Bruno C Perez, Marco C A M Bink, Karen L Svenson, Gary A Churchill, Mario P L Calus
{"title":"Adding gene transcripts into genomic prediction improves accuracy and reveals sampling time dependence.","authors":"Bruno C Perez, Marco C A M Bink, Karen L Svenson, Gary A Churchill, Mario P L Calus","doi":"10.1093/g3journal/jkac258","DOIUrl":"https://doi.org/10.1093/g3journal/jkac258","url":null,"abstract":"<p><p>Recent developments allowed generating multiple high-quality 'omics' data that could increase the predictive performance of genomic prediction for phenotypes and genetic merit in animals and plants. Here, we have assessed the performance of parametric and nonparametric models that leverage transcriptomics in genomic prediction for 13 complex traits recorded in 478 animals from an outbred mouse population. Parametric models were implemented using the best linear unbiased prediction, while nonparametric models were implemented using the gradient boosting machine algorithm. We also propose a new model named GTCBLUP that aims to remove between-omics-layer covariance from predictors, whereas its counterpart GTBLUP does not do that. While gradient boosting machine models captured more phenotypic variation, their predictive performance did not exceed the best linear unbiased prediction models for most traits. Models leveraging gene transcripts captured higher proportions of the phenotypic variance for almost all traits when these were measured closer to the moment of measuring gene transcripts in the liver. In most cases, the combination of layers was not able to outperform the best single-omics models to predict phenotypes. Using only gene transcripts, the gradient boosting machine model was able to outperform best linear unbiased prediction for most traits except body weight, but the same pattern was not observed when using both single nucleotide polymorphism genotypes and gene transcripts. Although the GTCBLUP model was not able to produce the most accurate phenotypic predictions, it showed the highest accuracies for breeding values for 9 out of 13 traits. We recommend using the GTBLUP model for prediction of phenotypes and using the GTCBLUP for prediction of breeding values.</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/PMC9635642/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33485871","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}
Johnathan Rylee, Simpla Mahato, John Aldrich, Emma Bergh, Brandon Sizemore, Lauren E Feder, Shaun Grega, Kennedy Helms, Megan Maar, Steven G Britt, Andrew C Zelhof
{"title":"A TRiP RNAi screen to identify molecules necessary for Drosophila photoreceptor differentiation.","authors":"Johnathan Rylee, Simpla Mahato, John Aldrich, Emma Bergh, Brandon Sizemore, Lauren E Feder, Shaun Grega, Kennedy Helms, Megan Maar, Steven G Britt, Andrew C Zelhof","doi":"10.1093/g3journal/jkac257","DOIUrl":"https://doi.org/10.1093/g3journal/jkac257","url":null,"abstract":"<p><p>Drosophila rhabdomeric terminal photoreceptor differentiation is an extended process taking several days to complete. Following ommatidial patterning by the morphogenetic furrow, photoreceptors are sequentially recruited and specified, and terminal differentiation begins. Key events of terminal differentiation include the establishment of apical and basolateral domains, rhabdomere and stalk formation, inter-rhabdomeral space formation, and expression of phototransduction machinery. While many key regulators of these processes have been identified, the complete network of transcription factors to downstream effector molecules necessary for regulating each of these major events remains incomplete. Here, we report an RNAi screen to identify additional molecules and cellular pathways required for photoreceptor terminal differentiation. First, we tested several eye-specific GAL4 drivers for correct spatial and temporal specificity and identified Pph13-GAL4 as the most appropriate GAL4 line for our screen. We screened lines available through the Transgenic RNAi Project and isolated lines that when combined with Pph13-GAL4 resulted in the loss of the deep pseudopupil, as a readout for abnormal differentiation. In the end, we screened 6,189 lines, representing 3,971 genes, and have identified 64 genes, illuminating potential new regulatory molecules and cellular pathways for the differentiation and organization of Drosophila rhabdomeric photoreceptors.