G3: Genes|Genomes|Genetics最新文献

Hybridization is a major force driving diversification, migration, and adaptation in Quercus species. While population genetics and phylogenetics have traditionally been used for studying these processes, advances in sequencing technology now enable us to incorporate comparative and pan-genomic approaches as well. Here we present a highly contiguous, chromosome-scale and haplotype-resolved genome assembly for the southern live oak, Quercus virginiana, the first reference genome for section Virentes, as part of the American Campus Tree Genomes (ACTG) program. Originating from a clone of Auburn University's historic "Toomer's Oak," this assembly contributes to the pool of genomic resources for investigating recombination, haplotype variation, and structural genomic changes influencing hybridization potential in this clade and across Quercus. It also provides insights into the architecture of the putative centromeric regions within the genus. Alongside other oak references, the Q. virginiana genome will support research into the evolution and adaptation of the Quercus genus.

Istocheta aldrichi Mesnil 1953 (Diptera: Tachinidae), is native to Japan, and has recently become an important biological control agent of the Japanese beetle, Popillia japonica (Coleoptera: Scarabaeidae), a pest with >300 host plants, including roses, linden trees, and numerous agricultural crops. During the past decade, I. aldrichi's range has greatly expanded across North America, particularly in Quebec and Ontario, Canada, and in the Midwest U.S. In Minnesota, parasitism of Japanese beetles by I. aldrichi was documented in commercial apple orchards in 2021, and has since spread to multiple locations, highlighting its importance as a natural enemy. To facilitate research on I. aldrichi and other tachinid flies we present a haploid reference genome generated from a single unsexed individual. The final genome assembly is 875.3 Mbp contained in 1,041 scaffolds, with an N50 of 4.77 Mbp, and 99.5% complete Diptera BUSCOs present. We also present a complete mitogenome and use comparative genomics across 19 tachinid species to identify unique features of I. aldrichi. Specifically, we find that tachinids as a whole have undergone rapid copy number changes in 935 gene families, largely related to metabolism and morphogenesis. While many tachinid lineages have experienced contractions in gene families, I. aldrichi is characterized by a relatively high number of gene family expansions, many of which are predicted to function in metal ion transport. The I. aldrichi reference genome will further research opportunities on these parasitic flies, including their potential for biocontrol of P. japonica.

A novel method for mapping the interphase genome architecture in Drosophila polytene chromosomes is proposed. The method is based on physical mapping of the boundaries between interbands, gray bands, and black bands. Mapping relies on three criteria: the 4HMM bioinformatic model that considers the associations between each of the four chromatin states and polytene chromosome structures and the findings of ChIP-seq analysis in salivary glands for two critical markers: the CHRIZ/CHRO protein localized in housekeeping gene promoters and H3K36me3 histone modification, a marker of transcriptional elongation. For mapping the 1AF region of the X chromosome, FISH probes were selected from AQUAMARINE chromatin (interbands) at the boundary with black bands, which provided precise coordinates of the edges of black bands (localization of the developmental genes). The localization of promoters and housekeeping gene bodies was then identified by ChIP-seq analysis for CHIRIZ and H3K36me3 in salivary glands (the interbands and gray bands, respectively). These maps will allow one to better understand the architecture of an actively functioning genome.

Genome sequence contamination has a variety of causes and can originate from within or between species. Previous research focused on contamination between distantly related species or on prokaryotes. Here we test for intra-species contamination by mapping short read genome data to a reference and visualizing the frequency of reads with single nucleotide di_erences from the reference. Out of 1,298 publicly available genome sequences investigated for Saccharomyces cerevisiae, a small number (8 genomes) show at least 5% contamination. Contamination rates di_ered however among sequencing centers: one unusually large study had a low contamination rate (below 0.2%) but the contamination rate was higher for other studies (2% or 15% of genomes). Using genome data contaminated in silico to known degrees, we showed that contamination is recognizable in plots with unexpected secondary allele (B-allele) frequencies of at least 5% and measured contamination e_ects on admixture and phylogenetic analysis in two fungal species. With a standard base calling pipeline, we found that contaminated genomes super_cially appeared to produce good quality genome data. Yet as little as 5-10% genome contamination was enough to change phylogenetic tree topologies and make contaminated strains appear as hybrids between lineages (genetically admixed). We recommend the use of B-allele frequency plots to screen genome resequencing data for intra-species contamination.

