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A reference quality genome assembly for the Jewel scarab Chrysina gloriosa G3 Genes Genomes Genet. (IF 2.6) Pub Date : 2024-04-17 Terrence Sylvester, Zachary Hoover, Carl E Hjelmen, Michelle M Jonika, Leslie T Blackmon, James M Alfieri, J Spencer Johnston, Sean Chien, Tahmineh Esfandani, Heath Blackmon
The jewel scarab Chrysina gloriosa is one of the most charismatic beetles in the United States and is found from the mountains of West Texas to the Southeastern Arizona sky islands. This species is highly sought by professional and amateur collectors worldwide due to its gleaming metallic coloration. However, the impact of the large-scale collection of this beetle on its populations is unknown, and
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What is a B chromosome? Early definitions revisited G3 Genes Genomes Genet. (IF 2.6) Pub Date : 2024-04-16 Patrick M Ferree, Jelena Blagojević, Andreas Houben, Cesar Martins, Vladimir A Trifonov, Mladen Vujošević
Since the discovery of B chromosomes, multiple different definitions of these selfish genetic elements have been put forth. We reconsidered early definitions in light of recently published studies. While there are many characteristics that vary among different B chromosomes, such as their evolutionary origins, size, segregation behaviors, gene content, and function, there is one defining trait of all
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Robustness in population-structure and demographic-inference results derived from the Aedes aegypti SNP chip and whole-genome sequencing data G3 Genes Genomes Genet. (IF 2.6) Pub Date : 2024-04-16 Andrés Gómez-Palacio, Gen Morinaga, Paul E Turner, Maria Victoria Micieli, Mohammed-Ahmed B Elnour, Bashir Salim, Sinnathamby Noble Surendran, Ranjan Ramasamy, Jeffrey R Powell, John Soghigian, Andrea Gloria-Soria
The mosquito Aedes aegypti is the primary vector of many human arboviruses such as dengue, yellow fever, chikungunya and Zika, which affect millions of people world-wide. Population genetics studies on this mosquito have been important in understanding its invasion pathways and success as a vector of human disease. The Axiom aegypti1 SNP chip was developed from a sample of geographically diverse Ae
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Museum Genomics approach to study the taxonomy and evolution of Woolly-necked storks using historic specimens G3 Genes Genomes Genet. (IF 2.6) Pub Date : 2024-04-16 Prashant Ghimire, Catalina Palacios, Jeremiah Trimble, Sangeet Lamichhaney
The accessibility of genomic tools in evolutionary biology has allowed for a thorough exploration of various evolutionary processes associated with adaptation and speciation. However, genomic studies in natural systems present numerous challenges, reflecting the inherent complexities of studying organisms in their native habitats. The utilization of museum specimens for genomics research has received
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A High-quality Genome of the convergent lady beetle, Hippodamia convergens G3 Genes Genomes Genet. (IF 2.6) Pub Date : 2024-04-15 Gavrila Ang, Andrew Zhang, John Obrycki, Arun Sethuraman
Here we describe a high quality genome assembly and annotation of the convergent lady beetle, Hippodamia convergens (Coleoptera: Coccinellidae). The highest quality unmasked genome comprises 619 Megabases (Mb) of chromosomal DNA, organized into 899 contigs, with a contig N50 score of 89 Mbps. The genome was assessed to be 96% complete (BUSCO). Reconstruction of a whole genome phylogeny resolved H.
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A chromosome-level genome assembly of the Asian house martin implies potential genes associated with the feathered-foot trait G3 Genes Genomes Genet. (IF 2.6) Pub Date : 2024-04-12 Yuan-Fu Chan, Chia-Wei Lu, Hao-Chih Kuo, Chih-Ming Hung
The presence of feathers is a vital characteristic among birds, yet most modern birds had no feather on their feet. The discoveries of feathers on the hind limbs of basal birds and dinosaurs have sparked an interest in the evolutionary origin and genetic mechanism of feathered feet. However, the majority of studies investigating the genes associated with this trait focused on domestic populations.
