Search Results (78)

Ochrolechia is a diverse and charismatic lineage of both sexually and asexually reproducing lichens, with centers of species richness in northern temperate areas of the world, including North America. As part of recent work to comprehensively inventory the lichens of the Indian Peaks Wilderness (Arapaho–Roosevelt National Forest, Front Range Mountains, Colorado), we discovered material of a sorediate member of the genus to which no existing names could be applied. This material was collected in very remote, extremely difficult-to-access mid-montane forests of the west slope of the Indian Peaks Wilderness, in a steep and jagged off-trail drainage (Hell Canyon). Subsequent study of this material along with review of pre-existing collections at the COLO Herbarium revealed it to represent a new scientific species. We here formally describe Ochrolechia raynori, in honor of Seth Raynor who led the Indian Peaks Wilderness lichen inventory. We additionally document the occurrence of Dactylospora parasitica on this new lichen species. Ochrolechia raynori is distinctive for its continuous, smooth, shiny thallus that bears discrete soralia and coarse soredia, its occurrence on mosses and other lichens that overgrow rocks, and its chemistry. We generated a molecular phylogeny of this and other members of Ochrolechia using the nrITS locus and show O. raynori to be sister to the widespread, sexually reproducing species O. upsaliensis. This occurrence of an asexual species that is sister to a sexual species is consistent with the “species pair” hypothesis in lichenology, which suggests an intimate role of reproductive mode divergence in the process of speciation. Examination of the phylogeny yielded evidence of four additional pairs in Ochrolechia, for a total of five species pairs, which indicates that this phenomenon may be a common occurrence in this lineage. IUCN Conservation Assessment of Ochrolechia raynori revealed the species to be best considered as Critically Endangered. However, we expect that continued efforts to inventory the lichens of the southern Rocky Mountains, especially in some of its wildest, most remote regions in similar habitats, will likely result in the discovery of additional populations of this remarkable new species. Full article

Wheat stripe rust (Puccinia striiformis f. sp. tritici, Pst) resistance and agronomic traits are crucial determinants of wheat yield. Elucidating the quantitative trait loci (QTLs) associated with these essential traits can furnish valuable genetic resources for improving both the yield potential and disease resistance in wheat. Lantian 31 is an excellent Chinese winter wheat cultivar; multi-environment phenotyping across three ecological regions (2022–2024) confirmed stable adult-plant resistance (IT 1–2; DS < 30%) against predominant Chinese Pst races (CYR31–CYR34), alongside superior thousand-kernel weight (TKW) and kernel morphology. Here, we dissected the genetic architecture of these traits using a total of 234 recombinant inbred lines (RILs) derived from a cross between Lantian 31 and the susceptible cultivar Avocet S (AvS). Genotyping with a 15K SNP array, complemented by 660K SNP-derived KASP and SSR markers, identified four stable QTLs for stripe rust resistance (QYrlt.swust-1B, -1D, -2D, -6B) and eight QTLs governing plant height (PH), spike length (SL), and kernel traits. Notably, QYrlt.swust-1B (1BL; 29.9% phenotypic variance) likely represents the pleiotropic Yr29/Lr46 locus, while QYrlt.swust-1D (1DL; 22.9% variance) is the first reported APR locus on chromosome 1DL. A pleiotropic cluster on 1B (670.4–689.9 Mb) concurrently enhanced the TKW and the kernel width and area, demonstrating Lantian 31’s dual utility as a resistance and yield donor. The integrated genotyping pipeline—combining 15K SNP discovery, 660K SNP fine-mapping, and KASP validation—precisely delimited QYrlt.swust-1B to a 1.5 Mb interval, offering a cost-effective model for QTL resolution in common wheat. This work provides breeder-friendly markers and a genetic roadmap for pyramiding durable resistance and yield traits in wheat breeding programs. Full article

