G3: Genes|Genomes|Genetics最新文献_第3页

A comprehensive atlas of pig RNA editome across 23 tissues reveals RNA editing affecting interaction mRNA-miRNAs. 横跨 23 种组织的猪 RNA 编辑组综合图谱揭示了影响 mRNA-miRNA 相互作用的 RNA 编辑。

IF 2.1 3区生物学

G3: Genes|Genomes|Genetics Pub Date : 2024-10-07 DOI: 10.1093/g3journal/jkae178

Jiajia Long, Weiwei Liu, Xinhao Fan, Yalan Yang, Xiaogan Yang, Zhonglin Tang

{"title":"A comprehensive atlas of pig RNA editome across 23 tissues reveals RNA editing affecting interaction mRNA-miRNAs.","authors":"Jiajia Long, Weiwei Liu, Xinhao Fan, Yalan Yang, Xiaogan Yang, Zhonglin Tang","doi":"10.1093/g3journal/jkae178","DOIUrl":"10.1093/g3journal/jkae178","url":null,"abstract":"RNA editing is a co-transcriptional/post-transcriptional modification that is mediated by the ADAR enzyme family. Profiling of RNA editing is very limited in pigs. In this study, we collated 3813 RNA-seq data from the public repositories across 23 tissues and carried out comprehensive profiling of RNA editing in pigs. In total, 127,927 A-to-I RNA-editing sites were detected. Our analysis showed that 98.2% of RNA-editing sites were located within repeat regions, primarily within the pig-specific SINE retrotransposon PRE-1/Pre0_SS elements. Subsequently, we focused on analyzing specific RNA-editing sites (SESs) in skeletal muscle tissues. Functional enrichment analyses suggested that they were enriched in signaling pathways associated with muscle cell differentiation, including DMD, MYOD1, and CAV1 genes. Furthermore, we discovered that RNA editing event in the 3'UTR of CFLAR mRNA influenced miR-708-5p binding in this region. In this study, the panoramic RNA-editing landscape of different tissues of pigs was systematically mapped, and RNA-editing sites and genes involved in muscle cell differentiation were identified. In summary, we identified modifications to pig RNA-editing sites and provided candidate targets for further validation.","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11457091/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141874570","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

Complementary approaches to dissect late leaf rust resistance in an interspecific raspberry population. 用互补方法剖析树莓种间群体的晚期叶锈病抗性。

IF 2.1 3区生物学

G3: Genes|Genomes|Genetics Pub Date : 2024-10-07 DOI: 10.1093/g3journal/jkae202

Melina Prado, Allison Vieira da Silva, Gabriela Romêro Campos, Karina Lima Reis Borges, Rafael Massahiro Yassue, Gustavo Husein, Felix Frederik Akens, Marcel Bellato Sposito, Lilian Amorim, Pariya Behrouzi, Daniela Bustos-Korts, Roberto Fritsche-Neto

{"title":"Complementary approaches to dissect late leaf rust resistance in an interspecific raspberry population.","authors":"Melina Prado, Allison Vieira da Silva, Gabriela Romêro Campos, Karina Lima Reis Borges, Rafael Massahiro Yassue, Gustavo Husein, Felix Frederik Akens, Marcel Bellato Sposito, Lilian Amorim, Pariya Behrouzi, Daniela Bustos-Korts, Roberto Fritsche-Neto","doi":"10.1093/g3journal/jkae202","DOIUrl":"10.1093/g3journal/jkae202","url":null,"abstract":"Over the last 10 years, global raspberry production has increased by 47.89%, based mainly on the red raspberry species (Rubus idaeus). However, the black raspberry (Rubus occidentalis), although less consumed, is resistant to one of the most important diseases for the crop, the late leaf rust caused by Acculeastrum americanum fungus. In this context, genetic resistance is the most sustainable way to control the disease, mainly because there are no registered fungicides for late leaf rust in Brazil. Therefore, the aim was to understand the genetic architecture that controls resistance to late leaf rust in raspberries. For that, we used an interspecific multiparental population using the species mentioned above as parents, 2 different statistical approaches to associate the phenotypes with markers [GWAS (genome-wide association studies) and copula graphical models], and 2 phenotyping methodologies from the first to the 17th day after inoculation (high-throughput phenotyping with a multispectral camera and traditional phenotyping by disease severity scores). Our findings indicate that a locus of higher effect, at position 13.3 Mb on chromosome 5, possibly controls late leaf rust resistance, as both GWAS and the network suggested the same marker. Of the 12 genes flanking its region, 4 were possible receptors, 3 were likely defense executors, 1 gene was likely part of signaling cascades, and 4 were classified as nondefense related. Although the network and GWAS indicated the same higher effect genomic region, the network identified other different candidate regions, potentially complementing the genetic control comprehension.","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11457092/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142035633","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

DNA methylation analysis reveals local changes in resistant and susceptible soybean lines in response to Phytophthora sansomeana. DNA 甲基化分析揭示了抗性和易感性大豆品系对 Phytophthora sansomeana 的局部反应变化。

IF 2.1 3区生物学

G3: Genes|Genomes|Genetics Pub Date : 2024-10-07 DOI: 10.1093/g3journal/jkae191

Charlotte N DiBiase, Xi Cheng, Gwonjin Lee, Richard C Moore, Austin G McCoy, Martin I Chilvers, Lianjun Sun, Dechun Wang, Feng Lin, Meixia Zhao

{"title":"DNA methylation analysis reveals local changes in resistant and susceptible soybean lines in response to Phytophthora sansomeana.","authors":"Charlotte N DiBiase, Xi Cheng, Gwonjin Lee, Richard C Moore, Austin G McCoy, Martin I Chilvers, Lianjun Sun, Dechun Wang, Feng Lin, Meixia Zhao","doi":"10.1093/g3journal/jkae191","DOIUrl":"10.1093/g3journal/jkae191","url":null,"abstract":"Phytophthora sansomeana is an emerging oomycete pathogen causing root rot in many agricultural species including soybean. However, as of now, only one potential resistance gene has been identified in soybean, and our understanding of how genetic and epigenetic regulation in soybean contributes to responses against this pathogen remains largely unknown. In this study, we performed whole genome bisulfite sequencing (WGBS) on two soybean lines, Colfax (resistant) and Williams 82 (susceptible), in response to P. sansomeana at two time points: 4 and 16 hours post-inoculation to compare their methylation changes. Our findings revealed that there were no significant changes in genome-wide CG, CHG (H = A, T, or C), and CHH methylation. However, we observed local methylation changes, specially an increase in CHH methylation around genes and transposable elements (TEs) after inoculation, which occurred earlier in the susceptible line and later in the resistant line. After inoculation, we identified differentially methylated regions (DMRs) in both Colfax and Williams 82, with a predominant presence in TEs. Notably, our data also indicated that more TEs exhibited changes in their methylomes in the susceptible line compared to the resistant line. Furthermore, we discovered 837 DMRs within or flanking 772 differentially expressed genes (DEGs) in Colfax and 166 DMRs within or flanking 138 DEGs in Williams 82. These DEGs had diverse functions, with Colfax primarily showing involvement in metabolic process, defense response, plant and pathogen interaction, anion and nucleotide binding, and catalytic activity, while Williams 82 exhibited a significant association with photosynthesis. These findings suggest distinct molecular responses to P. sansomeana infection in the resistant and susceptible soybean lines.","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11457093/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141982073","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

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":null,"pages":null},"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":null,"pages":null},"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

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

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":null,"pages":null},"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":null,"pages":null},"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":null,"pages":null},"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