G3 (Bethesda, Md.)最新文献_第5页

Correction to: Genetically induced redox stress occurs in a yeast model for Roberts syndrome. 更正:遗传诱导的氧化还原应激发生在罗伯茨综合征的酵母模型中。

IF 2.6

G3 (Bethesda, Md.) Pub Date : 2022-08-25 DOI: 10.1093/g3journal/jkac171

引用次数: 0

Analysis of transcriptome data and quantitative trait loci enables the identification of candidate genes responsible for fiber strength in Gossypium barbadense. 通过转录组数据和数量性状位点的分析，鉴定出了决定巴氏棉纤维强度的候选基因。

IF 2.6

G3 (Bethesda, Md.) Pub Date : 2022-08-25 DOI: 10.1093/g3journal/jkac167

Yajie Duan, Qin Chen, Quanjia Chen, Kai Zheng, Yongsheng Cai, Yilei Long, Jieyin Zhao, Yaping Guo, Fenglei Sun, Yanying Qu

{"title":"Analysis of transcriptome data and quantitative trait loci enables the identification of candidate genes responsible for fiber strength in Gossypium barbadense.","authors":"Yajie Duan, Qin Chen, Quanjia Chen, Kai Zheng, Yongsheng Cai, Yilei Long, Jieyin Zhao, Yaping Guo, Fenglei Sun, Yanying Qu","doi":"10.1093/g3journal/jkac167","DOIUrl":"https://doi.org/10.1093/g3journal/jkac167","url":null,"abstract":"Gossypium barbadense possesses a superior fiber quality because of its fiber length and strength. An in-depth analysis of the underlying genetic mechanism could aid in filling the gap in research regarding fiber strength and could provide helpful information for Gossypium barbadense breeding. Three quantitative trait loci related to fiber strength were identified from a Gossypium barbadense recombinant inbred line (PimaS-7 × 5917) for further analysis. RNA sequencing was performed in the fiber tissues of PimaS-7 × 5917 0-35 days postanthesis. Four specific modules closely related to the secondary wall-thickening stage were obtained using the weighted gene coexpression network analysis. In total, 55 genes were identified as differentially expressed from 4 specific modules. Gene Ontology and the Kyoto Encyclopedia of Genes and Genomes were used for enrichment analysis, and Gbar_D11G032910, Gbar_D08G020540, Gbar_D08G013370, Gbar_D11G033670, and Gbar_D11G029020 were found to regulate fiber strength by playing a role in the composition of structural constituents of cytoskeleton and microtubules during fiber development. Quantitative real-time PCR results confirmed the accuracy of the transcriptome data. This study provides a quick strategy for exploring candidate genes and provides new insights for improving fiber strength in cotton.","PeriodicalId":520629,"journal":{"name":"G3 (Bethesda, Md.)","volume":" ","pages":""},"PeriodicalIF":2.6,"publicationDate":"2022-08-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9434320/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40625036","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 4

Allele-specific alternative splicing of Drosophila Ribosomal protein S21 suppresses a lethal mutation in the Phosphorylated adaptor for RNA export (Phax) gene. 果蝇核糖体蛋白S21的等位基因特异性选择性剪接抑制了RNA输出磷酸化接头(Phax)基因的致命突变。

