G3: Genes|Genomes|Genetics最新文献

Estimating allele frequencies, ancestry proportions and genotype likelihoods in the presence of mapping bias.

IF 2.2 3区生物学

G3: Genes|Genomes|Genetics Pub Date : 2025-07-30 DOI: 10.1093/g3journal/jkaf172

Torsten Günther, Amy Goldberg, Joshua G Schraiber

{"title":"Estimating allele frequencies, ancestry proportions and genotype likelihoods in the presence of mapping bias.","authors":"Torsten Günther, Amy Goldberg, Joshua G Schraiber","doi":"10.1093/g3journal/jkaf172","DOIUrl":"https://doi.org/10.1093/g3journal/jkaf172","url":null,"abstract":"Population genomic analyses rely on an accurate and unbiased characterization of the genetic composition of the studied population. For short-read, high-throughput sequencing data, mapping sequencing reads to a linear reference genome can bias population genetic inference due to mismatches in reads carrying non-reference alleles. In this study, we investigate the impact of mapping bias on allele frequency estimates from pseudohaploid data and genotype likelihoods, two approaches commonly used in ultra-low to medium coverage sequencing. To mitigate mapping bias, we propose an empirical adjustment to genotype likelihoods. Using data from the 1000 Genomes Project, we find that our new method improves allele frequency estimation. To test a downstream application, we simulate ancient DNA data with realistic post-mortem damage to compare widely used methods for estimating ancestry proportions under different scenarios, including reference genome selection, population divergence, and sequencing depth. Our findings reveal that mapping bias can lead to differences in estimated admixture proportion of up to 4% depending on the reference population. However, the choice of method has a much stronger impact, with some methods showing differences of 10%. qpAdm appears to perform best at estimating simulated ancestry proportions, but it is sensitive to mapping bias and its applicability may vary across species due to its requirement for additional populations beyond the sources and target population. Our adjusted genotype likelihood approach largely mitigates the effect of mapping bias on genome-wide ancestry estimates from genotype likelihood-based tools. However, it cannot account for the bias introduced by the method itself or the noise in individual site allele frequency estimates due to low sequencing depth. Overall, our study provides valuable insights for obtaining more precise estimates of allele frequencies and ancestry proportions in empirical studies.","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2025-07-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144752928","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

The chromosome-level genome assembly of the slug Deroceras laeve facilitates its use as a comparative model of regeneration. slug Deroceras lave的染色体水平基因组组装便于其作为再生的比较模型使用。

IF 2.2 3区生物学

G3: Genes|Genomes|Genetics Pub Date : 2025-07-30 DOI: 10.1093/g3journal/jkaf164

Jerónimo R Miranda-Rodríguez, Javan Okendo, Wilbert Gutiérrez-Sarmiento, Tobiáš Ber, Josef Pasulka, Kateryna Nemesh, Aranza Torrado-Tapias, Emilio Ortiz-Ávila, Obed Ramírez-Sanchez, Carlos Lozano-Flores, Luis F Hernández-Ramírez, Maribel Hernández-Rosales, Petr Svoboda, Shawn M Burgess, Alfredo Varela-Echavarría

引用次数: 0

Ensemble of Bayesian alphabets via constraint weight optimization strategy improves genomic prediction accuracy. 基于约束权优化策略的贝叶斯字母表集成提高了基因组预测的准确性。

IF 2.2 3区生物学

G3: Genes|Genomes|Genetics Pub Date : 2025-07-29 DOI: 10.1093/g3journal/jkaf150

Prabina Kumar Meher, Upendra Kumar Pradhan, Mrinmoy Ray, Ajit Gupta, Rajender Parsad, Pushpendra Kumar Gupta

