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Harnessing the predicted maize pan-interactome for putative gene function prediction and prioritization of candidate genes for important traits G3 Genes Genomes Genet. (IF 2.6) Pub Date : 2024-03-16 Elly Poretsky, H Busra Cagirici, Carson M Andorf, Taner Z Sen
The recent assembly and annotation of the 26 maize nested association mapping (NAM) population founder inbreds have enabled large-scale pan-genomic comparative studies. These studies have expanded our understanding of agronomically important traits by integrating pan-transcriptomic data with trait-specific gene candidates from previous association mapping results. In contrast to the availability of
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Dietary Restriction Fails to Extend Lifespan of Drosophila Model of Werner Syndrome G3 Genes Genomes Genet. (IF 2.6) Pub Date : 2024-03-16 Eileen Sember, Ranga Chennakesavula, Breanna Beard, Mubaraq Opoola, Dae-Sung Hwangbo
Werner syndrome (WS) is a rare genetic disease in humans, caused by mutations in the WRN gene that encodes a protein containing helicase and exonuclease domains. WS is characterized by symptoms of accelerated aging in multiple tissues and organs, involving increased risk of cancer, heart failure, and metabolic dysfunction. These conditions ultimately lead to the premature mortality of patients with
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Identification of X chromatin is modulated by complementary pathways in Drosophila melanogaster G3 Genes Genomes Genet. (IF 2.6) Pub Date : 2024-03-16 Reem Makki, Victoria H Meller
Drosophila melanogaster males have one X chromosome while females have two. This creates an imbalance in X:A gene dosage between the sexes. This imbalance is corrected by increasing transcription from male X-linked genes approximately two-fold. This process involves the Male Specific Lethal (MSL) complex, which is recruited to Chromatin Entry Sites (CES) and transcribed X-linked genes where it modifies
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Parental thermal environment controls the offspring phenotype in Brook charr (Salvelinus fontinalis): insights from a transcriptomic study G3 Genes Genomes Genet. (IF 2.6) Pub Date : 2024-03-13 Ghizlane Banousse, Eric Normandeau, Christina Semeniuk, Louis Bernatchez, Céline Audet
Brook charr is a cold-water species which is highly sensitive to increased water temperatures, such as those associated with climate change. Environmental variation can potentially induce phenotypic changes that are inherited across generations, for instance, via epigenetic mechanisms. Here, we tested whether parental thermal regimes (intergenerational plasticity) and offspring-rearing temperatures
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Mapping of DDX11 genetic interactions defines sister chromatid cohesion as the major dependency G3 Genes Genomes Genet. (IF 2.6) Pub Date : 2024-03-13 Leanne Amitzi, Ecaterina Cozma, Amy Hin Yan Tong, Katherine Chan, Catherine Ross, Nigel O’Neil, Jason Moffat, Peter Stirling, Philip Hieter
DDX11/Chl1R is a conserved DNA helicase with roles in genome maintenance, DNA replication, and chromatid cohesion. Loss of DDX11 in humans leads to the rare cohesinopathy Warsaw Breakage Syndrome. DDX11 has also been implicated in human cancer where it has been proposed to have an oncogenic role and possibly to constitute a therapeutic target. Given the multiple roles of DDX11 in genome stability and
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The MAB-5/Hox family transcription factor is important for C. elegans Innate Immune Response to S. epidermidis Infection G3 Genes Genomes Genet. (IF 2.6) Pub Date : 2024-03-13 Christopher Kywe, Erik A Lundquist, Brian D Ackley, Patrick Lansdon
Innate immunity functions as a rapid defense against broad classes of pathogenic agents. While the mechanisms of innate immunity in response to antigen exposure are well-studied, how pathogen exposure activates the innate immune responses and the role of genetic variation in immune activity is currently being investigated. Previously we showed significant survival differences between the N2 and CB4856
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Regulatory features of Candida albicans hemin-induced filamentation G3 Genes Genomes Genet. (IF 2.6) Pub Date : 2024-03-12 Liping Xiong, Katharina Goerlich, Aaron P Mitchell
Candida albicans is a prominent fungal pathogen that can infect the bloodstream and deep tissues. One key pathogenicity trait is the ability to transition between yeast and hyphal growth. Hyphae are critical for the formation of biofilms, which in turn enable device-associated infection. Among signals that drive hypha formation is the presence of hemin, an oxidized Fe(III)-containing heme derivative
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A maternal-to-zygotic-transition gene block on the zebrafish sex chromosome G3 Genes Genomes Genet. (IF 2.6) Pub Date : 2024-03-11 Catherine A Wilson, John H Postlethwait
Wild zebrafish (Danio rerio) have a ZZ/ZW chromosomal sex determination system with the major sex locus on the right arm of chromosome-4 (Chr4R) near the largest heterochromatic block in the genome, suggesting that Chr4R transcriptomics might differ from the rest of the genome. To test this hypothesis, we conducted an RNA-seq analysis of adult ZW ovaries and ZZ testes in the Nadia strain and identified