IF 2.6

G3 (Bethesda, Md.) Pub Date : 2022-08-25 DOI: 10.1093/g3journal/jkac195

Eric L Garcia

{"title":"Allele-specific alternative splicing of Drosophila Ribosomal protein S21 suppresses a lethal mutation in the Phosphorylated adaptor for RNA export (Phax) gene.","authors":"Eric L Garcia","doi":"10.1093/g3journal/jkac195","DOIUrl":"https://doi.org/10.1093/g3journal/jkac195","url":null,"abstract":"Genetic disruptions to the biogenesis of spliceosomal small-nuclear ribonucleoproteins in Drosophila cause wide-spread alternative splicing changes, including changes to the splicing of pre-mRNA for Ribosomal protein S21 (RpS21). Using a transposon mutant for the Phosphorylated adaptor for RNA export (Phax) gene, we demonstrate that changes in the splicing of RpS21 transcripts have a strong influence on the developmental progression of PhaxSH/SH mutants. Different alleles of the Drosophila RpS21 gene are circulating in common laboratory strains and cell lines. These alleles exhibit differences in RpS21 intron retention and splicing efficiency. Differences in the splicing of RpS21 transcripts account for prior conflicting observations of the phenotypic severity of PhaxSH/SH mutant stocks. The alleles uncover a strong splicing enhancer in RpS21 transcripts that can fully suppress the larval lethality and partially suppress the pupal lethality exhibited by PhaxSH/SH mutant lines. In the absence of the splicing enhancer, the splicing of RpS21 transcripts can be modulated in trans by the SR-rich B52 splicing factor. As PhaxSH/SH mutants exhibit wide-spread splicing changes in transcripts for other genes, findings here establish the importance of a single alternative splicing event, RpS21 splicing or intron retention, to the developmental progression of Drosophila.","PeriodicalId":520629,"journal":{"name":"G3 (Bethesda, Md.)","volume":" ","pages":""},"PeriodicalIF":2.6,"publicationDate":"2022-08-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9434302/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40667141","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A comparative analysis of genomic and phenomic predictions of growth-related traits in 3-way coffee hybrids. 3-way咖啡杂交种生长相关性状的基因组和表型预测比较分析。

IF 2.6

G3 (Bethesda, Md.) Pub Date : 2022-08-25 DOI: 10.1093/g3journal/jkac170

Alain J Mbebi, Jean-Christophe Breitler, Mélanie Bordeaux, Ronan Sulpice, Marcus McHale, Hao Tong, Lucile Toniutti, Jonny Alonso Castillo, Benoît Bertrand, Zoran Nikoloski

{"title":"A comparative analysis of genomic and phenomic predictions of growth-related traits in 3-way coffee hybrids.","authors":"Alain J Mbebi, Jean-Christophe Breitler, Mélanie Bordeaux, Ronan Sulpice, Marcus McHale, Hao Tong, Lucile Toniutti, Jonny Alonso Castillo, Benoît Bertrand, Zoran Nikoloski","doi":"10.1093/g3journal/jkac170","DOIUrl":"https://doi.org/10.1093/g3journal/jkac170","url":null,"abstract":"Genomic prediction has revolutionized crop breeding despite remaining issues of transferability of models to unseen environmental conditions and environments. Usage of endophenotypes rather than genomic markers leads to the possibility of building phenomic prediction models that can account, in part, for this challenge. Here, we compare and contrast genomic prediction and phenomic prediction models for 3 growth-related traits, namely, leaf count, tree height, and trunk diameter, from 2 coffee 3-way hybrid populations exposed to a series of treatment-inducing environmental conditions. The models are based on 7 different statistical methods built with genomic markers and ChlF data used as predictors. This comparative analysis demonstrates that the best-performing phenomic prediction models show higher predictability than the best genomic prediction models for the considered traits and environments in the vast majority of comparisons within 3-way hybrid populations. In addition, we show that phenomic prediction models are transferrable between conditions but to a lower extent between populations and we conclude that chlorophyll a fluorescence data can serve as alternative predictors in statistical models of coffee hybrid performance. Future directions will explore their combination with other endophenotypes to further improve the prediction of growth-related traits for crops.","PeriodicalId":520629,"journal":{"name":"G3 (Bethesda, Md.)","volume":" ","pages":""},"PeriodicalIF":2.6,"publicationDate":"2022-08-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9434219/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40474718","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

Accounting for population structure in genomic predictions of Eucalyptus globulus. 巨桉基因组预测中种群结构的计算。

