G3: Genes|Genomes|Genetics最新文献_第10页

Transcriptional repression and enhancer decommissioning silence cell cycle genes in postmitotic tissues. 转录抑制和增强子退役抑制了有丝分裂后组织中的细胞周期基因。

IF 2.1 3区生物学

G3: Genes|Genomes|Genetics Pub Date : 2024-10-07 DOI: 10.1093/g3journal/jkae203

Elizabeth A Fogarty, Elli M Buchert, Yiqin Ma, Ava B Nicely, Laura A Buttitta

{"title":"Transcriptional repression and enhancer decommissioning silence cell cycle genes in postmitotic tissues.","authors":"Elizabeth A Fogarty, Elli M Buchert, Yiqin Ma, Ava B Nicely, Laura A Buttitta","doi":"10.1093/g3journal/jkae203","DOIUrl":"10.1093/g3journal/jkae203","url":null,"abstract":"The mechanisms that maintain a non-cycling status in postmitotic tissues are not well understood. Many cell cycle genes have promoters and enhancers that remain accessible even when cells are terminally differentiated and in a non-cycling state, suggesting their repression must be maintained long term. In contrast, enhancer decommissioning has been observed for rate-limiting cell cycle genes in the Drosophila wing, a tissue where the cells die soon after eclosion, but it has been unclear if this also occurs in other contexts of terminal differentiation. In this study, we show that enhancer decommissioning also occurs at specific, rate-limiting cell cycle genes in the long-lived tissues of the Drosophila eye and brain, and we propose this loss of chromatin accessibility may help maintain a robust postmitotic state. We examined the decommissioned enhancers at specific rate-limiting cell cycle genes and showed that they encode for dynamic temporal and spatial expression patterns that include shared, as well as tissue-specific elements, resulting in broad gene expression with developmentally controlled temporal regulation. We extend our analysis to cell cycle gene expression and chromatin accessibility in the mammalian retina using a published dataset and find that the principles of cell cycle gene regulation identified in terminally differentiating Drosophila tissues are conserved in the differentiating mammalian retina. We propose a robust, non-cycling status is maintained in long-lived postmitotic tissues through a combination of stable repression at most cell cycle genes, alongside enhancer decommissioning at specific rate-limiting cell cycle genes.","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2024-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11457063/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142016896","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

The role of uncertainty and negative feedback loops in the evolution of induced immune defenses. 不确定性和负反馈回路在诱导免疫防御进化中的作用。

IF 2.1 3区生物学

G3: Genes|Genomes|Genetics Pub Date : 2024-10-07 DOI: 10.1093/g3journal/jkae182

Danial Asgari, Alexander J Stewart, Richard P Meisel

{"title":"The role of uncertainty and negative feedback loops in the evolution of induced immune defenses.","authors":"Danial Asgari, Alexander J Stewart, Richard P Meisel","doi":"10.1093/g3journal/jkae182","DOIUrl":"10.1093/g3journal/jkae182","url":null,"abstract":"Organisms use constitutive or induced defenses against pathogens and other external threats. Constitutive defenses are constantly on, whereas induced defenses are activated when needed. Each of these strategies has costs and benefits, which can affect the type of defense that evolves in response to pathogens. In addition, induced defenses are usually regulated by multiple negative feedback mechanisms that prevent overactivation of the immune response. However, it is unclear how negative feedback affects the costs, benefits, and evolution of induced responses. To address this gap, we developed a mechanistic model of the well-characterized Drosophila melanogaster immune signaling network that includes 3 separate mechanisms of negative feedback as a representative of the widespread phenomenon of multilevel regulation of induced responses. We show that, under stochastic fly-bacteria encounters, an induced defense is favored when bacterial encounters are rare or uncertain, but in ways that depend on the bacterial proliferation rate. Our model also predicts that the specific negative regulators that optimize the induced response depend on the bacterial proliferation rate, linking negative feedback mechanisms to the factors that favor induction.","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2024-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11457078/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141897197","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

QTL discovery for agronomic and quality traits in diploid potato clones using PotatoMASH amplicon sequencing. 利用 PotatoMASH 扩增子测序发现二倍体马铃薯克隆中农艺和品质性状的 QTL。

