Genes最新文献

Background: The predictive performance of pre-screening phenotype-based algorithms in selecting patients with cerebral small vessel disease (cSVD), one of the main causes of ischaemic and haemorrhagic stroke and dementia, more likely to harbor clinically relevant genetic variants (CRGVs) has to date been poorly defined, making it a clinical challenge to decide which patients to screen for hereditary cSVD (hcSVD). Methods: We designed a high-throughput gene panel to identify variants in 27 candidate genes associated with cSVD and screened patients selected by a specific phenotype-based algorithm at one comprehensive stroke center from 2020 to 2023. We categorized participants into two sub-groups defined by pre-screening likelihood of hcSVD (hcSVD; High-Probability Group, HPG vs. Low-Probability Group, LPG) and compared the results of molecular analysis. Results: Among 65 probands, we detected four (6.1%) pathogenic CRGVs and seven (10.7%) variants of unknown significance (VUSs) in 11 (16.9%) patients. Pathogenic CRGVs were exclusively detected in the HPG (4/22 probands), corresponding to an 18.2% prevalence of hcSVD in this group. Of the seven VUSs, five (22.7%) were detected in the HPG vs. two (4.6%) in the LPG. Conclusions: The pragmatic algorithm we are proposing has the potential to help clinicians in identifying patients who are more likely to harbor monogenic disease.

Background: This study presents the sequencing and analysis of mitochondrial DNA (mtDNA) genomes from nine early medieval horse remains excavated across archaeological sites in Silesia region in present day Poland.

Methods: Using aDNA extraction protocols optimized for short fragments, combined with target enrichment and high-throughput sequencing, we reconstructed partial mtDNA sequences for seven of the specimens.

Results: The authenticity of the aDNA was confirmed through damage pattern analysis. Phylogenetic reconstruction revealed that the specimens belonged to six distinct mtDNA lineages (B, D, E, G, L, and M), indicating a high level of mitochondrial diversity within medieval Silesian horse population.

Conclusions: These findings highlight the extensive mtDNA variability among domestic horses, reflecting the diversity of their ancestral populations rather than modern breed differentiation. This research enhances our understanding of horse population structure in medieval Europe, emphasizing the genetic complexity present during this period.

Background: Tic spectrum disorder (TSD), encompassing Tourette syndrome and chronic tic disorder, is a childhood-onset neurodevelopmental condition with complex genetic and environmental contributions. Heritable components have been implicated in TSD, but no clear genetic mechanisms have been identified. Significant aspects of TSD etiology remain unclear, with key uncertainties concerning the role of environmental influences in its development. In this study, we aimed to identify environmentally induced epigenomic and transcriptomic changes contributing to TSD pathology by investigating genetically similar monozygotic twins discordant for TSD. Methods: To investigate environmentally driven mechanisms, we analyzed peripheral blood from eleven monozygotic twin pairs, either discordant or concordant for TSD, using RNA sequencing and DNA methylation analysis. Results: Differential expression analysis identified a dozen differentially expressed genes between TSD and non-TSD individuals, most of which were long non-coding RNAs or pseudogenes. Expression of the small RNA gene RNY1 was significantly associated with tic severity, suggesting involvement of immune-related processes. DNA methylation (DNAm) analysis revealed ~30,000 probes with a nominal p < 0.05, however none of these were significant after multiple testing correction. Expression quantitative trait methylation (eQTM) analysis identified 236 methylation-associated genes. Gene set enrichment analysis demonstrated broad downregulation in TSD individuals for pathways related to translation, RNA processing, and neurobiological functions, with Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways including ribosome, nucleocytoplasmic transport, pluripotency signaling, and nicotine addiction. Conclusions: These results suggest that environmentally influenced gene expression may contribute to TSD pathogenesis through dysregulation of immune and neuronal pathways. Despite a small sample size, the monozygotic twin design provides strong control for genetic background and identifies significant differences that contribute to the understanding of the underlying molecular mechanisms of TSD.

Background: Plant architecture, particularly branching patterns, plays a crucial role in plant growth, photosynthetic performance, and yield. Spur-type apple, characterized by compact growth, early fruiting, high productivity, and manageable canopy structure, represent valuable germplasm for establishing dwarf and high-density apple orchards. While hybrid breeding of spur-type varieties offers significant potential for genetic advancement, severe segregation of traits in hybrid progeny and the difficulty of combining multiple favorable traits still significantly limit breeding efficiency. Moreover, the genetic basis and molecular mechanisms of the spur-type trait remain poorly understood at the genomic level, hindering the development of precise molecular breeding approaches.

Methods: To address this, we used the spur-type line '0301-13-14' and the non-spur-type line '0301-50-32' from hybrid progenies of the spur-type cultivars 'Miyazaki Spur Fuji' and 'Starkrimson' to elucidate the regulatory mechanisms underlying apple branch formation and spur-type trait development by characterizing their branching traits, performing whole-genome resequencing analysis, and identifying candidate genes using bioinformatics analyses.

