G3: Genes|Genomes|Genetics最新文献_第10页

Testicular heterochrony in vgll3-mediated maturation age in Atlantic salmon. 大西洋鲑鱼睾丸异时性vgll3介导的成熟年龄。

IF 2.2 3区生物学

G3: Genes|Genomes|Genetics Pub Date : 2025-08-21 DOI: 10.1093/g3journal/jkaf196

Ehsan Pashay Ahi, Jukka-Pekka Verta, Johanna Kurko, Annukka Ruokolainen, Paul Vincent Debes, Craig R Primmer

{"title":"Testicular heterochrony in vgll3-mediated maturation age in Atlantic salmon.","authors":"Ehsan Pashay Ahi, Jukka-Pekka Verta, Johanna Kurko, Annukka Ruokolainen, Paul Vincent Debes, Craig R Primmer","doi":"10.1093/g3journal/jkaf196","DOIUrl":"https://doi.org/10.1093/g3journal/jkaf196","url":null,"abstract":"Heterochrony, or shifts in developmental timing, drives phenotypic diversity within and between species and shapes life history traits that can be selected for in changing environments which in turn promotes population resilience. Mutations in heterochronic genes that regulate these processes can induce stable timing shifts, impacting important life history traits like pubertal timing. Age at maturity is a key adaptive trait across species, with vgll3, a Hippo pathway co-factor, as a main determinant in Atlantic salmon. Recent studies show that early (E) and late (L) vgll3 alleles affect reproductive gene expression in salmon, reinforcing its role in regulating developmental timing. This study examines whether vgll3 influences testicular heterochrony in Atlantic salmon by analyzing gene expression related to the Hippo pathway. We observed heterochronic divergence in Hippo pathway gene transcription, indicating accelerated changes linked to spermatogenesis in vgll3*EE individuals. Our results position vgll3 as a heterochronic gene with a key role in regulating developmental timing in salmon.","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2025-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144949116","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Genome-wide discovery of multiple sclerosis genetic risk variant allelic regulatory activity. 全基因组发现多发性硬化症遗传风险变异等位基因调控活性。

IF 2.2 3区生物学

G3: Genes|Genomes|Genetics Pub Date : 2025-08-21 DOI: 10.1093/g3journal/jkaf192

Marissa Granitto, Lois Parks, Molly S Shook, Carmy Forney, Xiaoting Chen, Lee E Edsall, Omer A Donmez, Sreeja Parameswaran, Kristen S Fisher, Aram Zabeti, Lucinda P Lawson, Matthew T Weirauch, Leah C Kottyan

{"title":"Genome-wide discovery of multiple sclerosis genetic risk variant allelic regulatory activity.","authors":"Marissa Granitto, Lois Parks, Molly S Shook, Carmy Forney, Xiaoting Chen, Lee E Edsall, Omer A Donmez, Sreeja Parameswaran, Kristen S Fisher, Aram Zabeti, Lucinda P Lawson, Matthew T Weirauch, Leah C Kottyan","doi":"10.1093/g3journal/jkaf192","DOIUrl":"https://doi.org/10.1093/g3journal/jkaf192","url":null,"abstract":"Multiple Sclerosis (MS) is an immune-mediated demyelinating disease of the central nervous system (CNS) with a complex etiology involving environmental and genetic factors. Numerous genetic risk loci for MS have been nominated through genome-wide association studies, with most associated variants residing in non-coding regions. However, further work is needed to understand how genetic variation contributes to disease-related alterations to gene expression. Here, we use massively parallel reporter assays (MPRAs) to identify genetic risk variants with genotype-dependent enhancing or silencing activity within a set of 14,275 variants distributed among MS risk loci that have reached genome-wide or suggestive significance. We applied our MPRA library to EBV-transformed B cell lines derived from two patients with MS, as well as the ENCODE Tier 1 cell line GM12878. In total, our approach discovered 150 allelic enhancing variants and 286 allelic silencing variants, collectively representing 83 independent MS risk loci. Our systematic, genome-scale approach implicates potentially causal genotype-dependent gene regulatory mechanisms for over a third of the known MS risk loci, providing a unique resource for the discovery of the genetic mechanisms underlying this chronic inflammatory disease.","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2025-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144949123","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A Coffin-Siris syndrome-associated mutation modeled in C. elegans affects multiple developmental processes. 在秀丽隐杆线虫中模拟的棺材- siris综合征相关突变影响多个发育过程。