IF 2.1 3区生物学

G3: Genes|Genomes|Genetics Pub Date : 2024-10-07 DOI: 10.1093/g3journal/jkae164

Lea Vexler, Maria de la O Leyva-Perez, Agnieszka Konkolewska, Corentin R Clot, Stephen Byrne, Denis Griffin, Tom Ruttink, Ronald C B Hutten, Christel Engelen, Richard G F Visser, Vanessa Prigge, Silke Wagener, Gisele Lairy-Joly, Jan-David Driesprong, Ea Høegh Riis Sundmark, A Nico O Rookmaker, Herman J van Eck, Dan Milbourne

{"title":"QTL discovery for agronomic and quality traits in diploid potato clones using PotatoMASH amplicon sequencing.","authors":"Lea Vexler, Maria de la O Leyva-Perez, Agnieszka Konkolewska, Corentin R Clot, Stephen Byrne, Denis Griffin, Tom Ruttink, Ronald C B Hutten, Christel Engelen, Richard G F Visser, Vanessa Prigge, Silke Wagener, Gisele Lairy-Joly, Jan-David Driesprong, Ea Høegh Riis Sundmark, A Nico O Rookmaker, Herman J van Eck, Dan Milbourne","doi":"10.1093/g3journal/jkae164","DOIUrl":"10.1093/g3journal/jkae164","url":null,"abstract":"We genotyped a population of 618 diploid potato clones derived from six independent potato-breeding programmes from NW-Europe. The diploids were phenotyped for 23 traits, using standardized protocols and common check varieties, enabling us to derive whole population estimators for most traits. We subsequently performed a genome-wide association study (GWAS) to identify quantitative trait loci (QTL) for all traits with SNPs and short-read haplotypes derived from read-backed phasing. In this study, we used a marker platform called PotatoMASH (Potato Multi-Allele Scanning Haplotags); a pooled multiplex amplicon sequencing based approach. Through this method, neighboring SNPs within an amplicon can be combined to generate multiallelic short-read haplotypes (haplotags) that capture recombination history between the constituent SNPs and reflect the allelic diversity of a given locus in a different way than single bi-allelic SNPs. We found a total of 37 unique QTL across both marker types. A core of 10 QTL was detected with SNPs as well as with haplotags. Haplotags allowed to detect an additional 14 QTL not found based on the SNP set. Conversely, the bi-allelic SNP set also found 13 QTL not detectable using the haplotag set. We conclude that both marker types should routinely be used in parallel to maximize the QTL detection power. We report 19 novel QTL for nine traits: Skin Smoothness, Sprout Dormancy, Total Tuber Number, Tuber Length, Yield, Chipping Color, After-cooking Blackening, Cooking Type, and Eye depth.","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2024-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11457057/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141727049","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

Pseudomolecule-scale genome assemblies of Drepanocaryum sewerzowii and Marmoritis complanata. 基因组报告：Drepanocaryum sewerzowii 和 Marmoritis complanata 的假分子尺度基因组组装。

IF 2.1 3区生物学

G3: Genes|Genomes|Genetics Pub Date : 2024-10-07 DOI: 10.1093/g3journal/jkae172

Samuel J Smit, Caragh Whitehead, Sally R James, Daniel C Jeffares, Grant Godden, Deli Peng, Hang Sun, Benjamin R Lichman

引用次数: 0

Genomics of natural populations: gene conversion events reveal selected genes within the inversions of Drosophila pseudoobscura. 自然种群的基因组学：基因转换事件揭示了假鳞翅目果蝇逆转录中的部分基因。

