G3: Genes|Genomes|Genetics最新文献

Biological control to manage plant diseases is an environmentally friendly alternative to using chemical pesticides. However, little is known about the role of genetic variation in plants affecting the efficacy of biological control agents (BCAs). The aim of this study was to explore the genetic variation in winter wheat for disease susceptibility to fusarium foot rot caused by Fusarium graminearum and variation in biocontrol efficacy of the fungal BCA Clonostachys rosea to control the disease. In total, 190 winter wheat genotypes were evaluated under controlled conditions in two treatments, i.e. (i) F. graminearum (Fg) and (ii) F. graminearum infection on C. rosea treated seeds (FgCr). Alongside disease severity, plant growth-related traits such as shoot length and root length were also measured. Comparison of genotypes between the two treatments enabled the dissection of genotypic variation for disease resistance and C. rosea efficacy. The study revealed significant variation among plant genotypes for fusarium foot rot susceptibility and other growth traits in treatment Fg. Moreover, significant variation in C. rosea efficacy was also observed in genotype contrasts between the two treatments for all traits. Using a 20K marker array, a genome-wide association study was also performed. We identified a total of 18 significant marker-trait associations for disease resistance and C. rosea efficacy for all the traits. Moreover, the markers associated with disease resistance and C. rosea efficacy were not co-localized, highlighting the independent inheritance of these traits, which can facilitate simultaneous selection for cultivar improvement.

The Period genes (Per) play essential roles in modulating the molecular circadian clock timing in a broad range of species, which regulates the physiological and cellular rhythms through the transcription-translation feedback loop. While the Period gene paralogs are widely observed among vertebrates, the evolutionary history and the functional diversification of Per genes across vertebrates are not well known. In this study, we comprehensively investigated the evolution of Per genes at the copy number and sequence levels, including de novo binding motif discovery by comparative genomics. We also determined the lineage-specific transcriptome landscape across tissues and developmental stages and phenotypic effects in public RNA-seq data sets of model species. We observed multiple lineage-specific gain and loss events Per genes, though no simple association was observed between ecological factors and Per gene numbers in each species. Among salmonid fish species, the per3 gene has been lost in the majority, whereas those retaining the per3 gene exhibit not a signature of relaxed selective constraint but rather a signature of intensified selection. We also determined the signature of adaptive diversification of the CRY-binding region in Per1 and Per3, which modulates the circadian rhythm. We also discovered putative regulatory sequences, which are lineage-specific, suggesting that these cis-regulatory elements may have evolved rapidly and divergently across different lineages. Collectively, our findings revealed the evolution of Per genes and their fine-tuned contribution to the plastic and precise regulation of circadian rhythms in various vertebrate taxa.

An animal's locomotor rate is an important indicator of its motility. In studies of the nematode Caenorhabditis elegans (C. elegans), assays of the frequency of body bending waves have often been used to discern the effects of mutations, drugs, or aging. Traditional manual methods for measuring locomotor frequency are low in throughput and subject to human error. Most current automated methods depend on image segmentation, which requires high image quality and is prone to errors. Here, we describe an algorithm for automated estimation of C. elegans locomotor frequency using image invariants, i.e. shape-based parameters that are independent of object translation, rotation, and scaling. For each video frame, the method calculates a combination of 8 Hu's moment invariants and a set of maximally stable extremal regions (MSER) invariants. The algorithm then calculates the locomotor frequency by computing the autocorrelation of the time sequence of the invariant ensemble. Results of our method show excellent agreement with manual or segmentation-based results over a wide range of frequencies. We show that compared to a segmentation-based method that analyzes a worm's shape and a method based on video covariance, our technique is more robust to low image quality and background noise. We demonstrate the system's capabilities by testing the effects of serotonin and serotonin pathway mutations on C. elegans locomotor frequency.