IF 2.2 3区生物学

G3: Genes|Genomes|Genetics Pub Date : 2025-08-20 DOI: 10.1093/g3journal/jkaf194

Marissa Baccas, Jun Liu

{"title":"A Coffin-Siris syndrome-associated mutation modeled in C. elegans affects multiple developmental processes.","authors":"Marissa Baccas, Jun Liu","doi":"10.1093/g3journal/jkaf194","DOIUrl":"10.1093/g3journal/jkaf194","url":null,"abstract":"Coffin-Siris syndrome (CSS) is a rare human genetic disorder that is characterized by developmental delay, fifth digit abnormalities, and craniofacial defects. Heterozygous mutations in two SoxC proteins, SOX4 and SOX11, are associated with this disorder. C. elegans has a single SoxC protein, SEM-2, which is essential for development. In this study, we use C. elegans as a model system to explore the molecular effects of one CSS-associated SOX11 mutation, Y116C, on SoxC protein function in vivo. The equivalent amino acid of SOX11 Y116 is SEM-2 Y160, a residue in the C-terminal tail of the highly conserved DNA-binding domain. Homozygous, but not heterozygous, sem-2[Y160C] animals exhibit a high rate of embryonic and larval lethality, egg-laying defects, reduced brood size, bivulval phenotype and a low penetrance of hermaphrodite tail abnormalities. Additionally, sem-2[Y160C] animals have reduced expression of hlh-8/Twist, whose human counterparts, when mutated, are known to be associated with craniofacial disorders. All the phenotypes observed in sem-2[Y160C] animals resemble SEM-2 loss-of-function phenotypes, suggesting that SOX11[Y116C] is a loss-of-function, recessive mutation that likely causes defects due to haploinsufficiency. Our work suggests that using C. elegans as a model system to analyze the molecular effects of point mutations associated with craniofacial defects has the potential for unraveling the underlying mechanisms.","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2025-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144882550","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Integrated Ecdysone and O-Linked N-Acetylglucosamine Signaling Coordinates Intestinal Stem Cell Proliferation in Drosophila Midgut. 综合蜕皮激素和o -连接n -乙酰氨基葡萄糖信号协调果蝇中肠干细胞增殖。

IF 2.2 3区生物学

G3: Genes|Genomes|Genetics Pub Date : 2025-08-19 DOI: 10.1093/g3journal/jkaf190

Hyun-Jin Na, YiSeul Kim, Jong Min Kim, Mi Jeong Sung, Joung-Sun Park

{"title":"Integrated Ecdysone and O-Linked N-Acetylglucosamine Signaling Coordinates Intestinal Stem Cell Proliferation in Drosophila Midgut.","authors":"Hyun-Jin Na, YiSeul Kim, Jong Min Kim, Mi Jeong Sung, Joung-Sun Park","doi":"10.1093/g3journal/jkaf190","DOIUrl":"10.1093/g3journal/jkaf190","url":null,"abstract":"Steroid hormones and nutrient-sensitive signaling pathways play critical roles in the regulation of stem cell activity, maintenance of tissue homeostasis, and the coordination of metabolic functions. In Drosophila, the steroid hormone ecdysone and the nutrient-responsive post-translational modification O-linked N-acetylglucosamine (O-GlcNAcylation) are emerging as key regulators of intestinal stem cell (ISC) behavior. This study aimed to investigate how the interplay between ecdysone signaling and O-GlcNAcylation controls ISC proliferation and gut homeostasis, particularly in the context of aging. We showed that ecdysone receptor (EcR) expression increases during aging and upon increased O-GlcNAcylation, and that both genetic overexpression of EcR and exogenous 20-hydroxyecdysone treatment promote ISC proliferation and increase O-GlcNAc levels. Conversely, the knockdown of EcR or O-GlcNAc transferase suppressed ISC proliferation and reduced DNA damage accumulation. Our results show that EcR signaling induces DNA damage response and cooperates with O-GlcNAcylation to regulate ISC activity, suggesting a positive feedback loop involving hormones and nutrients. These results highlight the interaction between EcR and O-GlcNAc as a metabolic gatekeeper that balances regenerative activity and genomic integrity in the aging gut. These findings provide a potential mechanistic link for therapeutic strategies for age-related and metabolic diseases involving abnormal stem cell proliferation.","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2025-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144872403","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A chromosome-scale genome assembly and annotation of the tetraploid herb 'epazote' (Dysphania ambrosioides). 四倍体草本植物‘epazote’ （Dysphania ambrosioides）的染色体尺度基因组组装和注释。

