G3 (Bethesda, Md.)最新文献

{"title":"Analyses of mutational patterns induced by formaldehyde and acetaldehyde reveal similarity to a common mutational signature.","authors":"Mahanish J Thapa,&nbsp;Reena M Fabros,&nbsp;Salma Alasmar,&nbsp;Kin Chan","doi":"10.1093/g3journal/jkac238","DOIUrl":"https://doi.org/10.1093/g3journal/jkac238","url":null,"abstract":"<p><p>Formaldehyde and acetaldehyde are reactive small molecules produced endogenously in cells as well as being environmental contaminants. Both of these small aldehydes are classified as human carcinogens, since they are known to damage DNA and exposure is linked to cancer incidence. However, the mutagenic properties of formaldehyde and acetaldehyde remain incompletely understood, at least in part because they are relatively weak mutagens. Here, we use a highly sensitive yeast genetic reporter system featuring controlled generation of long single-stranded DNA regions to show that both small aldehydes induced mutational patterns characterized by predominantly C/G → A/T, C/G → T/A, and T/A → C/G substitutions, each in similar proportions. We observed an excess of C/G → A/T transversions when compared to mock-treated controls. Many of these C/G → A/T transversions occurred at TC/GA motifs. Interestingly, the formaldehyde mutational pattern resembles single base substitution signature 40 from the Catalog of Somatic Mutations in Cancer. Single base substitution signature 40 is a mutational signature of unknown etiology. We also noted that acetaldehyde treatment caused an excess of deletion events longer than 4 bases while formaldehyde did not. This latter result could be another distinguishing feature between the mutational patterns of these simple aldehydes. These findings shed new light on the characteristics of 2 important, commonly occurring mutagens.</p>","PeriodicalId":520629,"journal":{"name":"G3 (Bethesda, Md.)","volume":" ","pages":""},"PeriodicalIF":2.6,"publicationDate":"2022-11-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9635668/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33449449","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}

{"title":"NESM: a network embedding method for tumor stratification by integrating multi-omics data.","authors":"Feng Li,&nbsp;Zhensheng Sun,&nbsp;Jin-Xing Liu,&nbsp;Junliang Shang,&nbsp;Lingyun Dai,&nbsp;Xikui Liu,&nbsp;Yan Li","doi":"10.1093/g3journal/jkac243","DOIUrl":"https://doi.org/10.1093/g3journal/jkac243","url":null,"abstract":"<p><p>Tumor stratification plays an important role in cancer diagnosis and individualized treatment. Recent developments in high-throughput sequencing technologies have produced huge amounts of multi-omics data, making it possible to stratify cancer types using multiple molecular datasets. We introduce a Network Embedding method for tumor Stratification by integrating Multi-omics data. Network Embedding method for tumor Stratification by integrating Multi-omics pregroup the samples, integrate the gene features and somatic mutation corresponding to cancer types within each group to construct patient features, and then integrate all groups to obtain comprehensive patient information. The gene features contain network topology information, because it is extracted by integrating deoxyribonucleic acid methylation, messenger ribonucleic acid expression data, and protein-protein interactions through network embedding method. On the one hand, a supervised learning method Light Gradient Boosting Machine is used to classify cancer types based on patient features. When compared with other 3 methods, Network Embedding method for tumor Stratification by integrating Multi-omics has the highest AUC in most cancer types. The average AUC for stratifying cancer types is 0.91, indicating that the patient features extracted by Network Embedding method for tumor Stratification by integrating Multi-omics are effective for tumor stratification. On the other hand, an unsupervised clustering algorithm Density-Based Spatial Clustering of Applications with Noise is utilized to divide single cancer subtypes. The vast majority of the subtypes identified by Network Embedding method for tumor Stratification by integrating Multi-omics are significantly associated with patient survival.</p>","PeriodicalId":520629,"journal":{"name":"G3 (Bethesda, Md.)","volume":" ","pages":""},"PeriodicalIF":2.6,"publicationDate":"2022-11-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9635646/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40371113","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}

{"title":"Correction to: Austropuccinia psidii, causing myrtle rust, has a gigabase-sized genome shaped by transposable elements.","authors":"","doi":"10.1093/g3journal/jkac251","DOIUrl":"https://doi.org/10.1093/g3journal/jkac251","url":null,"abstract":"","PeriodicalId":520629,"journal":{"name":"G3 (Bethesda, Md.)","volume":" ","pages":""},"PeriodicalIF":2.6,"publicationDate":"2022-11-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9635664/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33482089","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}