Results: Anatomical observations revealed that the spur-type line '0301-13-14' possessed smaller cells with a more compact spatial arrangement compared to the non-spur-type line '0301-50-32'. Whole-genome resequencing generated 5,003,968 high-quality single-nucleotide polymorphisms (SNPs) and 577,886 high-quality insertions/deletions (InDels). We further identified 29,157 candidate genes harboring predicted deleterious mutations (classified as high or moderate impact). Gene Ontology (GO) enrichment analysis indicated that genes associated with the spur-type trait were mainly enriched in molecular function and biological process categories. Specifically, variant genes related to molecular function were enriched in transferase and catalytic activities, while those in biological process were mainly involved in phosphorylation and phosphorus metabolism. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis showed that candidate genes were significantly enriched in environmental information processing and metabolic pathways.

Conclusions: These results will provide a genomic foundation for identifying genes controlling spur-type branching traits and facilitate the genetic improvement of spur-type apple.

Background: Solenopsis invicta, commonly known as the red imported fire ant (RIFA), is an important global invasive pest, and its management is challenging because of insecticide resistance and environmental problems.

Methods: In this research, we applied transcriptomics to analyze the molecular responses of S. invicta worker ants exposed to different types of pesticides, beta-cypermethrin (BC) and the entomopathogenic fungus Cordyceps cicadae (CC), as well as to different concentrations of these pesticides.

Results: A total of 2727 differentially expressed genes (DEGs) were identified across all samples. The number of DEGs in the BC treatment group was significantly higher than that in the CC treatment group (2520 vs. 433), and higher concentrations resulted in more DEGs (an increase of 47 in the BC group and 229 in the CC group). KEGG pathway analysis revealed that the DEGs were significantly enriched in lipid metabolism, carbohydrate metabolism, amino acid metabolism, signal transduction, and membrane transport. Immune-related gene analysis showed more general down-regulation (average FPKM value in BC 741.37 to 756.06 vs. CK 1914.42) of pathogen recognition genes (PGRP-SC2) under BC stress conditions, while CC treatment resulted in increases in expression of important immune effectors such as various serine proteases.

Conclusions: Overall, this study provides useful insights into the molecular basis of responses to different pesticides in S. invicta and offers a basis to develop new approaches to control this pest.

Background: Sheep (Ovis aries) exhibit significant diversity in adipose tissue deposition, which influences meat quality, environmental adaptation, and economic value. Tail fat, in particular, varies widely among breeds, yet the transcriptomic basis of this variation remains incompletely understood. This study aims to systematically compare the transcriptional profiles of five adipose depots across five sheep breeds to identify molecular mechanisms underlying fat deposition and tail phenotype divergence.

Methods: We analyzed 250 publicly available RNA-seq samples from five adipose tissues (caul, subcutaneous, perirenal, intermuscular, and tail fat) of five sheep breeds (Altay, Tibetan, Merino, Wadi, Small-tailed Han). Data were processed using FastQC, STAR, and featureCounts. Differential expression analysis was performed with DESeq2, followed by GO and KEGG enrichment analyses. Breeds were grouped into three tail phenotypes: fat-tailed, short fat-tailed, and thin-tailed. Cross-tissue and phenotype-specific pathway analyses were conducted to identify key regulatory genes.

Results: Transcriptional divergence was most pronounced in subcutaneous and intermuscular fat, while tail fat exhibited both conserved and phenotype-specific pathways. Fat-tailed breeds showed enrichment in mitochondrial oxidative phosphorylation and lipid biosynthesis genes (TAFAZZIN, GPAM, COQ family). Short fat-tailed breeds were characterized by extracellular matrix remodeling genes (MMP9, MMP12, MMP19). Thin-tailed sheep lacked these pro-lipogenic and structural remodeling pathways. A dual-axis model of tail fat development is proposed to explain phenotypic diversity.

Conclusions: This study reveals that distinct molecular mechanisms underpin tail fat phenotypes in sheep: fat-tailed breeds prioritize metabolic efficiency, short fat-tailed breeds rely on ECM remodeling, and thin-tailed breeds lack these enhancements. The identified candidate genes may serve as potential targets for molecular breeding strategies aimed at optimizing fat deposition and adaptive traits in sheep.

Terpenes are major determinants of tea aroma, and terpene synthases (TPSs) catalyze key steps in terpenoid biosynthesis. To capture gene-family variation beyond a single reference, we performed a pan-genome-based analysis of TPS genes across nine Camellia genomes (three wild tea relatives and six cultivated Camellia sinensis accessions) and integrated pan-transcriptome profiling across eight tissues. We identified 381 TPS genes; wild species contained more TPSs than cultivated accessions (mean 58.3 vs. 34.3), suggesting a putative contraction. Phylogenetic analysis with Arabidopsis TPSs classified Camellia TPSs into five subfamilies, dominated by TPS-b (149) and TPS-a (140), whereas TPS-c was rare (8). Gene-structure and physicochemical analyses revealed marked subfamily divergence, with TPS-c showing highly conserved coding-region length. Orthology clustering assigned 355 TPSs to 19 orthogroups, including five core groups (190 genes, 53.5%) and 14 dispensable groups (165 genes, 46.5%); core/non-core status was significantly associated with subfamily composition. Tandem and proximal duplication contributed most to TPS expansion (29.4% and 29.1%), and all orthogroups exhibited copy-number variation, with pronounced lineage-specific expansions. Ka/Ks analyses indicated pervasive purifying selection (median 0.516) but heterogeneous constraints among subfamilies. Finally, cultivated tea showed higher TPS expression in most tissues, especially mature leaf and stem, and TPS-g displayed the broadest and strongest expression. Together, these results provide a pan-genome resource for Camellia TPSs and highlight how domestication, duplication, and CNV shape terpene-related genetic diversity.