The Galápagos Petrel (Pterodroma phaeopygia) is a critically endangered procellariiform seabird endemic to the Galápagos Islands. Once abundant, its populations have sharply declined due to invasive predators, habitat degradation, and destruction of nest burrows. Although the species is distributed across several islands, the demographics of each population and their genetic relationships are poorly understood. To facilitate future studies of population structure and connectivity, we present the first high-quality reference genome for the Galápagos Petrel. The genome was assembled solely from ultra-long Oxford Nanopore sequence data collected from an adult female sampled on San Cristóbal Island. Sequencing was performed at the Galapagos Science Center, building local capacity for the generation of genomic data in remote regions. The final nuclear genome assembly spans 1.35 Gb in length, with average coverage of 36.07x, scaffold N50 of 74.2 Mb, and a BUSCO completeness of 99.95%. The genome comprises 41 pseudo-chromosomes, with 23 spanning from telomere to telomere and 16, including W and Z chromosomes, containing a single telomere. Chromosomal-level scaffolding by reference was performed using the genome of Cory's Shearwater (Calonectris borealis) GCA_964196065.2 (Arànega et al., 2024), a closely related species. This reference genome provides a foundational tool for comparative genomics, conservation biology, and functional studies of island-endemic avifauna, and demonstrates that recent advances in basecalling and error correction now enable ONT-only datasets to achieve assemblies comparable in quality to those generated using short-read or PacBio HiFi data. It will also facilitate future efforts to characterize genetic diversity, structural variation, and adaptive responses in this critically endangered species.

Single nucleotide polymorphism (SNP) arrays have become increasingly popular due to their affordability, commercial availability, statistical power, and reproducibility. These arrays are being developed commercially for a wide range of species in various density formats. In this study, we evaluated the ability of commercially available medium-density (72,732 SNPs) and high-density SNP (702,183 SNPs) arrays for white-tailed deer (Odocoileus virginianus) to accurately identify known genetically related individuals within a wild population. We also assessed the impact of SNP filtering thresholds on relatedness analyses and compared the performance of four common relatedness softwares: KING, COLONY, Sequoia, and COANCESTRY, on these known related pairs. Our analysis revealed that the medium-density array exhibited greater tolerance to filtering and lower sensitivity to bioinformatic pipelines, making it a favorable balance between cost, computational time, and statistical power for analyses such as population structure. Additionally, we found that reducing missing data, specifically by using a subset of 600 loci with no missing data, combined with the relatedness estimator Sequoia (which allows the inclusion of life history data), yielded the most computationally efficient and accurate results. These findings offer valuable insights into the optimal SNP array size, appropriate filtering thresholds, and the most effective genetic relatedness methods for wildlife population studies.

Nutrition significantly influences various life-history traits in organisms, impacting decisions about growth, reproduction, and longevity. Accordingly, previous studies in Drosophila have demonstrated that diet affects transcription regulation, with many genes exhibiting altered expression for example between protein- and carbohydrate-rich diets. It remains challenging, however, to distinguish between metabolic adaptations to the different diets themselves and regulation pertaining to life history responses to nutrient availability. In this study, we explore the transcriptomic responses of virgin and mated flies to changes in nutritional environments, with the aim to differentiate changes in metabolism from changes due to altered reproductive investment. Using RNA-seq, we show that while males only respond to diet, both nutritional conditions and mating status affect gene expression in females. By comparing responses between males and females and virgin and mated flies, we are able to differentiate between basal dietary responses and reproductive adaptations, with the latter involving eight times as many genes as the former. We identify GATA family transcription factors and the heat-shock factor (Hsf) as crucial regulators of diet-dependent reproductive genes. These findings enhance our understanding of the complex interactions between nutrition and reproductive strategies in Drosophila.

The exchange of genetic material during meiosis requires the formation and repair of DNA double-strand breaks (DSBs), which may not be repaired with perfect fidelity. If meiotic exchange is mutagenic, this would add to the costs of sexual reproduction and affect patterns of genome evolution, but much of the evidence for this is indirect. In the fruit fly Drosophila melanogaster, it is possible to completely suppress endogenous DSBs while retaining normal fertility. We took advantage of this system to generate fly strains with and without a mutant allele of mei-P22, a gene that is essential for meiotic DSB formation, on a common genetic background. This allowed us to investigate the relationship between DSBs and genome-wide mutation patterns, using a mutation accumulation design to allow un-selected spontaneous mutations to be observed. Following 30 generations of mutation accumulation, we identified over 1800 mutations by whole-genome sequencing. The presence of meiotic DSBs had little effect on the rate and spectrum of point mutations. We found that mutations were more likely to occur in areas of the genome with higher rates of crossover recombination, regardless of whether meiotic DSBs were occurring. We also found that the rate of transposable element insertions across multiple TE families was substantially elevated in the group lacking meiotic DSBs, suggesting that host suppression of mobile genetic elements is closely associated with meiotic recombination mechanisms.

Natural isolates of the yeast Saccharomyces cerevisiae were evolved under a transfer protocol that selected for cell separation and against clumpy growth. Whole-genome sequencing of haploid populations revealed strong selection to deactivate AMN1, a known regulator of post-mitotic cell separation, as well as multiple instances of loss-of-function mutations on the Rim101 pathway, pointing to a previously unknown role of the Rim101 pathway in regulating cell separation. In diploid populations, we observed repeated large partial deletions of chromosome III caused by fusions of the mating type loci MAT and HMR (Hawthorne's deletion) or MAT and HML (Strathern's circle). We measured the spontaneous rate of Hawthorne's deletion and found that it is within an order of magnitude of previously measured rates of whole-chromosome aneuploidy. A diploid population in which neither large deletion was detected instead fixed a heterozygous nonsynonymous mutation to the calcium channel CCH1, also pointing to a novel role for this gene in relation to cell separation.

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.