IF 2.6

G3 (Bethesda, Md.) Pub Date : 2022-08-25 DOI: 10.1093/g3journal/jkac180

Andrew N Callister, Matias Bermann, Stephen Elms, Ben P Bradshaw, Daniela Lourenco, Jeremy T Brawner

{"title":"Accounting for population structure in genomic predictions of Eucalyptus globulus.","authors":"Andrew N Callister, Matias Bermann, Stephen Elms, Ben P Bradshaw, Daniela Lourenco, Jeremy T Brawner","doi":"10.1093/g3journal/jkac180","DOIUrl":"https://doi.org/10.1093/g3journal/jkac180","url":null,"abstract":"Genetic groups have been widely adopted in tree breeding to account for provenance effects within pedigree-derived relationship matrices. However, provenances or genetic groups have not yet been incorporated into single-step genomic BLUP (\"HBLUP\") analyses of tree populations. To quantify the impact of accounting for population structure in Eucalyptus globulus, we used HBLUP to compare breeding value predictions from models excluding base population effects and models including either fixed genetic groups or the marker-derived proxies, also known as metafounders. Full-sib families from 2 separate breeding populations were evaluated across 13 sites in the \"Green Triangle\" region of Australia. Gamma matrices (Γ) describing similarities among metafounders reflected the geographic distribution of populations and the origins of 2 land races were identified. Diagonal elements of Γ provided population diversity or allelic covariation estimates between 0.24 and 0.56. Genetic group solutions were strongly correlated with metafounder solutions across models and metafounder effects influenced the genetic solutions of base population parents. The accuracy, stability, dispersion, and bias of model solutions were compared using the linear regression method. Addition of genomic information increased accuracy from 0.41 to 0.47 and stability from 0.68 to 0.71, while increasing bias slightly. Dispersion was within 0.10 of the ideal value (1.0) for all models. Although inclusion of metafounders did not strongly affect accuracy or stability and had mixed effects on bias, we nevertheless recommend the incorporation of metafounders in prediction models to represent the hierarchical genetic population structure of recently domesticated populations.","PeriodicalId":520629,"journal":{"name":"G3 (Bethesda, Md.)","volume":" ","pages":""},"PeriodicalIF":2.6,"publicationDate":"2022-08-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9434241/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40580524","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

Correction to: A Genome-Wide Screen for Genes Affecting Spontaneous Direct-Repeat Recombination in Saccharomyces cerevisiae. 更正:在酿酒酵母中影响自发直接重复重组基因的全基因组筛选。

IF 2.6

G3 (Bethesda, Md.) Pub Date : 2022-08-25 DOI: 10.1093/g3journal/jkac181

引用次数: 0

Transcriptomic analysis of deceptively pollinated Arum maculatum (Araceae) reveals association between terpene synthase expression in floral trap chamber and species-specific pollinator attraction. 伪传粉Arum maculatum(天南星科)的转录组学分析揭示了诱花室中萜烯合成酶的表达与物种特异性传粉者的吸引之间的关系。

IF 2.6

G3 (Bethesda, Md.) Pub Date : 2022-08-25 DOI: 10.1093/g3journal/jkac175

Mark A Szenteczki, Adrienne L Godschalx, Jérémy Gauthier, Marc Gibernau, Sergio Rasmann, Nadir Alvarez