IF 2.1 3区生物学

G3: Genes|Genomes|Genetics Pub Date : 2024-10-07 DOI: 10.1093/g3journal/jkae176

Stephen W Schaeffer, Stephen Richards, Zachary L Fuller

{"title":"Genomics of natural populations: gene conversion events reveal selected genes within the inversions of Drosophila pseudoobscura.","authors":"Stephen W Schaeffer, Stephen Richards, Zachary L Fuller","doi":"10.1093/g3journal/jkae176","DOIUrl":"10.1093/g3journal/jkae176","url":null,"abstract":"When adaptive phenotypic variation or quantitative trait loci map within an inverted segment of a chromosome, researchers often despair because the suppression of crossing over will prevent the discovery of selective target genes that established the rearrangement. If an inversion polymorphism is old enough, then the accumulation of gene conversion tracts offers the promise that quantitative trait loci or selected loci within inversions can be mapped. The inversion polymorphism of Drosophila pseudoobscura is a model system to show that gene conversion analysis is a useful tool for mapping selected loci within inversions. D. pseudoobscura has over 30 different chromosomal arrangements on the third chromosome (Muller C) in natural populations and their frequencies vary with changes in environmental habitats. Statistical tests of five D. pseudoobscura gene arrangements identified outlier genes within inverted regions that had potentially heritable variation, either fixed amino acid differences or differential expression patterns. We use genome sequences of the inverted third chromosome (Muller C) to infer 98,443 gene conversion tracts for a total coverage of 142 Mb or 7.2× coverage of the 19.7 Mb chromosome. We estimated gene conversion tract coverage in the 2,668 genes on Muller C and tested whether gene conversion coverage was similar among arrangements for outlier vs non-outlier loci. Outlier genes had lower gene conversion tract coverage among arrangements than the non-outlier genes suggesting that selection removes exchanged DNA in the outlier genes. These data support the hypothesis that the third chromosome in D. pseudoobscura captured locally adapted combinations of alleles prior to inversion mutation events.","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2024-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11457094/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141787683","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

PyBrOpS: a Python package for breeding program simulation and optimization for multi-objective breeding. PyBrOpS：用于多目标育种程序模拟和优化的 Python 软件包。

IF 2.1 3区生物学

G3: Genes|Genomes|Genetics Pub Date : 2024-10-07 DOI: 10.1093/g3journal/jkae199

Robert Z Shrote, Addie M Thompson

{"title":"PyBrOpS: a Python package for breeding program simulation and optimization for multi-objective breeding.","authors":"Robert Z Shrote, Addie M Thompson","doi":"10.1093/g3journal/jkae199","DOIUrl":"10.1093/g3journal/jkae199","url":null,"abstract":"Plant breeding is a complex endeavor that is almost always multi-objective in nature. In recent years, stochastic breeding simulations have been used by breeders to assess the merits of alternative breeding strategies and assist in decision-making. In addition to simulations, visualization of a Pareto frontier for multiple competing breeding objectives can assist breeders in decision-making. This paper introduces Python Breeding Optimizer and Simulator (PyBrOpS), a Python package capable of performing multi-objective optimization of breeding objectives and stochastic simulations of breeding pipelines. PyBrOpS is unique among other simulation platforms in that it can perform multi-objective optimizations and incorporate these results into breeding simulations. PyBrOpS is built to be highly modular and has a script-based philosophy, making it highly extensible and customizable. In this paper, we describe some of the main features of PyBrOpS and demonstrate its ability to map Pareto frontiers for breeding possibilities and perform multi-objective selection in a simulated breeding pipeline.","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2024-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11457082/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141999721","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: Genetics of Bacteria: a call for papers. Correction to：细菌遗传学：论文征集。

IF 2.1 3区生物学

G3: Genes|Genomes|Genetics Pub Date : 2024-10-07 DOI: 10.1093/g3journal/jkae192

引用次数: 0

Comparative genomics of Metarhizium brunneum strains V275 and ARSEF 4556: unraveling intraspecies diversity. 布氏杆菌 V275 株和 ARSEF 4556 株的比较基因组学：揭示种内多样性。

IF 2.1 3区生物学

G3: Genes|Genomes|Genetics Pub Date : 2024-10-07 DOI: 10.1093/g3journal/jkae190

Alexandra M Kortsinoglou, Martyn J Wood, Antonis I Myridakis, Marios Andrikopoulos, Andreas Roussis, Dan Eastwood, Tariq Butt, Vassili N Kouvelis

{"title":"Comparative genomics of Metarhizium brunneum strains V275 and ARSEF 4556: unraveling intraspecies diversity.","authors":"Alexandra M Kortsinoglou, Martyn J Wood, Antonis I Myridakis, Marios Andrikopoulos, Andreas Roussis, Dan Eastwood, Tariq Butt, Vassili N Kouvelis","doi":"10.1093/g3journal/jkae190","DOIUrl":"10.1093/g3journal/jkae190","url":null,"abstract":"Entomopathogenic fungi belonging to the Order Hypocreales are renowned for their ability to infect and kill insect hosts, while their endophytic mode of life and the beneficial rhizosphere effects on plant hosts have only been recently recognized. Understanding the molecular mechanisms underlying their different lifestyles could optimize their potential as both biocontrol and biofertilizer agents, as well as the wider appreciation of niche plasticity in fungal ecology. This study describes the comprehensive whole genome sequencing and analysis of one of the most effective entomopathogenic and endophytic EPF strains, Metarhizium brunneum V275 (commercially known as Lalguard Met52), achieved through Nanopore and Illumina reads. Comparative genomics for exploring intraspecies variability and analyses of key gene sets were conducted with a second effective EPF strain, M. brunneum ARSEF 4556. The search for strain- or species-specific genes was extended to M. brunneum strain ARSEF 3297 and other species of genus Metarhizium, to identify molecular mechanisms and putative key genome adaptations associated with mode of life differences. Genome size differed significantly, with M. brunneum V275 having the largest genome amongst M. brunneum strains sequenced to date. Genome analyses revealed an abundance of plant-degrading enzymes, plant colonization-associated genes, and intriguing intraspecies variations regarding their predicted secondary metabolic compounds and the number and localization of Transposable Elements. The potential significance of the differences found between closely related endophytic and entomopathogenic fungi, regarding plant growth-promoting and entomopathogenic abilities, are discussed, enhancing our understanding of their diverse functionalities and putative applications in agriculture and ecology.","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2024-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11457142/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142106125","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

