G3: Genes|Genomes|Genetics最新文献_第10页

Flynotyper 2.0: an updated tool for rapid quantitative assessment of Drosophila eye phenotypes. Flynotyper 2.0：果蝇眼睛表型快速定量评估的最新工具。

IF 2.1 3区生物学

G3: Genes|Genomes|Genetics Pub Date : 2024-11-06 DOI: 10.1093/g3journal/jkae212

Johnathan Ray, Deepro Banerjee, Qingyu Wang, Santhosh Girirajan

引用次数: 0

Chromosome-scale genome assembly of Apocynum pictum, a drought-tolerant medicinal plant from the Tarim Basin. 塔里木盆地一种耐旱药用植物 Apocynum pictum 的染色体级基因组组装。

IF 2.1 3区生物学

G3: Genes|Genomes|Genetics Pub Date : 2024-11-05 DOI: 10.1093/g3journal/jkae237

Wenlong Xie, Baowei Bai, Yanqin Wang

{"title":"Chromosome-scale genome assembly of Apocynum pictum, a drought-tolerant medicinal plant from the Tarim Basin.","authors":"Wenlong Xie, Baowei Bai, Yanqin Wang","doi":"10.1093/g3journal/jkae237","DOIUrl":"10.1093/g3journal/jkae237","url":null,"abstract":"Apocynum pictum Schrenk is a semishrub of the Apocynaceae family with a wide distribution throughout the Tarim Basin that holds significant ecological, medicinal, and economic values. Here, we report the assembly of its chromosome-level reference genome using Nanopore long-read, Illumina HiSeq paired-end, and high-throughput chromosome conformation capture sequencing. The final assembly is 225.32 Mb in length with a scaffold N50 of 19.64 Mb. It contains 23,147 protein-coding genes across 11 chromosomes, 21,148 of which (91.36%) have protein functional annotations. Comparative genomics analysis revealed that A. pictum diverged from the closely related species Apocynum venetum approximately 2.2 million years ago and has not undergone additional polyploidizations after the core eudicot WGT-γ event. Karyotype evolution analysis was used to characterize interchromosomal rearrangements in representative Apocynaceae species and revealed that several A. pictum chromosomes were derived entirely from single chromosomes of the ancestral eudicot karyotype. Finally, we identified 50 members of the well-known stress-responsive WRKY transcription factor family and used transcriptomic data to document changes in their expression at 2 stages of drought stress, identifying a number of promising candidate genes. Overall, this study provides high-quality genomic resources for evolutionary and comparative genomics of the Apocynaceae, as well as initial molecular insights into the drought adaptation of this valuable desert plant.","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2024-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11631493/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142582680","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

Female germline expression of OVO transcription factor bridges Drosophila generations. OVO转录因子的雌性种系表达为果蝇的世代交替架起了桥梁。

IF 2.1 3区生物学

G3: Genes|Genomes|Genetics Pub Date : 2024-11-04 DOI: 10.1093/g3journal/jkae252

Leif Benner, Savannah Muron, Charli L Wingfield, Brian Oliver

{"title":"Female germline expression of OVO transcription factor bridges Drosophila generations.","authors":"Leif Benner, Savannah Muron, Charli L Wingfield, Brian Oliver","doi":"10.1093/g3journal/jkae252","DOIUrl":"10.1093/g3journal/jkae252","url":null,"abstract":"OVO is required for female germ cell viability but has no known function in the male germline in Drosophila. ovo is autoregulated by two antagonistic isoforms, OVO-A and OVO-B. All ovo- alleles were created as partial revertants of the antimorphic ovoD1 allele. Creation of new targeted alleles in an ovo+ background indicated that disrupting the germline-specific exon extension of ovo-B leads to an arrested egg chamber phenotype, rather than germ cell death. RNA-seq analysis, including >1K full length cDNAs, indicates that ovo has several unannotated splice variations in the extended exon and a minor population of ovo-B transcripts have an alternative splice. This indicates that classical ovo alleles such as ovoD1rv23, are not truly null for ovo, and are likely to be weak antimorphs. To generate bonafide nulls, we deleted the ovo-A and ovo-B promoters showing that only ovo-B is required for female germ cell viability and there is an early and continual developmental requirement for ovo-B in the female germline. To visualize OVO expression and localization, we endogenously tagged ovo and found nuclear OVO in all differentiating female germ cells throughout oogenesis in adults. We also found that OVO is maternally deposited into the embryo, where it showed nuclear localization in newly formed pole cells. Maternal OVO persisted in embryonic germ cells until zygotic OVO expression was detectable, suggesting that there is continuous nuclear OVO expression in the female germline in the transition from one generation to the next.","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2024-11-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142566339","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