The fungal family Mortierellaceae represents ubiquitous and ecologically significant components of soil ecosystems across terrestrial habitats. Through an integrative taxonomic approach combining multi-locus phylogenetic analyses (ITS, LSU, SSU rDNA, RPB1, and Act) with detailed morphological examinations of rhizosphere soil isolates, four novel species within this family were proposed. This study elucidates the morphological distinctions of novel species from allied species and the phylogenetic relationships among the novel and existing species within the family. Linnemannia rotunda sp. nov. (closely related to L. longigemmata) is distinguished by its globose sporangia and sporangiospores. Mortierella acuta sp. nov. (clustering with M. yunnanensis) is characterized by spiky collarettes. Mortierella oedema sp. nov. (a sister to M. macrocystis) exhibits distinctive ampulliform swellings. Mortierella tibetensis sp. nov. (clustering with M. parvispora) is named for its geographic origin in Tibet. As the eighth installment in a systematic investigation of early diverging fungal groups in China, this work expands the global taxonomic inventory of Mortierellaceae to 148 species, underscoring the ongoing discovery of cryptic biodiversity within this ecologically pivotal group. Full article

Background: Population differences in gut microbiota composition and related metabolites may influence their potential causal relationship with chronic kidney disease (CKD); however, this relationship remains poorly understood in the Chinese population. Materials and Methods: We conducted a two-sample Mendelian randomization (MR) study using summary statistics of 500 gut microbial features (9 phyla, 3 classes, 14 orders, 32 families, 95 genera, 248 species, and 99 gut metabolic modules (GMMs)) from the 4D-SZ (from Shenzhen, China) discovery cohort (n = 1539). CKD summary statistics were obtained from the China Kadoorie Biobank (CKB) (489 cases and 75,531 controls). Associations between gut microbiota and CKD were evaluated via inverse variance weighted, MR-Egger, weighted median, and MR-PRESSO. To validate our findings, we replicated the analyses in two independent East Asian CKD GWAS datasets: the Biobank of Japan (BBJ) dataset (2117 cases and 174,345 controls) and the J-Kidney-Biobank (JKB) dataset (382 cases and 3471 controls). We further validated the results via a meta-GWAS of BUN and eGFR in Biobank Japan (BBJ) and the Taiwan Biobank (TWB). Additionally, we analyzed 304 serum proteins from the Guangzhou Nutrition and Health Study (GNHS) and conducted mediation MR analyses to explore potential mediators. Result: At the locus-wide significance threshold, we identified 18 gut microbiome features associated with CKD onset in the China Kadoorie Biobank (CKB). Genus Alistipes (OR 1.02, 95% CI 1.00–1.03, p = 0.03) was associated with incident CKD risk in the JKB cohort. Species Bifidobacterium catenulatum–Bifidobacterium pseudocatenulatum complex (OR 1.0074, 95% CI 1.0070–1.0142, p = 0.01) was associated with incident CKD risk in a meta-GWAS of BUN. Sensitivity analyses, including Cochran’s Q test, MR-Egger intercept analysis, leave-one-out analysis, and funnel plots, yielded consistent results. Mediation analysis revealed that 26.7% (95% CI: 0.006–0.6700, p = 0.04) of the effect of Alistipes on CKD risk was mediated through the serum protein FBLN1. Conclusions: Our study provides Mendelian randomization-based evidence supporting a potential causal relationship between gut microbiota and CKD, highlighting the potential mediating role of FBLN1 in the association between genus Alistipes and CKD. Further studies are needed to explore whether and how genus Alistipes and FBLN1 contribute to CKD development. Full article

Background: Understanding the role of repetitive elements (REs) in cancer development is crucial for identifying novel biomarkers and therapeutic targets. Methods: This study investigated the locus-specific dysregulation of REs, including the differential expression and methylation of REs, across 12 TCGA cancer types stratified by their genomic context (i.e., genic and intergenic REs). Results: We found uniquely dysregulated genic REs co-regulated with their corresponding transcripts and associated with distinct biological functions in different cancer types. Uniquely dysregulated intergenic REs were identified in each cancer type and used to cluster different sample types. Recurrently dysregulated REs were identified in several cancer types, with genes associated with up-regulated genic REs involved in cell cycle processes and those associated with down-regulated REs involved in the extracellular matrix. Interestingly, four out of five REs consistently down-regulated in all 12 cancer types were located in the intronic region of the TMEM252, a recently discovered tumor suppressor gene. TMEM252 expression was also down-regulated in 10 of 12 cancer types, suggesting its potential importance across a wide range of cancer types. With the corresponding DNA methylation array data, we found a higher prevalence of hypo-methylated REs in most cancer types (10 out of 12). Despite the slight overlaps between differentially expressed REs and differentially methylated REs, we showed that the methylation of locus-specific REs negatively correlates with their expression in some of these 12 cancer types. Conclusions: Our findings highlight the cancer-specific and recurrent deregulation of REs, their functional associations, and the potential role of TMEM252 as a pan-cancer tumor suppressor, providing new insights into biomarker discovery and therapeutic development. Full article

