draper (Drpr) mediates clearance of apoptotic cells in Drosophila melanogaster, yet how distinct drpr alleles and RNAi constructs differ in efficiency and phenotypic outcomes has not been systematically compared. Here, we evaluate multiple drprRNAi lines across UAS/GAL4, QUAS/QF2, and LexA/LexAop systems, alongside a newly generated CRISPR allele (drprCR1). Immunostaining confirmed efficient protein knockdown for all RNAi lines, while qRT-PCR revealed variable transcript reduction, with short-hairpin (SH) constructs more effective in glia and long-hairpin (LH) constructs likely acting at the translational level. Despite these differences, all RNAi lines caused strong phenotypes with persisting nurse cell nuclei in the ovary, and apoptotic cell persistence and neurodegenerative vacuoles in the brain, with SH constructs producing more severe defects. The newly generated drprCR1, which selectively deletes exons 5-6, abolished full-length Drpr-I while preserving shorter isoforms. Unlike the widely used drprΔ5 allele, drprCR1 uncouples ovarian and brain phenotypes: both alleles display ovarian defects, but drprCR1 shows markedly reduced neurodegeneration compared to drprΔ5. Together, our findings reveal construct- and allele-specific differences in RNAi knockdown and drpr isoform function, demonstrating that full-length Drpr is indispensable for ovarian cell clearance but less critical for neurodegeneration.

Drosophila males exhibit a highly stereotypic courtship ritual towards virgin females, which is comprised of a sequence of specific behavioral elements that depend on inputs from diverse sensory modalities. Particularly, the visual system of the male plays an important role in detecting salient patterns, colors, and motion cues from conspecifics, which can promote or inhibit specific aspects of male courtship such as chase and song production. Here, we use a computer vision and machine learning-based approach, with a simplified courtship paradigm, to show that males also depend on visual cues to determine the anterior-posterior body axis of females, which drives the specific spatial patterns of distinct behavioral courtship elements. We show that the recognition of the female body axis depends, at least in part, on the visual recognition of female eyes as an anterior landmark. Furthermore, we find that in the absence of visual input, courting males adjust not only their relative spatial courtship positioning, but also the relative frequencies at which they engage in each specific courtship element. Finally, analyses of the contributions of specific visual projection neurons to the recognition of the female body axis indicate that, although it is driven by a seemingly simple visual cue, the spatiotemporal release patterns of each individual courtship element appear to depend on the activity of multiple independent populations of visual projection neurons. Together, our results provide novel insights into the possible role of visual anatomical features in driving complex social interactions between conspecifics.

Many insects can rapidly evolve resistance to artificial insecticides through changes in toxin target proteins. Over longer timescales, insects also evolve resistance to naturally occurring toxins to exploit new ecological niches, but the underlying mechanisms often remain poorly understood. A classic example is Drosophila sechellia, an extreme specialist for the ripe noni fruit of Morinda citrifolia. Noni is toxic for other insects - including D. sechellia's close relatives D. simulans and D. melanogaster - due to this fruit's high content of octanoic acid (OA). However, the mechanistic bases of OA susceptibility and resistance across species remain unclear. Here, we first show that the species-specific tolerance of OA is independent of these drosophilids' distinct microbiomes. Screening large, genetically-diverse panels of D. melanogaster and D. simulans strains revealed broad variation in OA resistance, with some lines surviving as well as D. sechellia. Resistance to OA does not correlate with resistance of these lines to other insecticides, implying a distinct toxicity mode-of-action. Genome-wide association and transcriptome-to-phenotype analyses identified multiple genes linked to OA resistance, with diverse expression patterns and functions, including epithelial septate junction formation, and lipid transport. Loss-of-function analysis in D. melanogaster confirmed that at least two of these - Bez, a CD36-family fatty acid transporter, and CG13003, a putative extracellular matrix component - positively contribute to OA resistance. Integration of our findings with those from previous complementary genetic approaches supports a model in which OA has no singular target, and that resistance is defined by multigenic and multi-tissue defense mechanisms.

Advances in long-read sequencing have made it easier and more cost effective to generate high-quality genome assemblies. However, assessing assembly quality remains a challenge, as existing tools often focus on a few metrics and/or require a reference assembly for comparison. Furthermore, the number of available metrics and associated tools for genome evaluation have expanded in recent years, making it more difficult for researchers to easily use and develop comprehensive pipelines. To address this, we developed the Post-Assembly Quality manager (PAQman), a tool that lowers the barrier to entry for assembly quality assessment by measuring seven reference-free features of genome quality within a single framework: Contiguity, Gene content, Completeness, Accuracy, Correctness, Coverage, and Telomerality. PAQman integrates multiple commonly used tools alongside custom scripts, requiring users to provide only a query genome assembly and its underlying long-read data, while providing a streamlined and consistent framework for quality assessment across datasets.

Analyzing genomic variants in large datasets composed of short-read sequencing data is a process that requires multiple steps and computational tools, which makes it a complicated task that is difficult to reproduce across projects and laboratories. To address this need, we developed a reproducible and scalable Snakemake workflow called WeavePop, which aligns samples to selected references, obtains reference-based assemblies, annotations, and sequences, and identifies small variants and copy-number variants in eukaryotic haploid organisms. All the results are integrated into a database that can be easily shared and explored through a graphical web interface provided alongside the workflow, making the discovery of variants in a population of study very simple. WeavePop is available from GitHub (https://github.com/magwenelab/WeavePop) for Linux operating systems. Here, we exemplify the use of WeavePop in a large collection of isolates of the pathogenic fungus Cryptococcus neoformans.