{"title":"Ensemble of Bayesian alphabets via constraint weight optimization strategy improves genomic prediction accuracy.","authors":"Prabina Kumar Meher, Upendra Kumar Pradhan, Mrinmoy Ray, Ajit Gupta, Rajender Parsad, Pushpendra Kumar Gupta","doi":"10.1093/g3journal/jkaf150","DOIUrl":"https://doi.org/10.1093/g3journal/jkaf150","url":null,"abstract":"This study proposes a weight optimization-based ensemble framework aimed at improving genomic prediction accuracy. It incorporates 8 Bayesian models-BayesA, BayesB, BayesC, BayesBpi, BayesCpi, BayesR, BayesL, and BayesRR in the ensemble framework, where the weight assigned to each model was optimized using genetic algorithm method. The performance of the ensemble model, named EnBayes, was evaluated on 18 datasets from 4 crop species, showing improved prediction accuracy compared to individual Bayesian models. New objective functions were proposed to improve prediction accuracy in terms of both Pearson's correlation coefficient and mean square error. The accuracy of the ensemble model was found to be associated with the number of models considered in the framework, where a few more accurate models achieved similar accuracy as that of more number of less accurate models. Additionally, over-bias and under-bias models also influenced the biasness of the ensemble model's accuracy. The study also explored a meta-learning approach using Bayesian models as base learners and random forest, quantile regression forest, and ridge regression as meta-learners, with the EnBayes model outperforming this approach. While traditional genomic prediction models GBLUP and rrBLUP and machine learning models support vector machine, random forest, extreme gradient boosting, and light gradient boosting were included in the ensemble framework in addition to Bayesian models, the ensemble model achieved higher accuracy as compared to the individual Bayesian, BLUP, and machine learning models. We believe that EnBayes would contribute significantly to ongoing efforts on improving genomic prediction accuracy.","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2025-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144729300","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

Somatic gonad morphogenesis in C. elegans requires the heterochronic pathway acting through HBL-1. 秀丽隐杆线虫的性腺形态发生需要通过HBL-1作用的异慢性途径。

IF 2.2 3区生物学

G3: Genes|Genomes|Genetics Pub Date : 2025-07-28 DOI: 10.1093/g3journal/jkaf170

Madeleine Minutillo, Kevin Kemper, Maria Ivanova, Erika Pianin, Eric G Moss

{"title":"Somatic gonad morphogenesis in C. elegans requires the heterochronic pathway acting through HBL-1.","authors":"Madeleine Minutillo, Kevin Kemper, Maria Ivanova, Erika Pianin, Eric G Moss","doi":"10.1093/g3journal/jkaf170","DOIUrl":"https://doi.org/10.1093/g3journal/jkaf170","url":null,"abstract":"The heterochronic genes are known for acting in succession to control the timing of stage-specific events of the developing Caenorhabditis elegans larva. While most heterochronic mutants have normal gonad development, in a few cases defective timing regulators lead to variations in gonad development, although with little to no effect on fertility. We found that a double mutant of two heterochronic genes, a lin-28 null allele and hbl-1 hypomorphic allele, results in a catastrophic failure of gonad morphogenesis resulting in sterility. This defect includes a high-penetrance disruption of normal gonad arm migration as well as frequent absence of one or both spermathecae. We demonstrate that the abnormal gonad morphology and novel sterility phenotype is ultimately due to loss of hbl-1 activity in larval development. To clarify the mechanism of how lin-28 positively influences hbl-1 activity, we demonstrate a direct interaction between the RNA-binding protein LIN-28 and the 5'UTR of lin-46, and in turn, a direct interaction between LIN-46 and two zinc fingers of HBL-1. Nevertheless, our genetic analysis indicates that lin-46 accounts for only part of lin-28's regulation of hbl-1 and that some portion of lin-28's effect is independent of lin-46.","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2025-07-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144729301","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

Limitations of Current Machine-Learning Models in Predicting Enzymatic Functions for Uncharacterized Proteins. 当前机器学习模型在预测未表征蛋白质的酶功能方面的局限性。