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A genome-wide cytotoxicity screen of Cluster F1 mycobacteriophage Girr reveals novel inhibitors of Mycobacterium smegmatis growth G3 Genes Genomes Genet. (IF 2.6) Pub Date : 2024-03-08 Richard S Pollenz, Kaylee Barnhill, Abbigail Biggs, Jackson Bland, Victoria Carter, Michael Chase, Hayley Clark, Caitlyn Coleman, Marshall Daffner, Caitlyn Deam, Alyssa Finocchiaro, Vanessa Franco, Thomas Fuller, Juan Gallardo Pinera, Mae Horne, Zoe Howard, Olivia Kanahan, Christopher Miklaszewski, Sydney Miller, Ryan Morgan, Oluwatobi Onalaja, Louis Otero, Shivani Padhye, Emily Rainey, Fareed Rasul
Over the past decade, thousands of bacteriophage genomes have been sequenced and annotated. A striking observation from this work is that known structural features and functions cannot be assigned for >65% of the encoded proteins. One approach to begin experimentally elucidating the function of these uncharacterized gene products is genome-wide screening to identify phage genes that confer phenotypes
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Fas2EB112: A Tale of Two Chromosomes G3 Genes Genomes Genet. (IF 2.6) Pub Date : 2024-03-06 Tara M Finegan, Christian Cammarota, Oscar Mendoza Andrade, Audrey M Garoutte, Dan T Bergstralh
The cell-cell adhesion molecule Fasciclin II (Fas2) has long been studied for its evolutionarily-conserved role in axon guidance. It is also expressed in the follicular epithelium, where together with a similar protein, Neuroglian (Nrg), it helps to drive the reintegration of cells born out of the tissue plane. Remarkably, one Fas2 protein null allele, Fas2G0336, demonstrates a mild reintegration phenotype
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The genetic basis of apple shape and size unraveled by digital phenotyping G3 Genes Genomes Genet. (IF 2.6) Pub Date : 2024-03-05 Beat Keller, Michaela Jung, Simone Bühlmann-Schütz, Marius Hodel, Bruno Studer, Giovanni A L Broggini, Andrea Patocchi
Great diversity of shape, size, and skin color is observed among the fruits of different apple genotypes. These traits are critical for consumers and therefore interesting targets for breeding new apple varieties. However, they are difficult to phenotype and their genetic basis, especially for fruit shape and ground color, is largely unknown. We used the FruitPhenoBox to digitally phenotype 525 genotypes
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Investigating genomic prediction strategies for grain carotenoid traits in a tropical/subtropical maize panel G3 Genes Genomes Genet. (IF 2.6) Pub Date : 2024-03-01 Mary-Francis LaPorte, Willy Bayuardi Suwarno, Pattama Hannok, Akiyoshi Koide, Peter Bradbury, José Crossa, Natalia Palacios-Rojas, Christine Helen Diepenbrock
Vitamin A deficiency remains prevalent on a global scale, including in regions where maize constitutes a high percentage of human diets. One solution for alleviating this deficiency has been to increase grain concentrations of provitamin A carotenoids in maize (Zea mays ssp. mays L.)—an example of biofortification. The International Maize and Wheat Improvement Center (CIMMYT) developed a Carotenoid
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Genetic variation for sexual dimorphism in developmental traits in Drosophila melanogaster G3 Genes Genomes Genet. (IF 2.6) Pub Date : 2024-03-01 Tianyu Li, Rebecca S Zhang, John R True
Sexual dimorphism in traits of insects during the developmental stages could potentially be the direct or indirect result of sex-specific selection provided that genetic variation for sexual dimorphism is present. We investigated genetic variation in sexual dimorphism in a set of Drosophila melanogaster inbred lines for 2 traits: egg to adult development time and pupation site preference. We observed
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Assembly and analysis of the genome of Notholithocarpus densiflorus G3 Genes Genomes Genet. (IF 2.6) Pub Date : 2024-03-01 Ying Cai, Ellis Anderson, Wen Xue, Sylvia Wong, Luman Cui, Xiaofang Cheng, Ou Wang, Qing Mao, Sophie Jia Liu, John T Davis, Paulo R Magalang, Douglas Schmidt, Takao Kasuga, Matteo Garbelotto, Radoje Drmanac, Chai-Shian Kua, Charles Cannon, Julin N Maloof, Brock A Peters
Tanoak (Notholithocarpus densiflorus) is an evergreen tree in the Fagaceae family found in California and southern Oregon. Historically, tanoak acorns were an important food source for Native American tribes and the bark was used extensively in the leather tanning process. Long considered a disjunct relictual element of the Asian stone oaks (Lithocarpus spp.), phylogenetic analysis has determined that
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Optimized protocols for RNA interference in Macrostomum lignano G3 Genes Genomes Genet. (IF 2.6) Pub Date : 2024-02-29 Stijn Mouton, Alexandra Mougel, Kirill Ustyantsev, Colette Dissous, Oleg Melnyk, Eugene Berezikov, Jérôme Vicogne
Macrostomum lignano, a marine free-living flatworm, has emerged as a potent invertebrate model in developmental biology for studying stem cells, germline, and regeneration processes. In recent years, many tools have been developed to manipulate this worm and to facilitate genetic modification. RNA interference is currently the most accessible and direct technique to investigate gene functions. It is