</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/PMC9635655/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33499145","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":"Extracellular matrix regulation of stress response genes during larval development in Caenorhabditis elegans.","authors":"Luke M Chandler, Keith P Choe","doi":"10.1093/g3journal/jkac221","DOIUrl":"https://doi.org/10.1093/g3journal/jkac221","url":null,"abstract":"<p><p>Mutation or loss of 6 extracellular matrix collagen genes disrupts annular furrows in adult C. elegans cuticles, causes a wide \"Dumpy\" body morphology, and activates osmotic, detoxification, and antimicrobial defense genes. High environmental osmolarity reduces internal turgor pressure, physically distorts the epidermis, and activates the same stress responses. Collagen gene mutations that cause Dumpy without furrow disruption do not activate stress responses. These results are consistent with an extracellular damage sensor associated with furrows in the adult cuticle that regulates environmental stress responses in adjacent cells. Several cuticle characteristics change between molts, but all stages have annular furrows and express furrow collagen genes. We compared body shape, furrow organization imaged with differential interference contrast microscopy, and stress response gene expression in furrow collagen gene mutants at all postembryonic stages. We find that most body shape and furrow disorganization phenotypes start at the L3 stage and increase in severity with each molt afterwards. Stress response genes were induced the strongest in adults, correlating with the greatest Dumpy and furrow phenotypes. Although weaker than in adults, osmolyte transporter gene hmit-1.1 and antimicrobial gene nlp-29 were also induced in some early larvae that had weak or undetectable cuticle phenotypes. Our data are consistent with progressive cuticle phenotypes in which each new cuticle is at least partially directed by organization of the former cuticle. Gene expression and cuticle data support the role of furrow disruption as a signal in L4 larvae and adults, but also suggest a role for other cuticle organization or epidermal cell effects in early larvae.</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/PMC9635657/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40438511","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":"Enteric bacterial infection in Drosophila induces whole-body alterations in metabolic gene expression independently of the immune deficiency signaling pathway.","authors":"Rujuta Deshpande, Byoungchun Lee, Savraj S Grewal","doi":"10.1093/g3journal/jkac163","DOIUrl":"https://doi.org/10.1093/g3journal/jkac163","url":null,"abstract":"<p><p>When infected by intestinal pathogenic bacteria, animals initiate both local and systemic defence responses. These responses are required to reduce pathogen burden and also to alter host physiology and behavior to promote infection tolerance, and they are often mediated through alterations in host gene expression. Here, we have used transcriptome profiling to examine gene expression changes induced by enteric infection with the Gram-negative bacteria Pseudomonas entomophila in adult female Drosophila. We find that infection induces a strong upregulation of metabolic gene expression, including gut and fat body-enriched genes involved in lipid transport, lipolysis, and beta-oxidation, as well as glucose and amino acid metabolism genes. Furthermore, we find that the classic innate immune deficiency (Imd)/Relish/NF-KappaB pathway is not required for, and in some cases limits, these infection-mediated increases in metabolic gene expression. We also see that enteric infection with Pseudomonas entomophila downregulates the expression of many transcription factors and cell-cell signaling molecules, particularly those previously shown to be involved in gut-to-brain and neuronal signaling. Moreover, as with the metabolic genes, these changes occurred largely independent of the Imd pathway. Together, our study identifies many metabolic, signaling, and transcription factor gene expression changes that may contribute to organismal physiological and behavioral responses to enteric pathogen infection.</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/PMC9635644/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40466719","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}
Karl Persson, Simon Stenberg, Markus J Tamás, Jonas Warringer
{"title":"Adaptation of the yeast gene knockout collection is near-perfectly predicted by fitness and diminishing return epistasis.","authors":"Karl Persson, Simon Stenberg, Markus J Tamás, Jonas Warringer","doi":"10.1093/g3journal/jkac240","DOIUrl":"https://doi.org/10.1093/g3journal/jkac240","url":null,"abstract":"<p><p>Adaptive evolution of clonally dividing cells and microbes is the ultimate cause of cancer and infectious diseases. The possibility of constraining the adaptation of cell populations, by inhibiting proteins enhancing the evolvability, has therefore attracted interest. However, our current understanding of how genes influence adaptation kinetics is limited, partly because accurately measuring adaptation for many cell populations is challenging. We used a high-throughput adaptive laboratory evolution platform to track the adaptation of >18,000 cell populations corresponding to single-gene deletion strains in the haploid yeast deletion collection. We report that the