Aquilaria sinensis (Lour.) Spreng. is an economically important tree specie that produces agarwood, a valuable medicinal and aromatic resin, when injured. However, its large-scale cultivation has led to confusion regarding its resources and genetic backgrounds, hindering the conservation and management of A. sinensis accessions. This study systematically developed and validated simple sequence repeat (SSR) molecular markers by using whole-genome resequencing (WGR) data from 60 A. sinensis accessions to elucidate their genetic diversity and population structure. A total of 56,657 SSR sequences (24,430 loci) were identified, which were dominated with dinucleotide repeat motifs (73.59%). After stringent quality control, 46 high-quality SSR loci were obtained, and 93 primer pairs were designed for amplification validation. Ultimately, 20 primer pairs with stable amplification and high polymorphism were selected, of which 11 exhibited high polymorphism (polymorphic information content: 0.554–0.688). These 20 primer pairs identified a total of 121 alleles, with an average of 6 alleles per locus. These primers successfully classified 149 A. sinensis accessions into three subpopulations, achieving a discrimination rate of 95.97%. The analysis of molecular variance revealed that genetic variation within the individuals accounted for 84% of the total variation. This study establishes a rapid and efficient SSR-based method by leveraging resequencing data for large-scale marker discovery in A. sinensis. It further provides a robust technical framework for the conservation and sustainable utilization of this valuable species. Full article

Natural gene variants of metabotropic glutamate receptor subtype 7 (Grm7), coding for mGluR7, affect individuals’ alcohol-drinking preference. Psychopharmacological investigations have suggested that mGluR7 is also involved in responses to cocaine, morphine, and nicotine exposures. We review the pleiotropic effects of Grm7 and the principle of recombinant quantitative trait locus introgression (RQI), which led to the discovery of the first mammalian quantitative gene accounting for alcohol-drinking preference. Grm7/GRM7 can play important roles in mammalian ontogenesis, brain development, and predisposition to addiction. It is also involved in other behavioral phenotypes, including emotion, stress, motivated cognition, defensive behavior, and pain-related symptoms. This review identified pleiotropy and the modulation of neurobehavioral processes by variations in the gene Grm7/GRM7. Patterns of pleiotropic genes can form oligogenic architectures whosecombined additive and interaction effects can significantly predispose individuals to the expressions of disorders. Identifying and characterizing pleiotropic genes are necessary for understanding the expressions of complex traits. This requires tasks, such as discovering and identifying novel genetic elements of the genetic architecture, which are unsuitable for AI but require classical experimental genetics. Full article

This paper explores the application of automated reasoning tools, specifically those implemented in GeoGebra Discovery, to the perimeter-area inequality in triangles. Focusing on the computational complex and real algebraic geometry methods behind these tools, this study analyzes a geometric construction involving a triangle with arbitrary side lengths and area, investigating the automated derivation of the relationship between the area and perimeter of a triangle, and showing that only equilateral triangles satisfy the exact perimeter-area equality. The main contribution of this work is to describe the challenges, and potential ways to approach their solutions, still posed by the use of such automated, symbolic computation, methods in dynamic geometry, in particular concerning the discovery of loci of points that satisfy specific geometric conditions, suggesting relevant improvements for the future development of these symbolic AI-based educational tools in geometry. Full article