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Ribonucleotide reductase inhibition improves the symptoms of a Caenorhabditis elegans model of Alzheimer’s Disease G3 Genes Genomes Genet. (IF 2.6) Pub Date : 2024-02-27 Ana M Brokate-Llanos, Mireya Sanchez-Ibañez, Mercedes M Pérez-Jiménez, José M Monje-Moreno, Carlos Gómez-Marín, Carlos Caro, Carlos Vivar-Rios, Miguel A Moreno-Mateo, María L García-Martín, Manuel J Muñoz, José L Royo
Alzheimer’s disease is the main cause of aging-associated dementia, for which there is no effective treatment. In this work, we reanalyze the information of a previous Genome Wide Association Study, using a new pipeline design to identify novel potential drugs. With this approach, ribonucleoside-diphosphate reductase gene (RRM2B) emerged as a candidate target and its inhibitor, 2’, 2'-difluoro 2'deoxycytidine
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The RU486-dependent activation of the GeneSwitch system in adult muscles leads to severe adverse effects in Drosophila G3 Genes Genomes Genet. (IF 2.6) Pub Date : 2024-02-27 Maria Paula Zappia, Deena Damschroder, Anton Westacott, Robert J Wessells, Maxim V Frolov
Robust genetic systems to control the expression of transgenes in a spatial and temporal manner are a valuable asset for researchers. The GeneSwitch system induced by the drug RU486 has gained widespread use in the Drosophila community. However, some concerns were raised as negative effects were seen depending on the stock, transgene, stage and tissue under study. Here, we characterized the adverse
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Relatedness coefficients and their applications for triplets and quartets of genetic markers G3 Genes Genomes Genet. (IF 2.6) Pub Date : 2024-02-27 Kermit Ritland
Relatedness coefficients which seek the identity-by-descent of genetic markers are described. The markers are in groups of two, three or four, and if four, can consist of two pairs. It is essential to use cumulants (not moments) for four-marker-gene probabilities, as the covariance of homozygosity, used in four-marker applications, can only be described with cumulants. A covariance of homozygosity
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Linkage mapping of root shape traits in two carrot populations G3 Genes Genomes Genet. (IF 2.6) Pub Date : 2024-02-27 Andrey Vega, Scott H Brainard, Irwin L Goldman
This study investigated the genetic basis of carrot root shape traits using composite interval mapping in two biparental populations (n = 119 and n = 128). The roots of carrot F2:3 progenies were grown over two years and analyzed using a digital imaging pipeline to extract root phenotypes that compose market class. Broad-sense heritability on an entry-mean basis ranged from 0.46 to 0.80 for root traits
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Enhancing grapevine breeding efficiency through genomic prediction and selection index G3 Genes Genomes Genet. (IF 2.6) Pub Date : 2024-02-24 Charlotte Brault, Vincent Segura, Maryline Roques, Pauline Lamblin, Virginie Bouckenooghe, Nathalie Pouzalgues, Constance Cunty, Matthieu Breil, Marina Frouin, Léa Garcin, Louise Camps, Marie-Agnès Ducasse, Charles Romieu, Gilles Masson, Sébastien Julliard, Timothée Flutre, Loïc Le Cunff
Grapevine (Vitis vinifera) breeding reaches a critical point. New cultivars are released every year with resistance to powdery and downy mildews. However, the traditional process remains time-consuming, taking 20 to 25 years, and demands the evaluation of new traits to enhance grapevine adaptation to climate change. Until now, the selection process has relied on phenotypic data and a limited number
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Chromosome-level assembly of the gray fox (Urocyon cinereoargenteus) confirms the basal loss of PRDM9 in Canidae G3 Genes Genomes Genet. (IF 2.6) Pub Date : 2024-02-17 Ellie E Armstrong, Ky L Bissell, H Sophia Fatima, Maya A Heikkinen, Anika Jessup, Maryam O Junaid, Dong H Lee, Emily C Lieb, Josef T Liem, Estelle M Martin, Mauricio Moreno, Khuslen Otgonbayar, Betsy W Romans, Kim Royar, Mary Beth Adler, David B Needle, Alex Harkess, Joanna L Kelley, Jazlyn A Mooney, Alexis M Mychajliw
Reference genome assemblies have been created from multiple lineages within the Canidae family, however, despite its phylogenetic relevance as a basal genus within the clade, there is currently no reference genome for the gray fox (Urocyon cinereoargenteus). Here, we present a chromosome-level assembly for the gray fox (U. cinereoargenteus), which represents the most contiguous, non-domestic canid
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A simple, robust, broadly applicable insertion mutagenesis method to create random fluorescent protein – target protein fusions G3 Genes Genomes Genet. (IF 2.6) Pub Date : 2024-02-17 Andrew Pike, Cassandra Pietryski, Padraig Deighan, Jason Kuehner, Derek Lau, Anupama Seshan, Paul E March
A simple broadly applicable method was developed using an in vitro transposition reaction followed by transformation into Escherichia coli and screening plates for fluorescent colonies. The transposition reaction catalyzes the random insertion of a fluorescent protein open reading frame into a target gene on a plasmid. The transposition reaction is employed directly in an E. coli transformation with
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A K-mer based Bulked Segregant Analysis approach to map seed traits in unphased heterozygous potato genomes G3 Genes Genomes Genet. (IF 2.6) Pub Date : 2024-02-17 Pajaree Sonsungsan, Mwaura Livingstone Nganga, Meric Lieberman, Kirk Amundson, Victoria Stewart, Kitiporn Plaimas, Luca Comai, Isabelle Henry