{"title":"Genomic selection for resistance to mammalian bark stripping and associated chemical compounds in radiata pine.","authors":"Judith S Nantongo,&nbsp;Brad M Potts,&nbsp;Jaroslav Klápště,&nbsp;Natalie J Graham,&nbsp;Heidi S Dungey,&nbsp;Hugh Fitzgerald,&nbsp;Julianne M O'Reilly-Wapstra","doi":"10.1093/g3journal/jkac245","DOIUrl":"https://doi.org/10.1093/g3journal/jkac245","url":null,"abstract":"<p><p>The integration of genomic data into genetic evaluations can facilitate the rapid selection of superior genotypes and accelerate the breeding cycle in trees. In this study, 390 trees from 74 control-pollinated families were genotyped using a 36K Axiom SNP array. A total of 15,624 high-quality SNPs were used to develop genomic prediction models for mammalian bark stripping, tree height, and selected primary and secondary chemical compounds in the bark. Genetic parameters from different genomic prediction methods-single-trait best linear unbiased prediction based on a marker-based relationship matrix (genomic best linear unbiased prediction), multitrait single-step genomic best linear unbiased prediction, which integrated the marker-based and pedigree-based relationship matrices (single-step genomic best linear unbiased prediction) and the single-trait generalized ridge regression-were compared to equivalent single- or multitrait pedigree-based approaches (ABLUP). The influence of the statistical distribution of data on the genetic parameters was assessed. Results indicated that the heritability estimates were increased nearly 2-fold with genomic models compared to the equivalent pedigree-based models. Predictive accuracy of the single-step genomic best linear unbiased prediction was higher than the ABLUP for most traits. Allowing for heterogeneity in marker effects through the use of generalized ridge regression did not markedly improve predictive ability over genomic best linear unbiased prediction, arguing that most of the chemical traits are modulated by many genes with small effects. Overall, the traits with low pedigree-based heritability benefited more from genomic models compared to the traits with high pedigree-based heritability. There was no evidence that data skewness or the presence of outliers affected the genomic or pedigree-based genetic estimates.</p>","PeriodicalId":520629,"journal":{"name":"G3 (Bethesda, Md.)","volume":" ","pages":""},"PeriodicalIF":2.6,"publicationDate":"2022-11-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9635650/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33500018","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}

{"title":"A chromosome-level assembly of the widely used Rockefeller strain of Aedes aegypti, the yellow fever mosquito.","authors":"Cera R Fisher,&nbsp;Michael Wilson,&nbsp;Jeffrey G Scott","doi":"10.1093/g3journal/jkac242","DOIUrl":"https://doi.org/10.1093/g3journal/jkac242","url":null,"abstract":"<p><p>Aedes aegypti is the vector of important human diseases, and genomic resources are crucial in facilitating the study of A. aegypti and its ecosystem interactions. Several laboratory-acclimated strains of this mosquito have been established, but the most used strain in toxicology studies is \"Rockefeller,\" which was originally collected and established in Cuba 130 years ago. A full-length genome assembly of another reference strain, \"Liverpool,\" was published in 2018 and is the reference genome for the species (AaegL5). However, genetic studies with the Rockefeller strain are complicated by the availability of only the Liverpool strain as the reference genome. Differences between Liverpool and Rockefeller have been known for decades, particularly in the expression of genes relevant to mosquito behavior and vector control (e.g. olfactory). These differences indicate that AaegL5 is likely not fully representative of the Rockefeller genome, presenting potential impediments to research. Here, we present a chromosomal-level assembly and annotation of the Rockefeller genome and a comparative characterization vs the Liverpool genome. Our results set the stage for a pan-genomic approach to understanding evolution and diversity within this important disease vector.</p>","PeriodicalId":520629,"journal":{"name":"G3 (Bethesda, Md.)","volume":" ","pages":""},"PeriodicalIF":2.6,"publicationDate":"2022-11-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9635639/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33457875","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}