Codon optimality influences homeostatic gene expression in zebrafish. 密码子最优性影响斑马鱼的平衡基因表达

IF 2.1 3区生物学

G3: Genes|Genomes|Genetics Pub Date : 2024-10-24 DOI: 10.1093/g3journal/jkae247

Michelle L DeVore, Ariel A Bazzini

{"title":"Codon optimality influences homeostatic gene expression in zebrafish.","authors":"Michelle L DeVore, Ariel A Bazzini","doi":"10.1093/g3journal/jkae247","DOIUrl":"10.1093/g3journal/jkae247","url":null,"abstract":"The ribosome plays a crucial role in translating mRNA into protein; however, the genetic code extends beyond merely specifying amino acids. Upon translation, codons, the three-nucleotide sequences interpreted by ribosomes, have regulatory properties affecting mRNA stability, a phenomenon known as codon optimality. Codon optimality has been previously observed in vertebrates during embryogenesis, where specific codons can influence the stability and degradation rates of mRNA transcripts. In our previous work, we demonstrated that codon optimality impacts mRNA stability in human cell lines. However, the extent to which codon content influences vertebrate gene expression in vivo remained unclear. In this study, we expand on our previous findings by demonstrating that codon optimality has a robust effect on homeostatic mRNA and protein levels in whole zebrafish during normal physiological conditions. Using reporters with nearly identical nucleotide sequences but different codon compositions, all expressed from the same genomic locus, we show that codon composition can significantly influence gene expression. This study provides new insights into the regulatory roles of codon usage in vertebrate gene expression and underscores the importance of considering codon optimality in genetic and translational research. These findings have broad implications for understanding the complexities of gene regulation and could inform the design of synthetic genes and therapeutic strategies targeting mRNA stability.","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2024-10-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11631405/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142498131","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

Loss of the Na+/K+ cation pump CATP-1 suppresses nekl-associated molting defects. Na+/K+阳离子泵CATP-1的缺失可抑制nekl相关的蜕皮缺陷。

IF 2.1 3区生物学

G3: Genes|Genomes|Genetics Pub Date : 2024-10-21 DOI: 10.1093/g3journal/jkae244

Shaonil Binti, Phil T Edeen, David S Fay

{"title":"Loss of the Na+/K+ cation pump CATP-1 suppresses nekl-associated molting defects.","authors":"Shaonil Binti, Phil T Edeen, David S Fay","doi":"10.1093/g3journal/jkae244","DOIUrl":"10.1093/g3journal/jkae244","url":null,"abstract":"The conserved Caenorhabditis elegans protein kinases NEKL-2 and NEKL-3 regulate membrane trafficking and are required for larval molting. Through a forward genetic screen we identified a mutation in catp-1 as a suppressor of molting defects in synthetically lethal nekl-2; nekl-3 double mutants. catp-1 encodes a membrane-associated P4-type ATPase involved in Na+-K+ exchange. A previous study found that wild-type worms exposed to the nicotinic agonist dimethylphenylpiperazinium (DMPP) exhibited larval arrest and molting-associated defects, which were suppressed by inhibition of catp-1. By testing a spectrum catp-1 alleles, we found that resistance to DMPP toxicity and the suppression of nekl defects did not strongly correlate, suggesting key differences in the mechanism of catp-1-mediated suppression. Through whole genome sequencing of additional nekl-2; nekl-3 suppressor strains, we identified two additional coding-altering mutations in catp-1. However, neither mutation, when introduced into nekl-2; nekl-3 mutants using CRISPR, was sufficient to elicit robust suppression of molting defects, suggesting the involvement of other loci. Endogenously tagged CATP-1 was primarily expressed in epidermal cells within punctate structures located near the apical plasma membrane, consistent with a role in regulating cellular processes within the epidermis. Based on previous studies, we tested the hypothesis that catp-1 inhibition induces entry into the pre-dauer L2d stage, potentially accounting for the ability of catp-1 mutants to suppress nekl molting defects. However, we found no evidence that loss of catp-1 leads to entry into L2d. As such, loss of catp-1 may suppress nekl-associated and DMPP-induced defects by altering electrochemical gradients within membrane-bound compartments.","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2024-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11631496/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142462208","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

Principal component analysis revisited: fast multitrait genetic evaluations with smooth convergence. 主成分分析重温：平稳收敛的快速多特征遗传评估