Chronic pain has an enormous impact on the quality of life of billions of patients, families, and caregivers worldwide. Current therapies do not adequately address pain for most patients. A basic understanding of the conserved genetic framework controlling pain may help us develop better, non-addictive pain therapies. Here, we identify new conserved and druggable analgesic targets using the tissue-specific functional genomic screening of candidate "pain" genes in fly. From these efforts, we describe 23 new pain genes for further consideration. This included Acsl, a fatty acid-metabolizing enzyme, and mammalian orthologs involved in arachidonic acid metabolism. The Acsl knockdown and mutant larvae showed delayed nocifensive responses to localized and global noxious heat. Mechanistically, the Acsl knockdown reduced dendritic branching of nociceptive neurons. Surprisingly, the pain phenotype in these animals could be rescued through dietary intervention with vitamin B5, highlighting the interplay between genetics, metabolism, and nutrient environment to establish sensory perception thresholds. Together, our functional genomic screening within the sensory nociceptor has identified new nociception genes that provide a better understanding of pain biology and can help guide the development of new painkillers.

The genetic effective size (Ne) is arguably one of the most important characteristics of a population as it impacts the rate of loss of genetic diversity. Methods that estimate Ne are important in population and conservation genetic studies as they quantify the risk of a population being inbred or lacking genetic diversity. Yet there are very few methods that can estimate the Ne from data from a single population and without extensive information about the genetics of the population, such as a linkage map, or a reference genome of the species of interest. We present ONeSAMP 3.0, an algorithm for estimating Ne from single nucleotide polymorphism data collected from a single population sample using approximate Bayesian computation and local linear regression. We demonstrate the utility of this approach using simulated Wright-Fisher populations, and empirical data from five endangered Channel Island fox (Urocyon littoralis) populations to evaluate the performance of ONeSAMP 3.0 compared to a commonly used Ne estimator. Our results show that ONeSAMP 3.0 is broadly applicable to natural populations and is flexible enough that future versions could easily include summary statistics appropriate for a suite of biological and sampling conditions. ONeSAMP 3.0 is publicly available under the GNU General Public License at https://github.com/AaronHong1024/ONeSAMP_3.

Drosophila prolongata is a member of the melanogaster species group and rhopaloa subgroup native to the subtropical highlands of Southeast Asia. This species exhibits an array of recently evolved male-specific morphological, physiological, and behavioral traits that distinguish it from its closest relatives, making it an attractive model for studying the evolution of sexual dimorphism and testing theories of sexual selection. The lack of genomic resources has impeded the dissection of the molecular basis of sex-specific development and behavior in this species. To address this, we assembled the genome of D. prolongata using long-read sequencing and Hi-C scaffolding, resulting in a highly complete and contiguous (scaffold N50 2.2 Mb) genome assembly of 220 Mb. The repetitive content of the genome is 24.6%, the plurality of which are long terminal repeats retrotransposons (33.2%). Annotations based on RNA-seq data and homology to related species revealed a total of 19,330 genes, of which 16,170 are protein-coding. The assembly includes 98.5% of Diptera BUSCO genes, including 93.8% present as a single copy. Despite some likely regional duplications, the completeness of this genome suggests that it can be readily used for gene expression, genome-wide association studies (GWAS), and other genomic analyses.

Understanding the signaling pathways in which genes participate is essential for discovering the etiology of diseases in humans. The model organism, Drosophila melanogaster, has been crucial in understanding the signaling pathways in humans, given the evolutionary conservation of a significant number of genes between the two species. Genetic screens using Drosophila are a useful way of testing large number of genes to study their function and roles within signaling pathways. We conducted a large-scale genetic screen to identify which human genes cause an alteration in the morphology of the Drosophila eye. The GMR-Gal4 was employed to activate a single UAS-human gene in the eye tissue. In total, we screened 802 UAS-human gene stocks, corresponding to 787 human protein-coding genes, for the ability to influence eye development. We found that overexpression of 64 human genes were capable of disrupting eye development, as determined by phenotypic changes in eye texture, size, shape, bristle morphology, and ommatidia organization. Subsequent analysis revealed that the fly genome encodes proteins that are homologous to a majority of the 64 human genes, raising the possibility that overexpression of these transgenes altered eye development by altering the activity of evolutionarily conserved developmental signaling pathways. Consistent with this hypothesis, a secondary screen demonstrated that overexpression of fly homologs produced phenotypes that mimicked those produced by overexpression of the human gene. Our screening has identified 64 human genes capable of inducing phenotypes in the fly, offering a foundation for ongoing research aimed at understanding functionally conserved pathways across species.