{"title":"A high-quality chromosome-level genome assembly of the bivalve mollusk Mactra veneriformis.","authors":"Yongxin Sun,&nbsp;Xiangfeng Liu,&nbsp;Xi Xie,&nbsp;Yongan Bai,&nbsp;Shuo Wang,&nbsp;Weiming Teng,&nbsp;Dacheng Li,&nbsp;Hualin Li,&nbsp;Zuoan Yu,&nbsp;Ming Zhang,&nbsp;Zunchun Zhou,&nbsp;Xu Liu,&nbsp;Hongtao Nie,&nbsp;Shaojun Du,&nbsp;Xiaodong Li,&nbsp;Qi Li,&nbsp;Qingzhi Wang","doi":"10.1093/g3journal/jkac229","DOIUrl":"https://doi.org/10.1093/g3journal/jkac229","url":null,"abstract":"<p><p>Mactra veneriformis (Bivalvia: Mactridae) is a bivalve mollusk of major economic importance in China. Decreased natural yields of M. veneriformis have led to an urgent need for genomic resources. To address this problem and the currently limited knowledge of molecular evolution in this genus, we here report a high-quality chromosome-level genome assembly of M. veneriformis. Our approach yielded a 939.32 Mb assembled genome with an N50 contig length of 7,977.84 kb. Hi-C scaffolding of the genome resulted in assembly of 19 pseudochromosomes. Repetitive elements made up ∼51.79% of the genome assembly. A total of 29,315 protein-coding genes (PCGs) were predicted in M. veneriformis. Construction of a genome-level phylogenetic tree demonstrated that M. veneriformis and Ruditapes philippinarum diverged around 231 million years ago (MYA). Inter-species comparisons revealed that 493 gene families have undergone expansion and 449 have undergone contraction in the M. veneriformis genome. Chromosome-based macrosynteny analysis revealed a high degree of synteny between the 19 chromosomes of M. veneriformis and those of Patinopecten yessoensis. These results suggested that M. veneriformis has a similar karyotype to that of P. yessoensis, and that a highly conserved 19-chromosome karyotype was formed in the early differentiation stages of bivalves. In summary, the genomic resources generated in this work serve as a valuable reference for investigating the molecular mechanisms underlying biological functions in M. veneriformis and will facilitate future genetic improvement and disease treatment in this economically important species. Furthermore, the assembled genome greatly improves our understanding of early genomic evolution of the Bivalvia.</p>","PeriodicalId":520629,"journal":{"name":"G3 (Bethesda, Md.)","volume":" ","pages":""},"PeriodicalIF":2.6,"publicationDate":"2022-11-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9635629/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40377720","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}

{"title":"Genetic screens identified dual roles of microtubule-associated serine threonine kinase and CREB within a single thermosensory neuron in the regulation of Caenorhabditis elegans thermotaxis behavior.","authors":"Shunji Nakano,&nbsp;Airi Nakayama,&nbsp;Hiroo Kuroyanagi,&nbsp;Riku Yamashiro,&nbsp;Yuki Tsukada,&nbsp;Ikue Mori","doi":"10.1093/g3journal/jkac248","DOIUrl":"https://doi.org/10.1093/g3journal/jkac248","url":null,"abstract":"<p><p>Animals integrate sensory stimuli presented at the past and present, assess the changes in their surroundings and navigate themselves toward preferred environment. Identifying the neural mechanisms of such sensory integration is pivotal to understand how the nervous system generates perception and behavior. Previous studies on thermotaxis behavior of Caenorhabditis elegans suggested that a single thermosensory neuron AFD plays an important role in integrating the past and present temperature information and is essential for the neural computation that drives the animal toward the preferred temperature region. However, the molecular mechanisms by which AFD executes this neural function remained elusive. Here we report multiple forward genetic screens to identify genes required for thermotaxis. We reveal that kin-4, which encodes the C. elegans homolog of microtubule-associated serine threonine kinase, plays dual roles in thermotaxis and can promote both cryophilic and thermophilic drives. We also uncover that a thermophilic defect of mutants for mec-2, which encodes a C. elegans homolog of stomatin, can be suppressed by a loss-of-function mutation in the gene crh-1, encoding a C. elegans homolog CREB transcription factor. Expression of crh-1 in AFD restored the crh-1-dependent suppression of the mec-2 thermotaxis phenotype, indicating that crh-1 can function in AFD to regulate thermotaxis. Calcium imaging analysis from freely moving animals suggest that mec-2 and crh-1 regulate the neuronal activity of the AIY interneuron, a postsynaptic partner of the AFD neuron. Our results suggest that a stomatin family protein can control the dynamics of neural circuitry through the CREB-dependent transcriptional regulation within a sensory neuron.</p>","PeriodicalId":520629,"journal":{"name":"G3 (Bethesda, Md.)","volume":" ","pages":""},"PeriodicalIF":2.6,"publicationDate":"2022-11-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9635662/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40356093","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}