Mutations in nuclear genes encoding mitochondrial ribosome proteins restore pollen fertility in S male-sterile maize. 编码线粒体核糖体蛋白的核基因突变可恢复 S 型雄性不育玉米的花粉育性。

IF 2.1 3区生物学

G3: Genes|Genomes|Genetics Pub Date : 2024-10-07 DOI: 10.1093/g3journal/jkae201

Yan Wang, Rosalind Williams-Carrier, Robert Meeley, Timothy Fox, Karen Chamusco, Mina Nashed, L Curtis Hannah, Susan Gabay-Laughnan, Alice Barkan, Christine Chase

{"title":"Mutations in nuclear genes encoding mitochondrial ribosome proteins restore pollen fertility in S male-sterile maize.","authors":"Yan Wang, Rosalind Williams-Carrier, Robert Meeley, Timothy Fox, Karen Chamusco, Mina Nashed, L Curtis Hannah, Susan Gabay-Laughnan, Alice Barkan, Christine Chase","doi":"10.1093/g3journal/jkae201","DOIUrl":"10.1093/g3journal/jkae201","url":null,"abstract":"The interaction of plant mitochondrial and nuclear genetic systems is exemplified by mitochondria-encoded cytoplasmic male sterility (CMS) under the control of nuclear restorer-of-fertility genes. The S type of CMS in maize is characterized by a pollen collapse phenotype and a unique paradigm for fertility restoration in which numerous nuclear restorer-of-fertility lethal mutations rescue pollen function but condition homozygous-lethal seed phenotypes. Two nonallelic restorer mutations recovered from Mutator transposon-active lines were investigated to determine the mechanisms of pollen fertility restoration and seed lethality. Mu Illumina sequencing of transposon-flanking regions identified insertion alleles of nuclear genes encoding mitochondrial ribosomal proteins RPL6 and RPL14 as candidate restorer-of-fertility lethal mutations. Both candidates were associated with lowered abundance of mitochondria-encoded proteins in developing maize pollen, and the rpl14 mutant candidate was confirmed by independent insertion alleles. While the restored pollen functioned despite reduced accumulation of mitochondrial respiratory proteins, normal-cytoplasm plants heterozygous for the mutant alleles showed a significant pollen transmission bias in favor of the nonmutant Rpl6 and Rpl14 alleles. CMS-S fertility restoration affords a unique forward genetic approach to investigate the mitochondrial requirements for, and contributions to, pollen and seed development.","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2024-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142008639","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

Functional and regulatory diversification of Period genes responsible for circadian rhythm in vertebrates. 脊椎动物昼夜节律周期基因的功能和调控多样化。

IF 2.1 3区生物学

G3: Genes|Genomes|Genetics Pub Date : 2024-10-07 DOI: 10.1093/g3journal/jkae162

Jun Soung Kwak, M Ángel León-Tapia, Celian Diblasi, Domniki Manousi, Lars Grønvold, Guro Katrine Sandvik, Marie Saitou

{"title":"Functional and regulatory diversification of Period genes responsible for circadian rhythm in vertebrates.","authors":"Jun Soung Kwak, M Ángel León-Tapia, Celian Diblasi, Domniki Manousi, Lars Grønvold, Guro Katrine Sandvik, Marie Saitou","doi":"10.1093/g3journal/jkae162","DOIUrl":"10.1093/g3journal/jkae162","url":null,"abstract":"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.","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2024-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11457068/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141727048","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