{"title":"Transcriptomic analysis of deceptively pollinated Arum maculatum (Araceae) reveals association between terpene synthase expression in floral trap chamber and species-specific pollinator attraction.","authors":"Mark A Szenteczki, Adrienne L Godschalx, Jérémy Gauthier, Marc Gibernau, Sergio Rasmann, Nadir Alvarez","doi":"10.1093/g3journal/jkac175","DOIUrl":"https://doi.org/10.1093/g3journal/jkac175","url":null,"abstract":"Deceptive pollination often involves volatile organic compound emissions that mislead insects into performing nonrewarding pollination. Among deceptively pollinated plants, Arum maculatum is particularly well-known for its potent dung-like volatile organic compound emissions and specialized floral chamber, which traps pollinators-mainly Psychoda phalaenoides and Psychoda grisescens-overnight. However, little is known about the genes underlying the production of many Arum maculatum volatile organic compounds, and their influence on variation in pollinator attraction rates. Therefore, we performed de novo transcriptome sequencing of Arum maculatum appendix and male floret tissue collected during anthesis and postanthesis, from 10 natural populations across Europe. These RNA-seq data were paired with gas chromatography-mass spectrometry analyses of floral scent composition and pollinator data collected from the same inflorescences. Differential expression analyses revealed candidate transcripts in appendix tissue linked to malodourous volatile organic compounds including indole, p-cresol, and 2-heptanone. In addition, we found that terpene synthase expression in male floret tissue during anthesis significantly covaried with sex- and species-specific attraction of Psychoda phalaenoides and Psychoda grisescens. Taken together, our results provide the first insights into molecular mechanisms underlying pollinator attraction patterns in Arum maculatum and highlight floral chamber sesquiterpene (e.g. bicyclogermacrene) synthases as interesting candidate genes for further study.","PeriodicalId":520629,"journal":{"name":"G3 (Bethesda, Md.)","volume":" ","pages":""},"PeriodicalIF":2.6,"publicationDate":"2022-08-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9434142/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40622597","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

Correlations of expression of nuclear and mitochondrial genes in triploid fish. 三倍体鱼细胞核和线粒体基因表达的相关性。

IF 2.6

G3 (Bethesda, Md.) Pub Date : 2022-08-25 DOI: 10.1093/g3journal/jkac197

Jialin Cui, Hong Zhang, Xin Gao, Xueyin Zhang, Mengxue Luo, Li Ren, Shaojun Liu

{"title":"Correlations of expression of nuclear and mitochondrial genes in triploid fish.","authors":"Jialin Cui, Hong Zhang, Xin Gao, Xueyin Zhang, Mengxue Luo, Li Ren, Shaojun Liu","doi":"10.1093/g3journal/jkac197","DOIUrl":"https://doi.org/10.1093/g3journal/jkac197","url":null,"abstract":"The expression of nuclear and mitochondrial genes, as well as their coordinated control, regulates cell proliferation, individual development, and disease in animals. However, the potential coregulation between nuclear and mitochondrial genes is unclear in triploid fishes. The two triploids (R2C and RC2) with distinct mitochondrial genomes but similar nuclear genomes exhibit different embryonic development times and growth rates. They are an excellent model for studying how nuclear and mitochondrial genes coordinate. Here, we performed the mRNA-seq of four stages of embryonic development (blastula, gastrula, segmentation, and hatching periods) in the two triploids (R2C and RC2) and their diploid inbred parents (red crucian carp and common carp). After establishing the four patterns of mitochondrial and nuclear gene expression, 270 nuclear genes regulated by mitochondrial genes were predicted. The expression levels of APC16 and Trim33 were higher in RC2 than in R2C, suggesting their potential effects on regulating embryonic development time. In addition, 308 differentially expressed genes filtered from the list of nuclear-encoded mitochondrial genes described by Mercer et al. in 2011 were considered potential genes for which nuclear genes regulate mitochondrial function. The findings might aid in our understanding of the correlation between mitochondrial and nuclear genomes as well as their synergistic effects on embryonic development.","PeriodicalId":520629,"journal":{"name":"G3 (Bethesda, Md.)","volume":" ","pages":""},"PeriodicalIF":2.6,"publicationDate":"2022-08-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9434317/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40691545","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Large RNP granules in Caenorhabditis elegans oocytes have distinct phases of RNA-binding proteins. 秀丽隐杆线虫卵母细胞中的大RNP颗粒具有不同的rna结合蛋白相。

IF 2.6

G3 (Bethesda, Md.) Pub Date : 2022-08-25 DOI: 10.1093/g3journal/jkac173

Mohamed T Elaswad, Brooklynne M Watkins, Katherine G Sharp, Chloe Munderloh, Jennifer A Schisa