High-throughput sequencing-based methods for bulked segregant analysis (BSA) allow for the rapid identification of genetic markers associated with traits of interest. BSA studies have successfully identified qualitative (binary) and quantitative trait loci using QTL mapping. However, most require population structures that fit the models available, and a reference genome. Instead, high throughput short
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High-density genetic linkage mapping in Sitka spruce advances the integration of genomic resources in conifers G3 Genes Genomes Genet. (IF 2.6) Pub Date : 2024-02-17 Hayley Tumas, Joana J Ilska, Sebastien Gérardi, Jerome Laroche, Stuart A’Hara, Brian Boyle, Mateja Janes, Paul McLean, Gustavo Lopez, Steve J Lee, Joan Cottrell, Gregor Gorjanc, Jean Bousquet, John A Woolliams, John J MacKay
In species with large and complex genomes such as conifers, dense linkage maps are a useful resource for supporting genome assembly and laying the genomic groundwork at the structural, populational, and functional levels. However, most of the 600+ extant conifer species still lack extensive genotyping resources, which hampers the development of high-density linkage maps. In this study, we developed
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Whole-genome sequencing and comparative genomic analyses of the medicinal fungus Sanguinoderma infundibulare in Ganodermataceae G3 Genes Genomes Genet. (IF 2.6) Pub Date : 2024-02-17 Yuxuan Fang, Dongmei Wu, Neng Gao, Mengxue Lv, Miao Zhou, Chuangui Ma, Yifei Sun, Baokai Cui
Sanguinoderma infundibulare is a newly discovered species of Ganodermataceae known to have high medicinal and ecological values. In this study, the whole-genome sequencing and comparative genomic analyses were conducted to further understand Ganodermataceae's genomic structural and functional characteristics. Using the Illumina NovaSeq and PacBio Sequel platforms, 88 scaffolds were assembled to obtain
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Lysine-36 of Drosophila histone H3.3 supports adult longevity G3 Genes Genomes Genet. (IF 2.6) Pub Date : 2024-02-17 John C Brown, Benjamin D McMichael, Vasudha Vandadi, Aadit Mukherjee, Harmony R Salzler, A Gregory Matera
Aging is a multifactorial process that disturbs homeostasis, increases disease susceptibility, and ultimately results in death. Although the definitive set of molecular mechanisms responsible for aging remain to be discovered, epigenetic change over time is proving to be a promising piece of the puzzle. Several posttranslational histone modifications (PTMs) have been linked to the maintenance of longevity
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Embryonic spatio-temporal expression pattern of Folded gastrulation (Fog) suggests roles in multiple morphogenetic events and regulation by AbdA G3 Genes Genomes Genet. (IF 2.6) Pub Date : 2024-02-17 Vrushali Katagade, Manisha Kandroo, Anuradha Ratnaparkhi
In Drosophila, the signaling pathway activated by the ligand Folded gastrulation (Fog) is amongst the few known G-protein coupled receptor (GPCR) pathways to regulate cell shape change with a well characterized role in gastrulation. However, an understanding of the spectrum of morphogenetic events regulated by Fog signaling is still lacking. Here, we present an analysis of the expression pattern and
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Revealing the genome of the microsporidian Vairimorpha bombi, a potential driver of bumble bee declines in North America G3 Genes Genomes Genet. (IF 2.6) Pub Date : 2024-02-09 Victoria L Webster, Samuel Hemmings, Marta Pérez, Matthew C Fisher, Mark J F Brown, Rhys A Farrer
Pollinators are vital for food security and the maintenance of terrestrial ecosystems. Bumblebees are important pollinators across northern temperate, arctic, and alpine ecosystems, yet are in decline across the globe. Vairimorpha bombi is a parasite belonging to the fungal class Microsporidia that has been implicated in rapid declines of bumblebees in North America, where it may be an emerging infectious
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A transcriptomics-based RNAi screen for regulators of meiosis and early stages of oocyte development in Drosophila melanogaster G3 Genes Genomes Genet. (IF 2.6) Pub Date : 2024-02-08 Stacie E Hughes, Andrew Price, Salam Briggs, Cynthia Staber, Morgan James, Madelyn Anderson, R Scott Hawley
A properly regulated series of developmental and meiotic events must occur to ensure the successful production of gametes. In Drosophila melanogaster ovaries, these early developmental and meiotic events include the production of the 16-cell cyst, meiotic entry, synaptonemal complex (SC) formation, recombination, and oocyte specification. In order to identify additional genes involved in early oocyte
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Long read genome assembly of Automeris io (Lepidoptera: Saturniidae) an emerging model for the evolution of deimatic displays G3 Genes Genomes Genet. (IF 2.6) Pub Date : 2024-02-07 Chelsea Skojec, R Keating Godfrey, Akito Y Kawahara
Automeris moths are a morphologically diverse group with 135 described species that have a geographic range that spans from the New World temperate zone to the Neotropics. Many Automeris have elaborate hindwing eyespots that are thought to deter or disrupt the attack of potential predators, allowing the moth time to escape. The Io moth (Automeris io), known for its striking eyespots, is a well-studied