IF 2.1 3区生物学

G3: Genes|Genomes|Genetics Pub Date : 2024-10-21 DOI: 10.1093/g3journal/jkae228

Jon Ahlinder, David Hall, Mari Suontama, Mikko J Sillanpää

{"title":"Principal component analysis revisited: fast multitrait genetic evaluations with smooth convergence.","authors":"Jon Ahlinder, David Hall, Mari Suontama, Mikko J Sillanpää","doi":"10.1093/g3journal/jkae228","DOIUrl":"10.1093/g3journal/jkae228","url":null,"abstract":"A cornerstone in breeding and population genetics is the genetic evaluation procedure, needed to make important decisions on population management. Multivariate mixed model analysis, in which many traits are considered jointly, utilizes genetic and environmental correlations between traits to improve the accuracy. However, the number of parameters in the multitrait model grows exponentially with the number of traits which reduces its scalability. Here, we suggest using principal component analysis to reduce the dimensions of the response variables, and then using the computed principal components as separate responses in the genetic evaluation analysis. As principal components are orthogonal to each other so that phenotypic covariance is abscent between principal components, a full multivariate analysis can be approximated by separate univariate analyses instead which should speed up computations considerably. We compared the approach to both traditional multivariate analysis and factor analytic approach in terms of computational requirement and rank lists according to predicted genetic merit on two forest tree datasets with 22 and 27 measured traits, respectively. Obtained rank lists of the top 50 individuals were in good agreement. Interestingly, the required computational time of the approach only took a few seconds without convergence issues, unlike the traditional approach which required considerably more time to run (7 and 10 h, respectively). The factor analytic approach took approximately 5-10 min. Our approach can easily handle missing data and can be used with all available linear mixed effect model softwares as it does not require any specific implementation. The approach can help to mitigate difficulties with multitrait genetic analysis in both breeding and wild populations.","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2024-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11631533/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142462209","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 white gene as a transgenesis marker for the cricket Gryllus bimaculatus. 白色基因作为蟋蟀 Gryllus bimaculatus 的转基因标记。

IF 2.1 3区生物学

G3: Genes|Genomes|Genetics Pub Date : 2024-10-15 DOI: 10.1093/g3journal/jkae235

Emmanuel Gonzalez-Sqalli, Matthieu Caron, Benjamin Loppin

引用次数: 0

A chromosome-scale genome assembly of Timorese crabgrass (Digitaria radicosa): a useful genomic resource for the Poaceae. 帝汶蟹草（Digitaria radicosa）染色体组规模的基因组组装：Poaceae 的有用基因组资源。

IF 2.1 3区生物学

G3: Genes|Genomes|Genetics Pub Date : 2024-10-10 DOI: 10.1093/g3journal/jkae242

Koki Minoji, Toshiyuki Sakai

{"title":"A chromosome-scale genome assembly of Timorese crabgrass (Digitaria radicosa): a useful genomic resource for the Poaceae.","authors":"Koki Minoji, Toshiyuki Sakai","doi":"10.1093/g3journal/jkae242","DOIUrl":"10.1093/g3journal/jkae242","url":null,"abstract":"Timorese crabgrass (Digitaria radicosa) is a grass species commonly found in Southeast Asia and Oceania. Digitaria species have high intraspecific and interspecific genetic and phenotypic diversity, suggesting their potential usefulness as a genetic resource. However, as the only high-quality reference genome available is for a tetraploid Digitaria species, a reference genome of the diploid species D. radicosa would be a useful resource for genomic studies of Digitaria and Poaceae plants. Here, we present a chromosome-level genome assembly of D. radicosa and describe its genetic characteristics; we also illustrate its usefulness as a genomic resource for Poaceae. We constructed a 441.6 Mb draft assembly consisting of 61 contigs with an N50 contig length of 41.5 Mb, using PacBio HiFi long reads. We predicted 26,577 protein-coding genes, reaching a BUSCO score of 96.5%. To demonstrate the usefulness of the D. radicosa reference genome, we investigated the evolution of Digitaria species and the genetic diversity of Japanese Digitaria plants based on our new reference genome. We also defined the syntenic blocks between D. radicosa and 2 Poaceae crops, fonio and rice, and the diverse distribution of representative resistance genes in D. radicosa. The D. radicosa reference genome presented here should help elucidate the genetic relatedness of Digitaria species and the genetic diversity of Digitaria plants. In addition, the D. radicosa genome will be an important genomic resource for Poaceae genomics and crop breeding.","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2024-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11631527/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142485677","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

Integrative multi-omic analysis identifies genes associated with cuticular wax biogenesis in adult maize leaves. 多组学综合分析确定了玉米成株叶片中与角质蜡生物发生相关的基因。