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A de novo genome assembly of Solanum bulbocastanum Dun., a Mexican diploid species reproductively isolated from the A-genome species, including cultivated potatoes G3 Genes Genomes Genet. (IF 2.6) Pub Date : 2024-04-12 Awie J Hosaka, Rena Sanetomo, Kazuyoshi Hosaka
Potato and its wild relatives are distributed mainly in the Mexican highlands and central Andes of South America. The South American A-genome species, including cultivated potatoes, are reproductively isolated from Mexican diploid species. Whole-genome sequencing has disclosed genome structure and similarity, mostly in cultivated potatoes and their closely related species. In this study, we generated
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Whole Genome Assembly of a Hybrid Trypanosoma cruzi Strain Assembled with Nanopore Sequencing Alone G3 Genes Genomes Genet. (IF 2.6) Pub Date : 2024-04-09 Jill M C Hakim, Sneider A Gutierrez Guarnizo, Edith Málaga Machaca, Robert H Gilman, Monica R Mugnier
Trypanosoma cruzi is the causative agent of Chagas disease, which causes 10,000 deaths per year. Despite the high mortality associated with Chagas, relatively few parasite genomes have been assembled to date, with genome assemblies unavailable even for some commonly used laboratory strains. This is at least partially due to T. cruzi’s highly complex and highly repetitive genome, which defies investigation
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Sse1, Hsp110 chaperone of yeast, controls the cellular fate during Endoplasmic reticulum stress G3 Genes Genomes Genet. (IF 2.6) Pub Date : 2024-04-05 Mainak Pratim Jha, Vignesh Kumar, Asmita Ghosh, Koyeli Mapa
Sse1 is a cytosolic Hsp110 molecular chaperone of yeast, Saccharomyces cerevisiae. Its multifaceted roles in cellular protein homeostasis as a Nucleotide Exchange Factor (NEF), as a protein-disaggregase and as a Chaperone linked to Protein Synthesis (CLIPS) are well documented. In the current study, we show that SSE1 genetically interacts with IRE1 and HAC1, the Endoplasmic Reticulum-Unfolded Protein
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Validation of positional candidates Rps6ka6 and Pou3f4 for a locus associated with skeletal muscle mass variability G3 Genes Genomes Genet. (IF 2.6) Pub Date : 2024-04-05 Konstantinos Lekkos, Afra A Bhuiyan, Abdullah M K Albloshi, Paige M Brooks, Thomas M Coate, Arimantas Lionikas
Genetic variability significantly contributes to individual differences in skeletal muscle mass; however, the specific genes involved in that process remain elusive. In this study, we examined the role of positional candidates, Rps6ka6 and Pou3f4, of a chromosome X locus, implicated in muscle mass variability in CFW laboratory mice. Histology of hindlimb muscles was studied in CFW male mice carrying
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Improved, reference quality genome sequence of the plastic-degrading greater wax moth, Galleria mellonella G3 Genes Genomes Genet. (IF 2.6) Pub Date : 2024-04-02 Reginald Young, Khandaker Asif Ahmed, Leon Court, Cynthia Castro-Vargas, Anna Marcora, Joseph Boctor, Cate Paull, Gene Wijffels, Rahul Rane, Owain Edwards, Tom Walsh, Gunjan Pandey
Galleria mellonella is a pest of honeybees in many countries because its larvae feed on beeswax. However, G. mellonella larvae can also eat various plastics, including polyethylene, polystyrene and polypropylene, so the species is garnering increasing interest as a tool for plastic biodegradation research. This paper presents an improved genome (99.3% completed lepidoptera_odb10 BUSCO; genome mode)
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Modulators of MAPK pathway activity during filamentous growth in Saccharomyces cerevisiae G3 Genes Genomes Genet. (IF 2.6) Pub Date : 2024-04-01 Atindra N Pujari, Paul J Cullen
Mitogen-activated protein kinase (MAPK) pathways control the response to intrinsic and extrinsic stimuli. In the budding yeast Saccharomyces cerevisiae, cells undergo filamentous growth, which is regulated by the fMAPK pathway. To better understand the regulation of the fMAPK pathway, a genetic screen was performed to identify spontaneous mutants with elevated activity of an fMAPK-pathway dependent
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Analysis of non-degradable cyclins reveals distinct roles of the mitotic cyclins in Drosophila meiosis G3 Genes Genomes Genet. (IF 2.6) Pub Date : 2024-03-29 Mohammed Bourouh, Rajdeep Dhaliwal, Rajni Rai, Hafsah Qureshi, Andrew Swan
Meiosis is a complex variant of the mitotic cell cycle, and as such relies on many of the same proteins involved in mitotis, but utilizes these in novel ways. As in mitosis, Cdk1 and its cyclin partners, Cyclin A, B and B3 are required at multiple steps in meiosis. Here we study the effect of stabilized forms of the three mitotic cyclins to study the consequences of failure to degrade the cyclins in
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Temporal challenges in detecting balancing selection from population genomic data G3 Genes Genomes Genet. (IF 2.6) Pub Date : 2024-03-29 Vivak Soni, Jeffrey D Jensen
The role of balancing selection in maintaining genetic variation remains an open question in population genetics. Recent years have seen numerous studies identifying candidate loci potentially experiencing balancing selection, most predominantly in human populations. There are however numerous alternative evolutionary processes that may leave similar patterns of variation, thereby potentially confounding
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The Landscape and Predicted Roles of Structural Variants in Fusarium Graminearum Genomes G3 Genes Genomes Genet. (IF 2.6) Pub Date : 2024-03-28 Upasana Dhakal, Hye-Seon Kim, Christopher Toomajian