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A haplotype-resolved chromosome-level assembly and annotation of European hazelnut (C. avellana cv. Jefferson) provides insight into mechanisms of eastern filbert blight resistance G3 Genes Genomes Genet. (IF 2.6) Pub Date : 2024-02-07 Samuel C Talbot, Kelly J Vining, Jacob W Snelling, Josh Clevenger, Shawn A Mehlenbacher
European hazelnut (Corylus avellana L.) is an important tree nut crop. Hazelnut production in North America is currently limited in scalability due to Anisogramma anomala, a fungal pathogen that causes Eastern Filbert Blight (EFB) disease in hazelnut. Successful deployment of EFB resistant cultivars has been limited to the state of Oregon, where the breeding program at Oregon State University (OSU)
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GWAS supported by computer vision identifies large numbers of candidate regulators of in planta regeneration in Populus trichocarpa G3 Genes Genomes Genet. (IF 2.6) Pub Date : 2024-02-07 Michael F Nagle, Jialin Yuan, Damanpreet Kaur, Cathleen Ma, Ekaterina Peremyslova, Yuan Jiang, Alexa Niño de Rivera, Sara Jawdy, Jin-Gui Chen, Kai Feng, Timothy B Yates, Gerald A Tuskan, Wellington Muchero, Li Fuxin, Steven H Strauss
Plant regeneration is an important dimension of plant propagation and a key step in the production of transgenic plants. However, regeneration capacity varies widely among genotypes and species, the molecular basis of which is largely unknown. While association mapping methods such as genome-wide association studies (GWAS) have long demonstrated abilities to help uncover the genetic basis of trait
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The haplolethal gene wupA of Drosophila exhibits potential as a target for an X-poisoning gene drive G3 Genes Genomes Genet. (IF 2.6) Pub Date : 2024-02-02 Clancy D Lawler, Ana Karla Parra Nuñez, Natalia Hernandes, Soumitra Bhide, Isabelle Lohrey, Simon Baxter, Charles Robin
A synthetic gene drive that targets haplolethal genes on the X-chromosome can skew the sex ratio towards males. Like an ‘X-shredder’ it does not involve ‘homing’ and that has advantages including the reduction of gene drive resistance allele formation. We examine this ‘X-poisoning’ strategy by targeting four of the 11 known X-linked haplolethal/haplosterile genes of Drosophila melanogaster with CRISPR/Cas9
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Genome assembly and annotation of the mermithid nematode Mermis nigrescens G3 Genes Genomes Genet. (IF 2.6) Pub Date : 2024-02-01 Upendra R Bhattarai, Robert Poulin, Neil J Gemmell, Eddy Dowle
Genetic studies of nematodes have been dominated by Caenorhabditis elegans as a model species. A lack of genomic resources has limited the expansion of genetic research to other groups of nematodes. Here, we report a draft genome assembly of a mermithid nematode, Mermis nigrescens. Mermithidae are insect parasitic nematodes with hosts including a wide range of terrestrial arthropods. We sequenced,
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Genome Report: Chromosome-scale Genome Assembly of the West Indian fruit fly Anastrepha obliqua (Diptera: Tephritidae) G3 Genes Genomes Genet. (IF 2.6) Pub Date : 2024-02-01 Sheina B Sim, Carlos Congrains, Sandra M Velasco-Cuervo, Renee L Corpuz, Angela N Kauwe, Brian Scheffler, Scott M Geib
The West Indian fruit fly, Anastrepha obliqua, is a major pest of mango in Central and South America and attacks more than 60 species of host fruits. To support current genetic and genomic research on A. obliqua, we sequenced the genome using high-fidelity (HiFi) long-read sequencing. This resulted in a highly contiguous contig assembly with 90% of the genome in 10 contigs. The contig assembly was
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GPI-anchored Gas1 protein regulates cytosolic proteostasis in budding yeast G3 Genes Genomes Genet. (IF 2.6) Pub Date : 2024-01-30 Yuhao Wang, Linhao Ruan, Rong Li
The decline in protein homeostasis (proteostasis) is a hallmark of cellular aging and aging-related diseases. Maintaining a balanced proteostasis requires a complex network of molecular machineries that govern protein synthesis, folding, localization, and degradation. Under proteotoxic stress, misfolded proteins that accumulate in cytosol can be imported into mitochondria for degradation through the
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Detecting genetic effects on phenotype variability to capture gene-by-environment interactions: a systematic method comparison G3 Genes Genomes Genet. (IF 2.6) Pub Date : 2024-01-30 Xiaopu Zhang, Jordana T Bell
Genetically associated phenotypic variability has been widely observed across organisms and traits, including in humans. Both gene-gene and gene-environment interactions can lead to an increase in genetically associated phenotypic variability. Therefore, detecting the underlying genetic variants, or variance Quantitative Trait Loci (vQTLs), can provide novel insights into complex traits. Established
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The unfolded protein response of the endoplasmic reticulum protects Caenorhabditis elegans against DNA damage caused by stalled replication forks G3 Genes Genomes Genet. (IF 2.6) Pub Date : 2024-01-25 Jiaming Xu, Brendil Sabatino, Junran Yan, Glafira Ermakova, Kelsie R S Doering, Stefan Taubert