IF 2.1 3区生物学

G3: Genes|Genomes|Genetics Pub Date : 2024-10-10 DOI: 10.1093/g3journal/jkae241

Meng Lin, Harel Bacher, Richard Bourgault, Pengfei Qiao, Susanne Matschi, Miguel F Vasquez, Marc Mohammadi, Sarah van Boerdonk, Michael J Scanlon, Laurie G Smith, Isabel Molina, Michael A Gore

{"title":"Integrative multi-omic analysis identifies genes associated with cuticular wax biogenesis in adult maize leaves.","authors":"Meng Lin, Harel Bacher, Richard Bourgault, Pengfei Qiao, Susanne Matschi, Miguel F Vasquez, Marc Mohammadi, Sarah van Boerdonk, Michael J Scanlon, Laurie G Smith, Isabel Molina, Michael A Gore","doi":"10.1093/g3journal/jkae241","DOIUrl":"10.1093/g3journal/jkae241","url":null,"abstract":"Studying the genetic basis of leaf wax composition and its correlation with leaf cuticular conductance (gc) is crucial for improving crop productivity. The leaf cuticle, which comprises a cutin matrix and various waxes, functions as an extracellular hydrophobic layer, protecting against water loss upon stomatal closure. To address the limited understanding of genes associated with the natural variation of adult leaf cuticular waxes and their connection to gc, we conducted statistical genetic analyses using leaf transcriptomic, metabolomic, and physiological data sets collected from a maize (Zea mays L.) panel of ∼300 inbred lines. Through a random forest analysis with 60 cuticular wax traits, it was shown that high molecular weight wax esters play an important role in predicting gc. Integrating results from genome-wide and transcriptome-wide studies (GWAS and TWAS) via a Fisher's combined test revealed 231 candidate genes detected by all three association tests. Among these, 11 genes exhibit known or predicted roles in cuticle-related processes. Throughout the genome, multiple hotspots consisting of GWAS signals for several traits from one or more wax classes were discovered, identifying four additional plausible candidate genes and providing insights into the genetic basis of correlated wax traits. Establishing a partially shared genetic architecture, we identified 35 genes for both gc and at least one wax trait, with four considered plausible candidates. Our study enhances the understanding of how adult leaf cuticle wax composition relates to gc and implicates both known and novel candidate genes as potential targets for optimizing productivity in maize.","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2024-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11631437/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142462207","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

Revealing the evolutionary history and contemporary population structure of Pacific salmon in the Fraser River through genome resequencing. 通过基因组重测序揭示菲沙河太平洋鲑鱼的进化史和当代种群结构。

IF 2.1 3区生物学

G3: Genes|Genomes|Genetics Pub Date : 2024-10-07 DOI: 10.1093/g3journal/jkae169

Kris A Christensen, Anne-Marie Flores, Dionne Sakhrani, Carlo A Biagi, Robert H Devlin, Ben J G Sutherland, Ruth E Withler, Eric B Rondeau, Ben F Koop

{"title":"Revealing the evolutionary history and contemporary population structure of Pacific salmon in the Fraser River through genome resequencing.","authors":"Kris A Christensen, Anne-Marie Flores, Dionne Sakhrani, Carlo A Biagi, Robert H Devlin, Ben J G Sutherland, Ruth E Withler, Eric B Rondeau, Ben F Koop","doi":"10.1093/g3journal/jkae169","DOIUrl":"10.1093/g3journal/jkae169","url":null,"abstract":"The Fraser River once supported massive salmon returns. However, over the last century, the largest returns have consistently been less than half of the recorded historical maximum. There is substantial interest from surrounding communities and governments to increase salmon returns for both human use and functional ecosystems. To generate resources for this endeavor, we resequenced genomes of Chinook (Oncorhynchus tshawytscha), coho (Oncorhynchus kisutch), and sockeye salmon (Oncorhynchus nerka) from the Fraser River at moderate coverage (∼16×). A total of 954 resequenced genomes were analyzed, with 681 collected specifically for this study from tissues sampled between 1997 and 2021. An additional 273 were collected from previous studies. At the species level, Chinook salmon appeared to have 1.6-2.1× more SNPs than coho or sockeye salmon, respectively. This difference may be attributable to large historical declines of coho and sockeye salmon. At the population level, 3 Fraser River genetic groups were identified for each species using principal component and admixture analyses. These were consistent with previous research and supports the continued use of these groups in conservation and management efforts. Environmental factors and a migration barrier were identified as major factors influencing the boundaries of these genetic groups. Additionally, 20 potentially adaptive loci were identified among the genetic groups. This information may be valuable in new management and conservation efforts. Furthermore, the resequenced genomes are an important resource for contemporary genomics research on Fraser River salmon and have been made publicly available.","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/PMC11457079/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141747901","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