Mutation is a major force of evolution and its accumulation is suggested to be influenced by environmental and genetic factors in both unicellular and multicellular species. While ample of evidence showed an effect of temperature on mutation rate, the influence of diet is less well characterized, especially in multicellular organisms. Here, we present mutation accumulation (MA) rate differences for the same nematode species comparing a variety of bacterial diets. MA rates were estimated from whole-genome sequencing data of MA lines of different natural isolates of the free-living nematode Pristionchus pacificus on various bacterial diets isolated from Pristionchus-associated environments. Average single-nucleotide mutation rates varied between 1.69*10-9 and 2.23*10-9 nucleotide site-1*generation-1, whereas the average insertion rates varied between 1.53*10-10 and 2.90*10-10 nucleotide site-1*generation-1 and the average deletion accumulation rates varied between 3.01*10-10 nucleotide site-1*generation-1 and 4.51*10-10 nucleotide site-1*generation-1. We observed around a 1.4-fold mutation rate difference among groups on bacterial diets. Despite mutation-rate differences, the mutation spectra are largely unchanged. These results suggest that bacterial diet influences MA rate without drastically changing other mutational features.

Manipulating gene expression in a tissue-specific and temporally controlled manner is essential for understanding the function of the focal genes. Still, in many cases, the limited availability of specific promotors to drive ectopic manipulation remains a restricting factor in developing organs, even in Drosophila. Developing external genitalia is one such organ with a complex anatomical structure shaped by a joint regulatory network of many transcription factors. To overcome the restriction, we employed the infrared laser-evoked gene operator system (IR-LEGO), in which infrared laser (1,480 nm) irradiation induces gene expression under the control of a heat shock promoter. Pupal genital structures were irradiated at approximately 24 or 48 hours after puparium formation. We tested a range of laser power and depth to the target structure by a reporter assay using green fluorescent protein, which was induced under the control of the heat shock protein 70 promoter (hs-GAL4). In previous studies, the IR-LEGO has been used as a tool to induce ectopic transgene expression. In this study, we attempted to knock down genes such as yellow (y) and odd-paired (opa) ectopically by RNAi using the GAL4/UAS system. The results demonstrated that this technique has a high potential in manipulating transcript abundance levels in small groups of cells in specific genital structures to unravel novel functions of genes involved in the morphogenesis of species-specific and rapidly evolving anatomical structures.

We developed a haplotype-resolved, chromosome-scale genome assembly of the Urochloa humidicola (Rendle) Morrone & Zuloaga cultivar Tully, an apomictic C4 forage grass cultivated in the tropics worldwide. We assembled a 4.1 Gb genome into 48 chromosomes (2n = 8x = 48), capturing 99.5% of the BUSCO markers, and annotating 259,254 protein-coding genes. Subgenome assignment revealed an octoploid AABBBBCC structure with three ancestral lineages (A, B, C), and an aneuploid composition of 14A, 22B, and 12C chromosomes. Comparative analyses with related Urochloa species identified U. dictyoneura and U. arrecta as potential progenitors of the B and C subgenomes, respectively. The likely progenitor of the A subgenome remains an unknown wild species from the Humidicola clade. Analysis of LTR-retrotransposons and gene collinearity further indicated a close relationship between A and B ancestries, and a distinct evolutionary path for C. Competitive read mapping across additional U. humidicola accessions supported multiple evolutionary histories in the species, with AABBBB (lacking C ancestry), being the most common. We found that previously described subpopulation structures can be explained by the presence or absence of C ancestry, and that sexual U. humidicola are likely to be autopolyploid from the B ancestry. The genome is available as assembly GCA_965614515.2. This assembly provides the first complete reference for U. humidicola and reveals a multi-ancestral origin and reticulated evolution in U. humidicola. It provides a foundation for studying complex polyploid evolution, regulation of apomixis and biological nitrification inhibition, and molecular breeding strategies.

The two-spotted cricket, Gryllus bimaculatus, is a key hemimetabolous model organism for developmental biology, neuroscience, and regeneration. The existing reference genome is, however, highly fragmented into 47,877 scaffolds, hampering chromosome-scale analyses for these fields. Here, we report a high-quality, chromosome-scale genome assembly for the white-eyed mutant strain of this cricket, generated using a combination of Nanopore and PacBio HiFi long reads, integrated with Hi-C data. The final 1.62 Gbp assembly achieves a scaffold N50 of 107.4 Mbp, a significant improvement in contiguity over the previous 6.3 Mbp N50. We anchored 94.45% of the assembly into 15 pseudomolecules, consistent with the known karyotype (n = 15). The genome completeness (BUSCO v6.0.0 insecta_odb12) reached 98.1%. We also updated the annotation, identifying 14,964 protein-coding genes. This gene set shows markedly improved completeness (BUSCO v6.0.0 insecta_odb12: 95.7%) compared with the previous annotation (81.2%) and successfully recovers all nine essential neuropeptide genes previously reported as missing from the draft assembly. This chromosome-scale genomic resource provides an essential foundation for comparative and functional genomics in G. bimaculatus.