All animals must maintain genome and proteome integrity, especially when experiencing endogenous or exogenous stress. To cope, organisms have evolved sophisticated and conserved response systems: unfolded protein responses (UPRs) ensure proteostasis while DNA damage responses (DDRs) maintains genome integrity. Emerging evidence suggests that UPRs and DDRs crosstalk, but this remains poorly understood
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Knockdown of Kmt2d leads to growth impairment by activating the Akt/β-catenin signaling pathway G3 Genes Genomes Genet. (IF 2.6) Pub Date : 2024-01-24 Huakun Shangguan, Xiaozhen Huang, Jinduan Lin, Ruimin Chen
The KMT2D variant–caused Kabuki syndrome (KS) is characterized by short stature as a prominent clinical characteristic. The initiation and progression of body growth are fundamentally influenced by chondrocyte proliferation. Uncertainty persists regarding the possibility that KMT2D deficiency affects growth by impairing chondrocyte proliferation. In this study, we used the CRISPR/Cas13d technique to
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Gene expression variation underlying tissue-specific responses to copper stress in Drosophila melanogaster G3 Genes Genomes Genet. (IF 2.6) Pub Date : 2024-01-24 Elizabeth R Everman, Stuart J Macdonald
Copper is one of a handful of biologically necessary heavy metals that is also a common environmental pollutant. Under normal conditions, copper ions are required for many key physiological processes. However, in excess, copper results in cell and tissue damage ranging in severity from temporary injury to permanent neurological damage. Because of its biological relevance, and because many conserved
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Friend turned foe: selfish behavior of a spontaneously arising mitochondrial deletion in an experimentally evolved C. elegans population G3 Genes Genomes Genet. (IF 2.6) Pub Date : 2024-01-23 Abigail N Sequeira, Ian P O’Keefe, Vaishali Katju, Ulfar Bergthorsson
Selfish mitochondrial DNA (mtDNA) mutations are variants that can proliferate within cells and enjoy a replication or transmission bias without fitness benefits for the host. MtDNA deletions in Caenorhabditis elegans can reach high heteroplasmic frequencies despite significantly reducing fitness, illustrating how new mtDNA variants can give rise to genetic conflict between different levels of selection
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Functional analysis of chromatin-associated proteins in Sordaria macrospora reveals similar roles for RTT109 and ASF1 in development and DNA damage response G3 Genes Genomes Genet. (IF 2.6) Pub Date : 2024-01-23 Jan Breuer, David Emanuel Antunes Ferreira, Mike Kramer, Jonas Bollermann, Minou Nowrousian
We performed a functional analysis of two potential partners of ASF1, a highly conserved histone chaperone that plays a crucial role in the sexual development and DNA damage resistance in the ascomycete Sordaria macrospora. ASF1 is known to be involved in nucleosome assembly and disassembly, binding histones H3 and H4 during transcription, replication and DNA repair and has direct and indirect roles
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Differences in transcription initiation directionality underlie distinctions between plants and animals in chromatin modification patterns at genes and cis-regulatory elements G3 Genes Genomes Genet. (IF 2.6) Pub Date : 2024-01-23 Brianna D Silver, Courtney G Willett, Kelsey A Maher, Dongxue Wang, Roger B Deal
Transcriptional initiation is among the first regulated steps controlling eukaryotic gene expression. High-throughput profiling of fungal and animal genomes has revealed that RNA Polymerase II (Pol II) often initiates transcription in both directions at the promoter transcription start site (TSS), but generally only elongates productively into the gene body. Additionally, Pol II can initiate transcription
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Multi-environment Genomic Prediction in Tetraploid Potato G3 Genes Genomes Genet. (IF 2.6) Pub Date : 2024-01-20 Stefan Wilson, Chaozhi Zheng, Chris Maliepaard, Han A Mulder, Richard G F Visser, Fred van Eeuwijk
Multi-environment genomic prediction was applied to tetraploid potato using 147 potato varieties, tested for two years, in three locations representative of three distinct regions in Europe. Different prediction scenarios were investigated to help breeders predict genotypic performance in the regions from one year to the next, for genotypes that were tested this year (scenario 1), as well as new genotypes
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Genome Report: First whole genome sequence and assembly of the Ecuadorian brown-headed spider monkey (Ateles fusciceps fusciceps), a critically endangered species, using Oxford Nanopore Technologies G3 Genes Genomes Genet. (IF 2.6) Pub Date : 2024-01-20 Gabriela Pozo, Martina Albuja-Quintana, Lizbeth Larreátegui, Bernardo Gutiérrez, Nathalia Fuentes, Felipe Alfonso-Cortés, Maria de Lourdes Torres
The Ecuadorian brown-headed spider monkey (Ateles fusciceps fusciceps) is currently considered one of the most endangered primates in the world and is classified as critically endangered (IUCN). It faces multiple threats, the most significant one being habitat loss due to deforestation in western Ecuador. Genomic tools are key for the management of endangered species, but this requires a reference