{"title":"Prioritizing candidate eQTL causal genes in Arabidopsis using RANDOM FORESTS.","authors":"Margi Hartanto,&nbsp;Asif Ahmed Sami,&nbsp;Dick de Ridder,&nbsp;Harm Nijveen","doi":"10.1093/g3journal/jkac255","DOIUrl":"https://doi.org/10.1093/g3journal/jkac255","url":null,"abstract":"<p><p>Expression quantitative trait locus mapping has been widely used to study the genetic regulation of gene expression in Arabidopsis thaliana. As a result, a large amount of expression quantitative trait locus data has been generated for this model plant; however, only a few causal expression quantitative trait locus genes have been identified, and experimental validation is costly and laborious. A prioritization method could help speed up the identification of causal expression quantitative trait locus genes. This study extends the machine-learning-based QTG-Finder2 method for prioritizing candidate causal genes in phenotype quantitative trait loci to be used for expression quantitative trait loci by adding gene structure, protein interaction, and gene expression. Independent validation shows that the new algorithm can prioritize 16 out of 25 potential expression quantitative trait locus causal genes within the top 20% rank. Several new features are important in prioritizing causal expression quantitative trait locus genes, including the number of protein-protein interactions, unique domains, and introns. Overall, this study provides a foundation for developing computational methods to prioritize candidate expression quantitative trait locus causal genes. The prediction of all genes is available in the AraQTL workbench (https://www.bioinformatics.nl/AraQTL/) to support the identification of gene expression regulators in Arabidopsis.</p>","PeriodicalId":520629,"journal":{"name":"G3 (Bethesda, Md.)","volume":" ","pages":""},"PeriodicalIF":2.6,"publicationDate":"2022-11-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9635658/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33478181","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}

{"title":"The cAMP-PKA pathway regulates prey sensing and trap morphogenesis in the nematode-trapping fungus Arthrobotrys oligospora.","authors":"Sheng-An Chen,&nbsp;Hung-Che Lin,&nbsp;Yen-Ping Hsueh","doi":"10.1093/g3journal/jkac217","DOIUrl":"https://doi.org/10.1093/g3journal/jkac217","url":null,"abstract":"<p><p>Sensing environmental factors and responding swiftly to them is essential for all living organisms. For instance, predators must act rapidly once prey is sensed. Nematode-trapping fungi (NTF) are predators that use \"traps\" differentiated from vegetative hyphae to capture, kill, and consume nematodes. These traps undergo drastic and rapid morphological changes upon nematode induction. Multiple signaling hubs have been shown to regulate this remarkable process. Here, we demonstrate that the conserved cAMP-PKA signaling pathway exerts a crucial role in trap morphogenesis of the nematode-trapping fungi Arthrobotrys oligospora. A gene deletion mutant of the PKA catalytic subunit TPK2 proved insensitive toward nematode presence. Moreover, we show that the G protein alpha subunit GPA2 acts upstream of adenylate cyclase, with GPA2 deletion resulting in substantially reduced trap formation, whereas exogenous provision of cAMP rescued the prey-sensing and trap morphogenesis defects of a gpa2 mutant. Thus, we show that cAMP production triggered by G protein signaling and downstream PKA activity are vital for prey-sensing and trap development in A. oligospora, demonstrating that this highly conserved signaling pathway is critical for nematode-trapping fungi and nematode predator-prey interactions.</p>","PeriodicalId":520629,"journal":{"name":"G3 (Bethesda, Md.)","volume":" ","pages":""},"PeriodicalIF":2.6,"publicationDate":"2022-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9526039/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40647569","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}

{"title":"Evolutionarily conserved role of hps1 in melanin production and blood coagulation in medaka fish.","authors":"Norimasa Iwanami,&nbsp;Yuka Ozaki,&nbsp;Hiyori Sakaguchi,&nbsp;Yuko Watanabe,&nbsp;Qi Meng,&nbsp;Kyoka Matsumoto,&nbsp;Tomohiro Suzuki,&nbsp;Kiyotaka Hitomi,&nbsp;Masaru Matsuda","doi":"10.1093/g3journal/jkac204","DOIUrl":"https://doi.org/10.1093/g3journal/jkac204","url":null,"abstract":"<p><p>Hermansky-Pudlak syndrome is an autosomal recessive disease characterized by albinism, visual impairment, and blood platelet dysfunction. One of the genes responsible for Hermansky-Pudlak syndrome, hps1, regulates organelle biogenesis and thus plays important roles in melanin production, blood clotting, and the other organelle-related functions in humans and mice. However, the function of hps1 in other species remains poorly understood. In this study, we discovered albino medaka fish during the maintenance of a wild-derived population and identified hps1 as the responsible gene using positional cloning. In addition to the specific absence of melanophore pigmentation, the hps1 mutant showed reduced blood coagulation, suggesting that hps1 is involved in clotting caused by both mammalian platelets and fish thrombocytes. Together, the findings of our study demonstrate that hps1 has an evolutionarily conserved role in melanin production and blood coagulation. In addition, our study presents a useful vertebrate model for understanding the molecular mechanisms of Hermansky-Pudlak syndrome.</p>","PeriodicalId":520629,"journal":{"name":"G3 (Bethesda, Md.)","volume":" ","pages":""},"PeriodicalIF":2.6,"publicationDate":"2022-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9526055/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40693139","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}