IF 2.2 3区生物学

G3: Genes|Genomes|Genetics Pub Date : 2025-07-24 DOI: 10.1093/g3journal/jkaf169

Valérie de Crécy-Lagard, Raquel Dias, Nick Sexson, Iddo Friedberg, Yifeng Yuan, Manal A Swairjo

{"title":"Limitations of Current Machine-Learning Models in Predicting Enzymatic Functions for Uncharacterized Proteins.","authors":"Valérie de Crécy-Lagard, Raquel Dias, Nick Sexson, Iddo Friedberg, Yifeng Yuan, Manal A Swairjo","doi":"10.1093/g3journal/jkaf169","DOIUrl":"10.1093/g3journal/jkaf169","url":null,"abstract":"Thirty to seventy percent of proteins in any given genome have no assigned function and have been labeled as the protein \"unknome\". This large knowledge shortfall is one of the final frontiers of biology. Machine-Learning (ML) approaches are enticing, with early successes demonstrating the ability to propagate functional knowledge from experimentally characterized proteins. An open question is the ability of machine-learning approaches to predict enzymatic functions unseen in the training sets. By integrating literature and a combination of bioinformatic approaches, we evaluated individually Enzyme Commission number predictions for over 450 Escherichia coli unknowns made using state-of-the-art machine-learning approaches. We found that current ML methods not only mostly fail to make novel predictions but also make basic logic errors in their predictions that human annotators avoid by leveraging the available knowledge base. This underscores the need to include assessments of prediction uncertainty in model output and to test for 'hallucinations' (logic failures) as a part of model evaluation. Explainable AI (XAI) analysis can be used to identify indicators of prediction errors, potentially identifying the most relevant data to include in the next generation of computational models.","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2025-07-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144698101","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

Comprehensive analysis of 1,771 transcriptomes from 7 tissues enhance genetic and biological interpretations of maize complex traits. 对来自7个组织的1771个转录组的综合分析增强了对玉米复合性状的遗传和生物学解释。

IF 2.1 3区生物学

G3: Genes|Genomes|Genetics Pub Date : 2025-07-22 DOI: 10.1093/g3journal/jkaf140

Mengyu Lei, Huan Si, Mingjia Zhu, Yu Han, Wei Liu, Yifei Dai, Yan Ji, Zhengwen Liu, Fan Hao, Ran Hao, Jiarui Zhao, Guoyou Ye, Yanjun Zan

{"title":"Comprehensive analysis of 1,771 transcriptomes from 7 tissues enhance genetic and biological interpretations of maize complex traits.","authors":"Mengyu Lei, Huan Si, Mingjia Zhu, Yu Han, Wei Liu, Yifei Dai, Yan Ji, Zhengwen Liu, Fan Hao, Ran Hao, Jiarui Zhao, Guoyou Ye, Yanjun Zan","doi":"10.1093/g3journal/jkaf140","DOIUrl":"https://doi.org/10.1093/g3journal/jkaf140","url":null,"abstract":"By reanalyzing 1,771 RNA-seq datasets from 7 tissues in a maize diversity panel, we explored the landscape of multi-tissue transcriptome variation, evolution patterns of tissue-specific genes, and built a comprehensive multi-tissue gene regulation atlas to understand the genetic regulation of maize complex traits. Through an integrative analysis of tissue-specific gene regulatory variation with genome-wide association studies, we detected relevant tissue types and several candidate genes for a number of agronomic traits, including leaf during the day for the anthesis-silking interval, leaf during the day for kernel Zeinoxanthin level, and root for ear height, highlighting the potential contribution of tissue-specific gene expression to variation in agronomic traits. Using transcriptome-wide association and colocalization analysis, we associated tissue-specific expression variation of 74 genes to agronomic traits variation. Our findings provide novel insights into the genetic and biological mechanisms underlying maize complex traits, and the multi-tissue regulatory atlas serves as a primary source for biological interpretation, functional validation, and genomic improvement of maize.","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144682314","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