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Expression and potential regulatory functions of Drosophila octopamine receptors in the female reproductive tract G3 Genes Genomes Genet. (IF 2.6) Pub Date : 2024-01-20 Ethan W Rohrbach, Elizabeth M Knapp, Sonali A Deshpande, David E Krantz
Aminergic signaling is known to play a critical role in regulating female reproductive processes in both mammals and insects. In Drosophila, the ortholog of noradrenaline, octopamine (OA), is required for ovulation as well as several other female reproductive processes. Two OA receptors have already been shown to be expressed in the Drosophila reproductive tract and to be required for egg-laying: OAMB
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ProbBreed: A novel tool for calculating the risk of cultivar recommendation in multi-environment trials G3 Genes Genomes Genet. (IF 2.6) Pub Date : 2024-01-20 Saulo F S Chaves, Matheus D Krause, Luiz A S Dias, Antonio A F Garcia, Kaio O G Dias
Neglecting genotype-by-environment interactions in multi-environment trials (MET) increases the risk of flawed cultivar recommendations for growers. Recent advancements in probability theory coupled with cutting-edge software offer a more streamlined decision-making process for selecting suitable candidates across diverse environments. Here, we present the user-friendly ProbBreed package in R, which
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Evaluating evidence for co-geography in the Anopheles-Plasmodium host-parasite system G3 Genes Genomes Genet. (IF 2.6) Pub Date : 2024-01-17 Clara T Rehmann, Peter L Ralph, Andrew D Kern
The often tight association between parasites and their hosts means that under certain scenarios, the evolutionary histories of the two species can become closely coupled both through time and across space. Using spatial genetic inference, we identify a potential signal of common dispersal patterns in the Anopheles gambiae and Plasmodium falciparum host-parasite system as seen through a between-species
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An RNAi screen for conserved kinases that enhance microRNA activity after dauer in C. elegans G3 Genes Genomes Genet. (IF 2.6) Pub Date : 2024-01-16 Himal Roka Pun, Xantha Karp
Gene regulation in changing environments is critical for maintaining homeostasis. Some animals undergo a stress-resistant diapause stage to withstand harsh environmental conditions encountered during development. MicroRNAs (miRNAs) are one mechanism for regulating gene expression during and after diapause. MicroRNAs downregulate target genes post-transcriptionally through the activity of the miRNA-Induced
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The relationship between Intra-Flagellar Transport and upstream protein trafficking pathways and macrocyclic lactone resistance in Caenorhabditis elegans G3 Genes Genomes Genet. (IF 2.6) Pub Date : 2024-01-16 Robert A Brinzer, Alan D Winter, Antony P Page
Parasitic nematodes are globally important and place a heavy disease burden on infected humans, crops and livestock, while commonly administered anthelmintics used for treatment are being rendered ineffective by increasing levels of resistance. It has recently been shown in the model nematode Caenorhabditis elegans that the sensory cilia of the amphid neurons play an important role in resistance towards
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Genomic insights into the evolution and adaptation of secondary metabolite gene clusters in fungicolous species Cladobotryum mycophilum ATHUM6906 G3 Genes Genomes Genet. (IF 2.6) Pub Date : 2024-01-12 Anastasia C Christinaki, Antonis I Myridakis, Vassili N Kouvelis
Mycophilic or fungicolous fungi can be found wherever fungi exist since they are able to colonize other fungi, which occupy a diverse range of habitats. Some fungicolous species cause important diseases on basidiomycetes and thus, they are the main reason for the destruction of mushroom cultivations. Nonetheless, despite their ecological significance, their genomic data remain limited. Cladobotrum
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Genetic screens in Saccharomyces cerevisiae identify a role for 40S ribosome recycling factors Tma20/22 in nonsense mediated decay G3 Genes Genomes Genet. (IF 2.6) Pub Date : 2024-01-10 Miguel Pacheco, Karole N D’Orazio, Laura N Lessen, Anthony J Veltri, Zachary Neiman, Raphael Loll-Krippleber, Grant W Brown, Rachel Green
The decay of messenger RNA with a premature termination codon (PTC) by nonsense mediated decay (NMD) is an important regulatory pathway for eukaryotes and an essential pathway in mammals. NMD is typically triggered by the ribosome terminating at a stop codon that is aberrantly distant from the poly-A tail. Here, we use a fluorescence screen to identify factors involved in NMD in S. cerevisiae. In addition
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Unusual predominance of maintenance DNA methylation in Spirodela polyrhiza G3 Genes Genomes Genet. (IF 2.6) Pub Date : 2024-01-08 Alex Harkess, Adam J Bewick, Zefu Lu, Paul Fourounjian, Todd P Michael, Robert J Schmitz, Blake C Meyers
Duckweeds are among the fastest reproducing plants, able to clonally divide at exponential rates. However, the genetic and epigenetic impact of clonality on plant genomes is poorly understood. 5-methylcytosine (5mC) is a modified base often described as necessary for the proper regulation of certain genes and transposons and for the maintenance of genome integrity in plants. However, the extent of