Background: The genus Artocarpus includes about 70 species, such as the economically important jackfruit and breadfruit, which serve as vital sources of food, timber, and medicine in the tropics. However, systematic research and genetic improvement have been restricted by the scarcity and fragmentation of available genomic data.

Methods: Here, we developed the Artocarpus Genome Database (ArGD), a publicly accessible, comprehensive research platform dedicated to this genus. ArGD centrally integrates high-quality genomic sequences from seven Artocarpus genomes, along with related transcriptomic data and detailed functional annotations.

Results: Beyond basic data retrieval, ArGD features a suite of advanced visualization and analysis modules, including BLAST, JBrowse, expression heatmaps, volcano plots, synteny viewers, ArtocarpusCYC metabolic interface, and Gene Ontology (GO)/KEGG enrichment analyses. Additionally, ArGD provides online identification tools for gene families related to fruit aroma and secondary metabolism.

Conclusions: Overall, ArGD serves as a valuable resource for functional genomics and comparative studies in Artocarpus, facilitating future research and data-driven studies of genetic improvement.

Background: The zinc finger-homeodomain (ZF-HD) transcription factor family exerts pivotal regulatory functions in plant development and stress responses, yet a systematic genome-wide survey is lacking for Rosa chinensis.

Methods: In this study, we performed a comprehensive genome-wide identification and analysis of RcZF-HD genes in R. chinensis using bioinformatics approaches. Nine RcZF-HD loci were mined from the rose genome and comprehensively profiled for physicochemical parameters, phylogenetic affiliations, chromosomal positions, exon-intron architectures, conserved motifs, and spatiotemporal expression landscapes.

Results: The results showed that RcZF-HD genes were unevenly distributed across four chromosomes (Chr2, Chr4, Chr6, and Chr7), with tandem duplication events detected on chromosomes 2 and 7, suggesting their contribution to gene family expansion. Maximum-likelihood phylogeny placed RcZF-HD proteins within nine well-supported sub-clades alongside Arabidopsis orthologs, implying both evolutionary conservation and lineage-specific divergence. All members retain canonical zinc-finger domains, yet acquire unique motif signatures predictive of functional specialization. Gene structure analysis revealed considerable diversity in exon-intron organization. Expression profiling across six different tissues (root, stem, leaf, bud, flower, and fruit) demonstrated remarkable tissue-specific expression patterns. Notably, RchiOBHm_Chr2g0168531 exhibited extremely high expression in stem tissue, while RchiOBHm_Chr7g0181371 showed preferential expression in flower tissue, suggesting specialized roles in stem development and floral organ formation, respectively. The cold-stress challenge of 'Old Blush' petals further disclosed pronounced up-regulation of seven RcZF-HD genes, attesting to their critical contribution to low-temperature tolerance.

Conclusions: Integrative analyses furnish a multidimensional blueprint of the rose RcZF-HD repertoire, providing molecular landmarks for future functional dissection and ornamental trait engineering.

Background: Varroa destructor is the major threat to honey bee health, and selective breeding for resistance traits such as Varroa-sensitive hygiene represents a promising long-term strategy for controlling mite populations. However, breeding programs that rely on highly controlled mating schemes, including single-drone instrumental insemination, may reduce allelic diversity at the complementary sex determiner (csd) locus, potentially increasing the production of non-viable diploid males and compromising colony fitness. Methods: To evaluate whether csd diversity can be maintained under these conditions, we characterized the hypervariable region of csd in a selectively bred Apis mellifera population subjected to four years of selection. Using a validated de novo assembly pipeline, we reconstructed 43 amino-acid sequences from 33 diploid worker pupae sampled across 13 colonies. Results: Seven distinct alleles were identified, five of which were shared among multiple colonies and corresponded to variants already described in the literature, while two were private to individual colonies and novel in the literature. Colony-level frequency data revealed a moderate diversity: the most common allele was detected in nine colonies, with an allelic frequency of 31%. Moreover, the expected heterozygosity of the population was estimated at 0.79. Conclusions: Overall, these findings show that csd diversity can be partially maintained even under strong selective pressure when multiple maternal lines are retained, and they underscore the importance of incorporating genetic information into breeding decisions to support the long-term sustainability of selective breeding programs.