preadaptation fitness of gene knockouts near-perfectly (R2= 0.91) predicts their adaptation to arsenic, leaving at the most a marginal role for dedicated evolvability gene functions. We tracked the adaptation of another >23,000 gene knockout populations to a diverse range of selection pressures and generalized the almost perfect (R2=0.72-0.98) capacity of preadaptation fitness to predict adaptation. We also reconstructed mutations in FPS1, ASK10, and ARR3, which together account for almost all arsenic adaptation in wild-type cells, in gene deletions covering a broad fitness range and show that the predictability of arsenic adaptation can be understood as a by global epistasis, where excluding arsenic is more beneficial to arsenic unfit cells. The paucity of genes with a meaningful evolvability effect on adaptation diminishes the prospects of developing adjuvant drugs aiming to slow antimicrobial and chemotherapy resistance.</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/PMC9635671/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33455471","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":"Comparative genomics reveals putative evidence for high-elevation adaptation in the American pika (Ochotona princeps).","authors":"Bryson M F Sjodin, Michael A Russello","doi":"10.1093/g3journal/jkac241","DOIUrl":"https://doi.org/10.1093/g3journal/jkac241","url":null,"abstract":"<p><p>High-elevation environments have lower atmospheric oxygen content, reduced temperatures, and higher levels of UV radiation than found at lower elevations. As such, species living at high elevations must overcome these challenges to survive, grow, and reproduce. American pikas (Ochotona princeps) are alpine lagomorphs that are habitat specialists typically found at elevations >2,000 m. Previous research has shown putative evidence for high-elevation adaptation; however, investigations to date have been limited to a fraction of the genome. Here, we took a comparative genomics approach to identify putative regions under selection using a chromosomal reference genome assembly for the American pika relative to 8 other mammalian species targeted based on phylogenetic relatedness and (dis)similarity in ecology. We first identified orthologous gene groups across species and then extracted groups containing only American pika genes as well as unclustered pika genes to inform functional enrichment analyses; among these, we found 141 enriched terms with many related to hypoxia, metabolism, mitochondrial function/development, and DNA repair. We identified 15 significantly expanded gene families within the American pika across all orthologous gene groups that displayed functionally enriched terms associated with hypoxia adaptation. We further detected 196 positively selected genes, 41 of which have been associated with putative adaptation to hypoxia, cold tolerance, and response to UV following a literature review. In particular, OXNAD1, NRDC, and those genes critical in DNA repair represent important targets for future research to examine their functional implications in the American pika, especially as they may relate to adaptation to rapidly changing environments.</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/PMC9635661/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33458226","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}
Christian H Gauthier, Steven G Cresawn, Graham F Hatfull
{"title":"PhaMMseqs: a new pipeline for constructing phage gene phamilies using MMseqs2.","authors":"Christian H Gauthier, Steven G Cresawn, Graham F Hatfull","doi":"10.1093/g3journal/jkac233","DOIUrl":"https://doi.org/10.1093/g3journal/jkac233","url":null,"abstract":"<p><p>The diversity and mosaic architecture of phage genomes present challenges for whole-genome phylogenies and comparative genomics. There are no universally conserved core genes, ∼70% of phage genes are of unknown function, and phage genomes are replete with small (<500 bp) open reading frames. Assembling sequence-related genes into \"phamilies\" (\"phams\") based on amino acid sequence similarity simplifies comparative phage genomics and facilitates representations of phage genome mosaicism. With the rapid and substantial increase in the numbers of sequenced phage genomes, computationally efficient pham assembly is needed, together with strategies for including newly sequenced phage genomes. Here, we describe the Python package PhaMMseqs, which uses MMseqs2 for pham assembly, and we evaluate the key parameters for optimal pham assembly of sequence- and functionally related proteins. PhaMMseqs runs efficiently with only modest hardware requirements and integrates with the pdm_utils package for simple genome entry and export of datasets for evolutionary analyses and phage genome map construction.</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/PMC9635663/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33486081","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}