Background: Black adults have higher incidence of all-cause mortality and worse cardiovascular disease (CVD) outcomes when compared to other U.S. populations. The Duffy chemokine receptor is not expressed on erythrocytes in a large majority of Black adults, but the clinical implications of this are unclear. Methods: Here, we investigated the relationship of Duffy receptor status, high-sensitivity C-reactive protein (hs-CRP), and mortality and incident CVD events (coronary heart disease, stroke, and heart failure) in self-identified Black members of three contemporary, longitudinal cohort studies (the Women’s Health Initiative, Jackson Heart Study, and Multi-Ethnic Study of Atherosclerosis). Data on 14,358 Black participants (9023 Duffy-null and 5335 Duffy-receptor-positive, as defined using single-nucleotide polymorphism (SNP) rs2814778) were included in this analysis. Results: Duffy null was strongly associated with higher hs-CRP (meta-analysis p = 2.62 × 10⁻⁹), but the association was largely attenuated, though still marginally significant (p = 0.005), after conditioning on known CRP locus alleles in linkage disequilibrium with the Duffy gene. In our discovery cohorts, Duffy-null status appeared to be associated with a higher risk of all-cause mortality and incident stroke, though these associations were attenuated and non-significant following adjustment for traditional risk factors including hs-CRP. Moreover, the association of Duffy-null status with mortality could not be replicated in an independent sample of Black adults from the UK Biobank. Conclusions: These findings suggest that the higher levels of hs-CRP found in Duffy-null individuals may be in part independent of CRP alleles known to influence circulating levels of hs-CRP. During the follow-up of this community-based sample of Black participants, Duffy-null status was not associated with mortality or incident CVD events independently of traditional risk factors including hs-CRP. Full article

Autoimmune polyglandular syndrome (APS) comprises a complex association of autoimmune pathological conditions. APS Type 1 originates from loss-of-function mutations in the autoimmune regulator (AIRE) gene. APS2, APS3 and APS4 are linked to specific HLA alleles within the major histocompatibility complex, with single-nucleotide polymorphisms (SNPs) in non-HLA genes also contributing to disease. In general, variability in the AIRE locus and the presence of heterozygous loss-of-function mutations can impact self-antigen presentation in the thymus. In this study, whole-exome sequencing (WES) was performed on a sixteen-year-old female APS3A/B patient to investigate the genetic basis of her complex phenotype. The analysis identified two variants (p.Arg111Trp and p.Thr101Ile) of the hepatitis A virus cell receptor 2 gene (HAVCR2) encoding for the TIM-3 (T cell immunoglobulin and mucin domain 3) protein. These variants were predicted, through in silico analysis, to impact protein structure and stability, potentially influencing the patient’s autoimmune phenotype. While confocal microscopy analysis revealed no alteration in TIM-3 fluorescence intensity between the PBMCs isolated from the patient and those of a healthy donor, RT-qPCR showed reduced TIM-3 expression in the patient’s unfractionated PBMCs. A screening conducted on a cohort of thirty APS patients indicated that the p.Thr101Ile and p.Arg111Trp mutations were unique to the proband. This study opens the pathway for the search of TIM-3 variants possibly linked to complex autoimmune phenotypes, highlighting the potential of novel variant discovery in contributing to APS classification and diagnosis. Full article

Characterization of fungal spider pathogens lags far behind their insect counterparts. In addition, little to nothing is known concerning the ecological reservoir and/or fungal entomopathogen community surrounding infection sites. Five infected spider cadavers were identified in the neo-tropical climate of north-central Florida, USA, from three of which viable cultures were obtained. Multi-locus molecular phylogenetic and morphological characterization identified one isolate as a new Gibellula species, here named, Gibellula floridensis, and the other isolates highly similar to Parengyodontium album. The fungal entomopathogen community surrounding infected spiders was sampled at different habitats/trophic levels, including soil, leaf litter, leaf, and twig, and analyzed using ITS amplicon sequencing. These data revealed broad but differential distribution of insect-pathogenic fungi between habitats and variation between sites, with members of genera belonging to Metarhizium and Metacordyceps from Clavicipitaceae, Purpureocillium and Polycephalomyces from Ophiocordyceps, and Akanthomyces and Simplicillium from Cordycipitaceae predominating. However, no sequences corresponding to Gibellula or Parengyodontium, even at the genera levels, could be detected. Potential explanations for these findings are discussed. These data highlight novel discovery of fungal spider pathogens and open the broader question regarding the environmental distribution and ecological niches of such host-specific pathogens. Full article