IF 2.2 3区生物学

G3: Genes|Genomes|Genetics Pub Date : 2025-08-19 DOI: 10.1093/g3journal/jkaf191

Paul B Frandsen, Abigail Borgmeier, Sam Bratsman, Brian J Cox, Sarah J Gottfredson, Robert Hadfield, Garrett Harding, Andrea L Kokkonen, Ying Fei Lin, Jackson Linde, Teagan Mulford, Andrew Parker, Shane Smith, Kaitlin Torres, Lauren Young, Hayley Mangelson, Eric N Jellen, Peter J Maughan, David E Jarvis

{"title":"A chromosome-scale genome assembly and annotation of the tetraploid herb 'epazote' (Dysphania ambrosioides).","authors":"Paul B Frandsen, Abigail Borgmeier, Sam Bratsman, Brian J Cox, Sarah J Gottfredson, Robert Hadfield, Garrett Harding, Andrea L Kokkonen, Ying Fei Lin, Jackson Linde, Teagan Mulford, Andrew Parker, Shane Smith, Kaitlin Torres, Lauren Young, Hayley Mangelson, Eric N Jellen, Peter J Maughan, David E Jarvis","doi":"10.1093/g3journal/jkaf191","DOIUrl":"10.1093/g3journal/jkaf191","url":null,"abstract":"Epazote (Dysphania ambrosiodes L.) is a perennial plant from the tropics of the Americas and is of regional importance due to both culinary and medicinal applications. However, few genomic resources exist to facilitate the identification of genes and pathways underlying the production of functionally important compounds in epazote. Here, we present a chromosome-scale assembly of the tetraploid epazote genome using PacBio HiFi reads and Hi-C. The final genome assembly contains 191 scaffolds spanning a total length of 469.23 Mbp, with 98.17% of the total length in the 16 largest chromosome-scale scaffolds. A BUSCO analysis identified 99.01% of the universal, single-copy orthologs, indicating that the genome is largely complete. We identified 51.81% of the genome as repetitive and annotated 24,424 genes. Collinearity of homologous genes has degraded to the point that, with few exceptions, homoeologous chromosome pairs cannot be identified, suggesting that the whole-genome duplication in epazote is relatively old. Analysis of epazote and related species suggests that the whole-genome duplication in epazote is independent and is older than the whole-genome duplication in quinoa but younger than that of amaranth.","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2025-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144882549","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Characterizing fatty acid oxidation genes in Drosophila. 果蝇脂肪酸氧化基因的表征。

IF 2.2 3区生物学

G3: Genes|Genomes|Genetics Pub Date : 2025-08-06 DOI: 10.1093/g3journal/jkaf139

Juliana Geronazzo, Abigail Heimerl, Linnea Lindell, Skye McCrimmon, Clara Stormer, Brooke Horvai, Ian P Johnson, Tia M Peterson, Jocelyn Zuckerman, Anna I Scott, Meredith M Course

{"title":"Characterizing fatty acid oxidation genes in Drosophila.","authors":"Juliana Geronazzo, Abigail Heimerl, Linnea Lindell, Skye McCrimmon, Clara Stormer, Brooke Horvai, Ian P Johnson, Tia M Peterson, Jocelyn Zuckerman, Anna I Scott, Meredith M Course","doi":"10.1093/g3journal/jkaf139","DOIUrl":"10.1093/g3journal/jkaf139","url":null,"abstract":"In this study, we leverage the power and tractability of Drosophila genetics to better understand the molecular mechanisms underlying a group of rare genetic diseases known as fatty acid oxidation disorders. We use CRISPR-Cas9 to generate mutations in 6 putative fatty acid oxidation genes in Drosophila, then analyze the phenotypes and acylcarnitine profiles of these flies. We find that while Arc42 and CG4860 are both predicted orthologs of human ACADS, only Arc42 loss of function mirrors the acylcarnitine profile of ACADS loss of function. Acylcarnitine profiles also support our previous identification of Mcad as the likely ACADM ortholog, and reveal the deleterious effects of a single codon deletion in Mtpα (the predicted human HADHA ortholog). Finally, we observe that loss of function in Etf-QO and in CG7834-predicted orthologs of human ETFDH and ETFB, respectively-is homozygous lethal in flies. Producing animal models like these will enable new approaches to studying fatty acid oxidation disease progression, symptomatic variability, and therapeutic intervention.","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2025-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12341901/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144301596","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Correction to: Convergent Evolution of Calcineurin Pathway Roles in Thermotolerance and Virulence in Candida glabrata. 修正：钙调磷酸酶途径在光假丝酵母耐热性和毒力中的趋同进化。