Cathy C Westhues, Henner Simianer, Timothy M Beissinger
{"title":"learnMET: an R package to apply machine learning methods for genomic prediction using multi-environment trial data.","authors":"Cathy C Westhues, Henner Simianer, Timothy M Beissinger","doi":"10.1093/g3journal/jkac226","DOIUrl":"https://doi.org/10.1093/g3journal/jkac226","url":null,"abstract":"<p><p>We introduce the R-package learnMET, developed as a flexible framework to enable a collection of analyses on multi-environment trial breeding data with machine learning-based models. learnMET allows the combination of genomic information with environmental data such as climate and/or soil characteristics. Notably, the package offers the possibility of incorporating weather data from field weather stations, or to retrieve global meteorological datasets from a NASA database. Daily weather data can be aggregated over specific periods of time based on naive (for instance, nonoverlapping 10-day windows) or phenological approaches. Different machine learning methods for genomic prediction are implemented, including gradient-boosted decision trees, random forests, stacked ensemble models, and multilayer perceptrons. These prediction models can be evaluated via a collection of cross-validation schemes that mimic typical scenarios encountered by plant breeders working with multi-environment trial experimental data in a user-friendly way. The package is published under an MIT license and accessible on GitHub.</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/PMC9635651/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40369132","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":"Robust linear DNA degradation supports replication-initiation-defective mutants in Escherichia coli.","authors":"T V Pritha Rao, Andrei Kuzminov","doi":"10.1093/g3journal/jkac228","DOIUrl":"https://doi.org/10.1093/g3journal/jkac228","url":null,"abstract":"<p><p>RecBCD helicase/nuclease supports replication fork progress via recombinational repair or linear DNA degradation, explaining recBC mutant synthetic lethality with replication elongation defects. Since replication initiation defects leave chromosomes without replication forks, these should be insensitive to the recBCD status. Surprisingly, we found that both Escherichia coli dnaA46(Ts) and dnaC2(Ts) initiation mutants at semi-permissive temperatures are also recBC-colethal. Interestingly, dnaA46 recBC lethality suppressors suggest underinitiation as the problem, while dnaC2 recBC suppressors signal overintiation. Using genetic and physical approaches, we studied the dnaA46 recBC synthetic lethality, for the possibility that RecBCD participates in replication initiation. Overproduced DnaA46 mutant protein interferes with growth of dnaA+ cells, while the residual viability of the dnaA46 recBC mutant depends on the auxiliary replicative helicase Rep, suggesting replication fork inhibition by the DnaA46 mutant protein. The dnaA46 mutant depends on linear DNA degradation by RecBCD, rather than on recombinational repair. At the same time, the dnaA46 defect also interacts with Holliday junction-moving defects, suggesting reversal of inhibited forks. However, in contrast to all known recBC-colethals, which fragment their chromosomes, the dnaA46 recBC mutant develops no chromosome fragmentation, indicating that its inhibited replication forks are stable. Physical measurements confirm replication inhibition in the dnaA46 mutant shifted to semi-permissive temperatures, both at the level of elongation and initiation, while RecBCD gradually restores elongation and then initiation. We propose that RecBCD-catalyzed resetting of inhibited replication forks allows replication to displace the \"sticky\" DnaA46(Ts) protein from the chromosomal DNA, mustering enough DnaA for new initiations.</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/PMC9635670/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40377719","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: Local genetic covariance between serum urate and kidney function estimated with Bayesian multitrait models.","authors":"","doi":"10.1093/g3journal/jkac259","DOIUrl":"https://doi.org/10.1093/g3journal/jkac259","url":null,"abstract":"This is a correction to: Alexa S Lupi, Nicholas A Sumpter, Megan P Leask, Justin O’Sullivan, Tayaza Fadason, Gustavo de los Campos, Tony R Merriman, Richard J Reynolds, Ana I Vazquez, Local genetic covariance between serum urate and kidney function estimated with Bayesian multitrait models, G3 GenesjGenomesjGenetics, Volume 12, Issue 9, September 2022, jkac158, https://doi.org/10. 1093/g3journal/jkac158 In the originally published version of this manuscript, a footnote to the author byline was missing:","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/PMC9635656/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40393953","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}