Genome-wide association studies (GWAS) have accelerated the exploration of genotype–phenotype associations, facilitating the discovery of replicable genetic markers associated with specific traits or complex diseases. This narrative review explores the statistical methodologies developed using GWAS data to investigate relationships between various phenotypes, focusing on endometrial cancer, the most prevalent gynecological malignancy in developed nations. Advancements in analytical techniques such as genetic correlation, colocalization, cross-trait locus identification, and causal inference analyses have enabled deeper exploration of associations between different phenotypes, enhancing statistical power to uncover novel genetic risk regions. These analyses have unveiled shared genetic associations between endometrial cancer and many phenotypes, enabling identification of novel endometrial cancer risk loci and furthering our understanding of risk factors and biological processes underlying this disease. The current status of research in endometrial cancer is robust; however, this review demonstrates that further opportunities exist in statistical genetics that hold promise for advancing the understanding of endometrial cancer and other complex diseases. Full article

Fusarium head blight (FHB) can cause serious yield loss and significant mycotoxin contamination, which seriously threaten global food security and safety. Breeding stable and durable cultivars that are resistant to FHB is one of the most effective approaches to controlling this disease. Fhb1 is a well-known genetic locus for FHB resistance, but its resistance is not always effective across diverse wheat genetic backgrounds. To achieve a high and durable level of resistance, the discovery and use of additional quantitative trait loci (QTL) for FHB resistance are essentially needed in breeding programs. In this study, two independent wheat natural populations of different origins were used for mining resistance QTL with a major and stable effect. Using genome-wide association analysis (GWAS), a total of 58 marker–trait associations (MTAs) on chromosomes 1A, 2B, 3A, 3B, 4A, 4B, 4D, 5A, 5B, 5D, 6A, 6B, 6D, 7A and 7B were found to be significant for type II resistance to FHB. These 58 MTAs represent 24 putative QTL. Among these QTL, Qfhb.yzu.3B.1 and Qfhb.yzu.6B.3 were stably detected in the two natural populations across three consecutive experimental years. The favorable haplotypes at the two QTL could significantly reduce the disease severity, either individually or in combination. These two QTL are also additive to Fhb1 in cultivars with different genetic backgrounds. Breeder-friendly markers were designed to differentiate the contrasting alleles at these two loci, thus proving very useful for improving FHB resistance in wheat by marker-assisted selection. Full article

Although Chalcidoidea is one of the megadiverse superfamilies in Hymenoptera, numerous species are still being discovered and described. However, the difficulties in delimiting intra- and interspecific variation hinder this process. In this study, DNA barcoding methods using the COI gene were employed to investigate the morphological variation within Dzhanokmenia Kostjukov, 1977. The nuclear locus, 28S D2, was used to infer a phylogeny to gain an understanding of the relationship of Dzhanokmenia with other potentially close genera. Through a preliminary DNA barcode library established here, including eight species, we calibrated the intraspecific variation in certain diagnostic characters for the new species described here, D. brevifunis Ganbaatar & Cao sp. nov. Maximum likelihood results show that Dzhanokmenia is clustered with the genera associated with Tetrastichus, such as Chaenotetrastichus Graham, 1987, Baryscapus Förster, 1856, Tetrastichus Haliday, 1844, and Oomyzus Rondani, 1870 involved in this study. Our results indicate that the species diversity of Dzhanokmenia is understudied and tentatively confirm that Dzhanokmenia has a potential close relationship with Baryscapus. Along with the DNA barcode library, the referenced phylogeny datasets improve the understanding of the systematic position of Dzhanokmenia within the subfamily Tetrastichinae and the definition of this genus in terms of morphology, thereby facilitating species delimitation, discovery, and description within Dzhanokmenia. Full article

Autism spectrum disorder (ASD) is a common and highly heritable neurodevelopmental disorder. During the last 15 years, advances in genomic technologies and the availability of increasingly large patient cohorts have greatly expanded our knowledge of the genetic architecture of ASD and its neurobiological mechanisms. Over two hundred risk regions and genes carrying rare de novo and transmitted high-impact variants have been identified. Additionally, common variants with small individual effect size are also important, and a number of loci are now being uncovered. At the same time, these new insights have highlighted ongoing challenges. In this perspective article, we summarize developments in ASD genetic research and address the enormous impact of large-scale genomic initiatives on ASD gene discovery. Full article