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A chromosome-scale assembly for ‘d’Anjou’ pear G3 Genes Genomes Genet. (IF 2.6) Pub Date : 2024-01-08 Alan Yocca, Mary Akinyuwa, Nick Bailey, Brannan Cliver, Harrison Estes, Abigail Guillemette, Omar Hasannin, Jennifer Hutchison, Wren Jenkins, Ishveen Kaur, Risheek Rahul Khanna, Madelene Loftin, Lauren Lopes, Erika Moore-Pollard, Oluwakemisola Olofintila, Gideon Oluwaseye Oyebode, Jinesh Patel, Parbati Thapa, Martin Waldinger, Jie Zhang, Qiong Zhang, Leslie Goertzen, Sarah B Carey, Heidi Hargarten
Cultivated pear consists of several Pyrus species with P. communis (European pear) representing a large fraction of worldwide production. As a relatively recently domesticated crop and perennial tree, pear can benefit from genome-assisted breeding. Additionally, comparative genomics within Rosaceae promises greater understanding of evolution within this economically important family. Here, we generate
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Profiling The Compendium Of Changes In Saccharomyces cerevisiae Due To Mutations That Alter Availability Of The Main Methyl Donor S-Adenosylmethionine G3 Genes Genomes Genet. (IF 2.6) Pub Date : 2024-01-07 McKayla Remines, Makailyn Schoonover, Zoey Knox, Kailee Kenwright, Kellyn M Hoffert, Amila Coric, James Mead, Joseph Ampfer, Serigne Seye, Erin D Strome
The SAM1 and SAM2 genes encode for S-AdenosylMethionine (AdoMet) synthetase enzymes, with AdoMet serving as the main cellular methyl donor. We have previously shown that independent deletion of these genes alters chromosome stability and AdoMet concentrations in opposite ways in Saccharomyces cerevisiae. To characterize other changes occurring in these mutants, we grew wildtype, sam1Δ/sam1Δ, and sam2Δ/sam2Δ
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A fast algorithm to factorize high-dimensional Tensor Product matrices used in Genetic Models G3 Genes Genomes Genet. (IF 2.6) Pub Date : 2024-01-05 Marco Lopez-Cruz, Paulino Pérez-Rodríguez, Gustavo de los Campos
Many genetic models (including models for epistatic effects as well as genetic-by-environment) involve covariance structures that are Hadamard products of lower rank matrices. Implementing these models require factorizing large Hadamard product matrices. The available algorithms for factorization do not scale well for big data, making the use of some of these models not feasible with large sample sizes
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Allelic combinations of Hd1, Hd16, and Ghd7 exhibit pleiotropic effects on agronomic traits in rice G3 Genes Genomes Genet. (IF 2.6) Pub Date : 2024-01-03 Seung Young Lee, Ji-Ung Jeung, Youngjun Mo
Heading date is a critical agronomic trait that significantly affects grain yield and quality in rice. As early heading is typically associated with reduced yield due to shorter growth duration, it is essential to harness optimum heading date genes and their allelic combinations to promote heading while minimizing yield penalties. In this study, we identified quantitative trait loci (QTLs) for heading
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Genome report: Whole genome sequence and annotation of Penstemon davidsonii G3 Genes Genomes Genet. (IF 2.6) Pub Date : 2023-12-29 Kate L Ostevik, Magdy Alabady, Mengrui Zhang, Mark D Rausher
Penstemon is the most speciose flowering plant genus endemic to North America. Penstemon species’ diverse morphology and adaptation to various environments have made them a valuable model system for studying evolution. Here we report the first full reference genome assembly and annotation for Penstemon davidsonii. Using PacBio long-read sequencing and Hi-C scaffolding technology, we constructed a de
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A comprehensive evolutionary scenario for the origin and neofunctionalization of the Drosophila speciation gene Odysseus (OdsH) G3 Genes Genomes Genet. (IF 2.6) Pub Date : 2023-12-29 William Vilas Boas Nunes, Daniel Siqueira de Oliveira, Guilherme de Rezende Dias, Antonio Bernardo Carvalho, Ícaro Putinhon Caruso, Joice Matos Biselli, Nathalie Guegen, Abdou Akkouche, Nelly Burlet, Cristina Vieira, Claudia M A Carareto
Odysseus (OdsH) was the first speciation gene described in Drosophila related to hybrid sterility in offspring of mating between D. mauritiana and D. simulans. Its origin is attributed to the duplication of the gene unc-4 in the subgenus Sophophora. By using a much larger sample of Drosophilidae species, we showed that contrary to what has been previously proposed, OdsH origin occurred 62 million years
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PBRM-1/PBAF-regulated genes in a multipotent progenitor in C. elegans G3 Genes Genomes Genet. (IF 2.6) Pub Date : 2023-12-27 Laura D Mathies, Andrew C Kim, Evan M Soukup, Alan’da E Thomas, Jill C Bettinger
The Caenorhabditis elegans somatic gonadal precursors (SGPs) are multipotent progenitors that generate all somatic cells of the adult reproductive system. The two SGPs originate in the mesodermal layer and are born through a division that produces one SGP and one head mesodermal cell (hmc). One hmc terminally differentiates and the other dies by programmed cell death. The PBAF chromatin remodeling