IF 2.2 3区生物学

G3: Genes|Genomes|Genetics Pub Date : 2025-08-06 DOI: 10.1093/g3journal/jkaf124

引用次数: 0

Correction to: Genome-wide association mapping dissects the selective breeding of determinacy and photoperiod sensitivity in common bean (Phaseolus vulgaris L.). 修正：全基因组关联图谱剖析了普通豆（Phaseolus vulgaris L.）的确定性和光周期敏感性的选择性育种。

IF 2.2 3区生物学

G3: Genes|Genomes|Genetics Pub Date : 2025-08-06 DOI: 10.1093/g3journal/jkaf141

引用次数: 0

diplo-locus: a lightweight toolkit for inference and simulation of time-series genetic data under general diploid selection. diploi -locus：一个轻量级的工具箱，用于推断和模拟一般二倍体选择下的时间序列遗传数据。

IF 2.2 3区生物学

G3: Genes|Genomes|Genetics Pub Date : 2025-08-06 DOI: 10.1093/g3journal/jkaf123

Xiaoheng Cheng, Matthias Steinrücken

引用次数: 0

The genome of the American dog tick (Dermacentor variabilis). 美国狗蜱的基因组。

IF 2.2 3区生物学

G3: Genes|Genomes|Genetics Pub Date : 2025-08-06 DOI: 10.1093/g3journal/jkaf130

Jacob Cassens, Matt Villalta, Saul Aguirre, Lauren Ecklund, Trek Stenger, Idil Abdi, Sree Venigalla, Elizabeth Shiffman, Kristen Bastug, Beth K Thielen, Christopher Faulk

{"title":"The genome of the American dog tick (Dermacentor variabilis).","authors":"Jacob Cassens, Matt Villalta, Saul Aguirre, Lauren Ecklund, Trek Stenger, Idil Abdi, Sree Venigalla, Elizabeth Shiffman, Kristen Bastug, Beth K Thielen, Christopher Faulk","doi":"10.1093/g3journal/jkaf130","DOIUrl":"10.1093/g3journal/jkaf130","url":null,"abstract":"The American dog tick (Dermacentor variabilis) is a vector of zoonotic pathogens in North America that poses emerging threats to public health. Despite its medical importance, genomic resources for D. variabilis remain scarce. Leveraging long-read nanopore sequencing, we generated a high-quality genome assembly for D. variabilis with a final size of 2.15 Gb, an N50 of 445 kb, and a benchmarking universal single-copy ortholog (BUSCO) completeness score of 95.2%. Comparative BUSCO analyses revealed fewer duplicate genes in our assembly than in other Dermacentor genomes, indicating improved haplotype resolution. The mitochondrial genome, assembled as a single circular contig, clustered monophyletically with D. variabilis isolates from the Upper Midwest, corroborating regional phylogenetic relationships. Repetitive element analysis identified 61% of the genome as repetitive, dominated by long interspersed nuclear elements and long terminal repeat elements, with 24% remaining unclassified, underscoring the need for further exploration of transposable elements in tick genomes. Gene annotation predicted 21,722 putative genes, achieving a protein BUSCO completeness of 80.88%. Additionally, genome-wide methylation analysis revealed 9.9% global 5mC methylation, providing the first insights into epigenetic modifications in D. variabilis. Further, nanopore sequencing detected Rickettsia montanensis and a nonpathogenic Francisella-like endosymbiont. These findings expand our understanding of tick genomics and epigenetics, offering valuable resources for comparative studies and evolutionary analyses.","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2025-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12341941/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144257809","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0