{"title":"Large RNP granules in Caenorhabditis elegans oocytes have distinct phases of RNA-binding proteins.","authors":"Mohamed T Elaswad, Brooklynne M Watkins, Katherine G Sharp, Chloe Munderloh, Jennifer A Schisa","doi":"10.1093/g3journal/jkac173","DOIUrl":"https://doi.org/10.1093/g3journal/jkac173","url":null,"abstract":"The germ line provides an excellent in vivo system to study the regulation and function of RNP granules. Germ granules are conserved germ line-specific RNP granules that are positioned in the Caenorhabditis elegans adult gonad to function in RNA maintenance, regulation, and surveillance. In Caenorhabditis elegans, when oogenesis undergoes extended meiotic arrest, germ granule proteins and other RNA-binding proteins assemble into much larger RNP granules whose hypothesized function is to regulate RNA metabolism and maintain oocyte quality. To gain insight into the function of oocyte RNP granules, in this report, we characterize distinct phases for four protein components of RNP granules in arrested oocytes. We find that the RNA-binding protein PGL-1 is dynamic and has liquid-like properties, while the intrinsically disordered protein MEG-3 has gel-like properties, similar to the properties of the two proteins in small germ granules of embryos. We find that MEX-3 exhibits several gel-like properties but is more dynamic than MEG-3, while CGH-1 is dynamic but does not consistently exhibit liquid-like characteristics and may be an intermediate phase within RNP granules. These distinct phases of RNA-binding proteins correspond to, and may underlie, differential responses to stress. Interestingly, in oocyte RNP granules, MEG-3 is not required for the condensation of PGL-1 or other RNA-binding proteins, which differs from the role of MEG-3 in small, embryonic germ granules. Lastly, we show that the PUF-5 translational repressor appears to promote MEX-3 and MEG-3 condensation into large RNP granules; however, this role may be associated with regulation of oogenesis.","PeriodicalId":520629,"journal":{"name":"G3 (Bethesda, Md.)","volume":" ","pages":""},"PeriodicalIF":2.6,"publicationDate":"2022-08-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9434171/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40492605","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 2

Quantitative evaluation of nonlinear methods for population structure visualization and inference. 人口结构可视化与推理非线性方法的定量评价。

IF 2.6

G3 (Bethesda, Md.) Pub Date : 2022-08-25 DOI: 10.1093/g3journal/jkac191

Jordan Ubbens, Mitchell J Feldmann, Ian Stavness, Andrew G Sharpe

{"title":"Quantitative evaluation of nonlinear methods for population structure visualization and inference.","authors":"Jordan Ubbens, Mitchell J Feldmann, Ian Stavness, Andrew G Sharpe","doi":"10.1093/g3journal/jkac191","DOIUrl":"https://doi.org/10.1093/g3journal/jkac191","url":null,"abstract":"Population structure (also called genetic structure and population stratification) is the presence of a systematic difference in allele frequencies between subpopulations in a population as a result of nonrandom mating between individuals. It can be informative of genetic ancestry, and in the context of medical genetics, it is an important confounding variable in genome-wide association studies. Recently, many nonlinear dimensionality reduction techniques have been proposed for the population structure visualization task. However, an objective comparison of these techniques has so far been missing from the literature. In this article, we discuss the previously proposed nonlinear techniques and some of their potential weaknesses. We then propose a novel quantitative evaluation methodology for comparing these nonlinear techniques, based on populations for which pedigree is known a priori either through artificial selection or simulation. Based on this evaluation metric, we find graph-based algorithms such as t-SNE and UMAP to be superior to principal component analysis, while neural network-based methods fall behind.","PeriodicalId":520629,"journal":{"name":"G3 (Bethesda, Md.)","volume":" ","pages":""},"PeriodicalIF":2.6,"publicationDate":"2022-08-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9434256/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40664551","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0