We report a virus infecting Entomophthora muscae, a behavior-manipulating fungal pathogen of dipterans. The virus, which we name Berkeley Entomophthovirus, is a positive-strand RNA virus in the iflaviridae family of capsid-forming viruses, which are mostly known to infect insects. The viral RNA is expressed at high levels in fungal cells in vitro and during in vivo infections of Drosophila melanogaster, and virus particles can be seen intracellularly in E. muscae. This virus, of which we find two closely related variants in our culture of E. muscae, is also closely related to three different viruses reported from metagenomic surveys, two of which were isolated from wild dipterans, and a third isolated from wild ticks. By analyzing sequencing data from these earlier reports, we find abundant reads aligning to E. muscae specifically in the samples from which viral reads were sequenced. These data establish a wide and perhaps obligate association with E. muscae in the wild, consistent with our laboratory data that E. muscae is the host for these closely related viruses. Because of this, we propose the name Entomophthovirus (EV) for this group of highly related virus variants. As other members of the iflaviridae have been reported to cause behavioral changes in insects, we speculate on the possibility that EV plays a role in the behavioral manipulation of flies infected with E. muscae.

Flavonoids are secondary metabolites associated with plant seed coat and flower color. These compounds provide health benefits to humans as anti-inflammatory and antioxidant compounds. The expression of the late biosynthetic genes in the flavonoid pathway is controlled by a ternary MBW protein complex consisting of interfacing MYB, beta-helix-loop-helix (bHLH), and WD40 Repeat (WDR) proteins. P, the master regulator gene of the flavonoid expression in common bean (Phaseolus vulgaris L.), was recently determined to encode a bHLH protein. The T and Z genes control the distribution of color in bean seeds and flowers and have historically been considered regulators of the flavonoid gene expression. T and Z candidates were identified using reverse genetics based on genetic mapping, phylogenetic analysis, and mutant analysis. Domain and AlphaFold2 structure analyses determined that T encodes a seven-bladed β-propeller WDR protein, while Z encodes a R2R3 MYB protein. Deletions and SNPs in T and Z mutants, respectively, altered the 3D structure of these proteins. Modeling of the Z MYB/P bHLH/T WDR MBW complex identified interfacing sequence domains and motifs in all three genes that are conserved in dicots. One Z MYB motif is a possible beta-molecular recognition feature (β-MoRF) that only appears in a structured state when Z MYB is modeled as a component of a MBW complex. Complexes containing mutant T and Z proteins changed the interaction of members of the complex in ways that would alter their role in regulating the expression of genes in the flavonoid pathway.

Island species are highly vulnerable due to habitat destruction and their often small population sizes with reduced genetic diversity. The Hawaiian Islands constitute the most isolated archipelago on the planet, harboring many endemic species. Kokia is an endangered flowering plant genus endemic to these islands, encompassing 3 extant and 1 extinct species. Recent studies provided evidence of unexpected genetic diversity within Kokia. Here, we provide high-quality genome assemblies for all 3 extant Kokia species, including an improved genome for Kokia drynarioides. All 3 Kokia genomes contain 12 chromosomes exhibiting high synteny within and between Kokia and the sister taxon Gossypioides kirkii. Gene content analysis revealed a net loss of genes in K. cookei compared to other species, whereas the gene complement in K. drynarioides remains stable and that of Kokia kauaiensis displays a net gain. A dated phylogeny estimates the divergence time from the last common ancestor for the 3 Kokia species at ∼1.2 million years ago (mya), with the sister taxa (K. cookei + K. drynarioides) diverging ∼0.8 mya. Kokia appears to have followed a stepping-stone pattern of colonization and diversification of the Hawaiian archipelago, likely starting on low or now submerged older islands. The genetic resources provided may benefit conservation efforts of this endangered endemic genus.