Structural rearrangements, such as inversions, translocations, duplications, and large insertions and deletions, are large-scale genomic variants that can play an important role in shaping phenotypic variation and in genome adaptation and evolution. We used chromosomal-level assemblies from eight Fusarium graminearum isolates to study structural variants and their role in fungal evolution. We generated
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Chromosome-level genome assembly of the European green woodpecker Picus viridis G3 Genes Genomes Genet. (IF 2.6) Pub Date : 2024-03-27 Thomas Forest, Guillaume Achaz, Martial Marbouty, Amaury Bignaud, Agnès Thierry, Romain Koszul, Marine Milhes, Joanna Lledo, Jean-Marc Pons, Jérôme Fuchs
The European green woodpecker, Picus viridis, is a widely distributed species found in the Western Palearctic region. Here, we assembled a highly contiguous genome assembly for this species using a combination of short- and long-read sequencing and scaffolded with chromatin conformation capture (Hi-C). The final genome assembly was 1.28 Gb and features a scaffold N50 of 37 Mb and a scaffold L50 of
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A Genome Sequence for the Threatened Whitebark Pine G3 Genes Genomes Genet. (IF 2.6) Pub Date : 2024-03-25 David B Neale, Aleksey V Zimin, Amy Meltzer, Akriti Bhattarai, Maurice Amee, Laura Figueroa Corona, Brian J Allen, Daniela Puiu, Jessica Wright, Amanda R De La Torre, Patrick E McGuire, Winston Timp, Steven L Salzberg, Jill L Wegrzyn
Whitebark pine (WBP, Pinus albicaulis) is a white pine of subalpine regions in western contiguous US and Canada. WBP has become critically threatened throughout a significant part of its natural range due to mortality from the introduced fungal pathogen white pine blister rust (WPBR, Cronartium ribicola) and additional threats from mountain pine beetle (Dendroctonus ponderosae), wildfire, and maladaptation
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Identification of different classes of genome instability suppressor genes through analysis of DNA damage response markers G3 Genes Genomes Genet. (IF 2.6) Pub Date : 2024-03-25 Bin-Zhong Li, Richard D Kolodner, Christopher D Putnam
Cellular pathways that detect DNA damage are useful for identifying genes that suppress DNA damage, which can cause genome instability and cancer predisposition syndromes when mutated. We identified 199 high-confidence and 530 low-confidence DNA damage suppressing (DDS) genes in Saccharomyces cerevisiae through a whole genome screen for mutations inducing Hug1 expression, a focused screen for mutations
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A long-read draft assembly of the Chinese mantis (Mantodea: Mantidae: Tenodera sinensis) genome reveals patterns of ion channel gain and loss across Arthropoda G3 Genes Genomes Genet. (IF 2.6) Pub Date : 2024-03-22 Jay K Goldberg, R Keating Godfrey, Meghan Barrett
Praying mantids (Mantodea: Mantidae) are iconic insects that have captivated biologists for decades, especially the species with cannibalistic copulatory behavior. This behavior has been cited as evidence that insects lack nociceptive capacities and cannot feel pain; however, this behaviorally driven hypothesis has never been rigorously tested at the genetic or functional level. To enable future studies
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Estimating Between Country Migration in Pneumococcal Populations G3 Genes Genomes Genet. (IF 2.6) Pub Date : 2024-03-20 Sophie Belman, Henri Pesonen, Nicholas J Croucher, Stephen D Bentley, Jukka Corander
Streptococcus pneumoniae (the pneumococcus) is a globally distributed, human obligate opportunistic bacterial pathogen which, although often carried commensally, is also a significant cause of invasive disease. Apart from multi-drug resistant and virulent clones, the rate and direction of pneumococcal dissemination between different countries remains largely unknown. The ability for the pneumococcus
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Strain-specific evolution and host-specific regulation of transposable elements in the model plant symbiont Rhizophagus irregularis G3 Genes Genomes Genet. (IF 2.6) Pub Date : 2024-03-20 Jordana Inácio Nascimento Oliveira, Nicolas Corradi
Transposable elements (TEs) are repetitive DNA that can create genome structure and regulation variability. The genome of Rhizophagus irregularis, a widely studied arbuscular mycorrhizal fungus (AMF), comprises approximately 50% repetitive sequences that include transposable elements. Despite their abundance, two-thirds of TEs remain unclassified, and their regulation among AMF life stages remains
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The evolution of the gliotoxin biosynthetic gene cluster in Penicillium fungi G3 Genes Genomes Genet. (IF 2.6) Pub Date : 2024-03-20 Charu Balamurugan, Jacob L Steenwyk, Gustavo H Goldman, Antonis Rokas
Fungi biosynthesize diverse secondary metabolites, small organic bioactive molecules with key roles in fungal ecology. Fungal secondary metabolites are often encoded by physically clustered genes known as biosynthetic gene clusters (BGCs). Fungi in the genus Penicillium produce a cadre of secondary metabolites, some of which are useful (e.g., the antibiotic penicillin and the cholesterol-lowering drug
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Identification of chemosensory genes in the stingless bee Tetragonisca fiebrigi G3 Genes Genomes Genet. (IF 2.6) Pub Date : 2024-03-18 María Sol Balbuena, Jose M Latorre-Estivalis, Walter M Farina
Reception of chemical information from the environment is crucial for insects’ survival and reproduction. The chemosensory reception mainly occurs by the antennae and mouth parts of the insect, when the stimulus contacts the chemoreceptors located within the sensilla. Chemosensory receptor genes have been well-studied in some social hymenopterans such as ants, honeybees, and wasps. However, although
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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