Characterization and mapping of a rust resistance locus in the common bean landrace G19833. 菜豆地方品种G19833抗锈病位点的鉴定与定位。

IF 2.1 3区生物学

G3: Genes|Genomes|Genetics Pub Date : 2025-07-21 DOI: 10.1093/g3journal/jkaf168

Giseli Valentini, Marcial A Pastor-Corrales, Oscar P Hurtado-Gonzales, Larissa F S Xavier, Upinder Gill, Qijian Song

{"title":"Characterization and mapping of a rust resistance locus in the common bean landrace G19833.","authors":"Giseli Valentini, Marcial A Pastor-Corrales, Oscar P Hurtado-Gonzales, Larissa F S Xavier, Upinder Gill, Qijian Song","doi":"10.1093/g3journal/jkaf168","DOIUrl":"https://doi.org/10.1093/g3journal/jkaf168","url":null,"abstract":"The Andean common bean landrace, G19833 exhibits broad and effective resistance to multiple virulent races of Uromyces appendiculatus, the fungus that causes the rust disease of common bean. In this study, with the combination of high throughput phenotyping and genotyping of large segregating populations, we characterize and map the rust resistance locus present on chromosome Pv04 in G19833. Our results revealed one single dominant gene in G19833 conditioning resistance to the races 16-1 (52), 31-1 (53), 30-1 (55), and 37-1 (84) of U. appendiculatus. Further, we fine mapped the resistance locus in a 747 kb genomic interval using 650 F2 and 1,975 F3 plants from the cross G19833 × Olathe. This region is previously known to have low levels of recombination and contains several disease resistance genes against multiple diseases, including bean rust. To identify candidate genes, we also performed in silico gene expression analysis using the available data from G19833 to identify functional nucleotide-binding sites with leucine-rich repeats (NLRs). Our analysis revealed that some NLR genes were highly expressed across all 11 plant tissues examined, while others showed higher expression in specific tissues. These insights enhance our understanding of rust resistance in common beanand will facilitate the development of cultivars with durable rust resistance.","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-07-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144682313","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

Bar-seq: A robust, platform-agnostic method for massively parallel cell-based screens. Bar-seq：用于大规模并行细胞筛选的稳健、平台无关的方法。

IF 2.1 3区生物学

G3: Genes|Genomes|Genetics Pub Date : 2025-07-18 DOI: 10.1093/g3journal/jkaf166

Marjan Barazandeh, Hamid Kian Gaikani, Rutuja Pattanshetti, Joseph Uche Ogbede, Sunita Sinha, Rachel Moore, Christopher E Carr, Guri Giaever, Corey Nislow

引用次数: 0

Chromosome-scale genome assembly of the bed bug Cimex lectularius sheds light on a key insecticide resistance locus. 臭虫的染色体尺度基因组组装揭示了一个关键的杀虫剂抗性位点。

IF 2.1 3区生物学

G3: Genes|Genomes|Genetics Pub Date : 2025-07-18 DOI: 10.1093/g3journal/jkaf161

Chloé Haberkorn, Julien Varaldi, Oriane Plantec, Nelly Burlet, Ines Amdouni, Elsa Baligand, Albert Ndour, Louis Sanglier, Christine Oger-Desfeux, Fabrice Vavre

{"title":"Chromosome-scale genome assembly of the bed bug Cimex lectularius sheds light on a key insecticide resistance locus.","authors":"Chloé Haberkorn, Julien Varaldi, Oriane Plantec, Nelly Burlet, Ines Amdouni, Elsa Baligand, Albert Ndour, Louis Sanglier, Christine Oger-Desfeux, Fabrice Vavre","doi":"10.1093/g3journal/jkaf161","DOIUrl":"https://doi.org/10.1093/g3journal/jkaf161","url":null,"abstract":"The population densities of the common bed bug Cimex lectularius have recently exploded worldwide. This demographic boom is mostly due to the evolution of insecticide resistance, which appears to be mainly driven by one autosomal locus in this species, identified by a QTL analysis. However, the exact gene content of this locus is still unclear, in particular regarding the inclusion of the Voltage-Gated Sodium Channel (VGSC) gene, due to uncertainty in previous assemblies available. To resolve this ambiguity, and more generally to provide useful resources to fight this hematophagous human parasite, we combined short, long and Hi-C reads to produce a chromosome-scale assembly for this species. Three competing assembly strategies were used, all of which resulted in 13 autosomes plus two X chromosomes, consistent with previous cytological studies and a very recent chromosome-scale assembly. The best assembly had a total length of 507 Mb, an N50 of 35 Mb, encoded 98% of complete BUSCO genes, and covered 99% of the previous reference genome. This chromosome-scale assembly revealed that the main insecticide-resistance locus does indeed contain the VGSC gene, as well as other genes possibly involved in insecticide resistance. Additionally, a population genomics analysis showed that this 7.65 Mb locus is highly differentiated between insecticide-resistant and susceptible strains, confirming previous results. We hope this high-quality, complete and annotated genome of C. lectularius will serve as a useful resource to understand the mechanisms of insecticide resistance evolution and, more generally, better control bed bug populations.","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-07-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144663889","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

Pleiotropic Effects of Red and Purple Pericarp Genes on Seed Coating Patterns, Flavonoids, Dormancy and Germination in Rice. 红色和紫色果皮基因对水稻种皮形态、黄酮类化合物、休眠和萌发的多效性影响。

IF 2.1 3区生物学

G3: Genes|Genomes|Genetics Pub Date : 2025-07-18 DOI: 10.1093/g3journal/jkaf158

Wenwu Tang, Min Guo, Yue Zhu, Rupak Chakraborty, Bhupinder S Batth, Kamal Bhattarai, Guiquan Zhang, De-Yu Xie, Xing-You Gu

{"title":"Pleiotropic Effects of Red and Purple Pericarp Genes on Seed Coating Patterns, Flavonoids, Dormancy and Germination in Rice.","authors":"Wenwu Tang, Min Guo, Yue Zhu, Rupak Chakraborty, Bhupinder S Batth, Kamal Bhattarai, Guiquan Zhang, De-Yu Xie, Xing-You Gu","doi":"10.1093/g3journal/jkaf158","DOIUrl":"https://doi.org/10.1093/g3journal/jkaf158","url":null,"abstract":"Seeds are coated with pigments presumably to promote plant adaptation. To understand the adaptive mechanisms of seed pigment traits, allelic variants of the red (Rc/rc) and purple (Pb/pb) pericarp color genes were assembled into the same genetic background to identify the trait development patterns and pleiotropies of the loci on seed flavonoids, dormancy and germination in rice (Oryza sativa). Non-allelic recombination and epistasis of the loci dictated four patterns of the trait development from 5 to 40 days post anthesis (DPA). The Rc- and Pb-controlled pigments were synthesized in the same lower epidermal cells but compartmented in the cells and lignified wall area, respectively, after 10 d. Four flavan-3-ols (catechin, epicatechin and their dimeric procyanidins) and anthocyanins (AC) were detected in the Pb and Rc systems, respectively, with catechin being most abundant. Both genes affected seed primary dormancy, and imbibition and germination velocities of the dormancy-released seeds. Additive effects of the loci contributed most to the variances for all the pleiotropic traits, the development time and its interaction with the additive components influenced the flavonoid contents, and the additive-by-additive epistasis modified the AC content and dormancy level. Thus, seed pigment traits influence plant adaptation likely through a series of pleiotropies, including the coat structure, enhanced dormancy, and reduced germination speed. The differences between the Rc and Pb loci in the flavonoid type/content and the size of pleiotropic effects could partly explain the predominance of red pericarp-colored genotypes in wild and weedy rice and in pigmented specialty cultivars.","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-07-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144663890","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