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The Arabidopsis Information Resource in 2024. Genetics (IF 3.3) Pub Date : 2024-03-08 Leonore Reiser, Erica Bakker, Sabarinath Subramaniam, Xingguo Chen, Swapnil Sawant, Kartik Khosa, Trilok Prithvi, Tanya Z Berardini
Since 1999, The Arabidopsis Information Resource (www.arabidopsis.org) has been curating data about the Arabidopsis thaliana genome. Its primary focus is integrating experimental gene function information from the peer-reviewed literature and codifying it as controlled vocabulary annotations. Our goal is to produce a "gold standard" functional annotation set that reflects the current state of knowledge
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The contribution of an X chromosome QTL to non-Mendelian inheritance and unequal chromosomal segregation in A. freiburgense. Genetics (IF 3.3) Pub Date : 2024-03-02 Talal Al-Yazeedi, Sally Adams, Sophie Tandonnet, Anisa Turner, Jun Kim, Junho Lee, Andre Pires-daSilva
Auanema freiburgense is a nematode with males, females, and selfing hermaphrodites. When XO males mate with XX females, they typically produce a low proportion of XO offspring because they eliminate nullo-X spermatids. This process ensures that most sperm carry an X chromosome, increasing the likelihood of X chromosome transmission compared to random segregation. This occurs because of an unequal distribution
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COP9 signalosome component CSN-5 stabilizes PUF proteins FBF-1 and FBF-2 in Caenorhabditis elegans germline stem and progenitor cells. Genetics (IF 3.3) Pub Date : 2024-03-01 Emily Osterli, Mary Ellenbecker, Xiaobo Wang, Mikaya Terzo, Ketch Jacobson, DeAnna Cuello, Ekaterina Voronina
RNA-binding proteins FBF-1 and FBF-2 (FBFs) are required for germline stem cell maintenance and the sperm/oocyte switch in Caenorhabditis elegans, though the mechanisms controlling FBF protein levels remain unknown. We identified an interaction between both FBFs and CSN-5, a component of the COP9 (constitutive photomorphogenesis 9) signalosome best known for its role in regulating protein degradation
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A fluorescent assay for cryptic transcription in Saccharomyces cerevisiae reveals novel insights into factors that stabilize chromatin structure on newly replicated DNA. Genetics (IF 3.3) Pub Date : 2024-02-26 Ellia Gao, Joshua A R Brown, Stephanie Jung, LeAnn J Howe
The disruption of chromatin structure can result in transcription initiation from cryptic promoters within gene bodies. While the passage of RNA polymerase II is a well-characterized chromatin-disrupting force, numerous factors, including histone chaperones, normally stabilize chromatin on transcribed genes, thereby repressing cryptic transcription. DNA replication, which employs a partially overlapping
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Bursts of coalescence within population pedigrees whenever big families occur. Genetics (IF 3.3) Pub Date : 2024-02-26 Dimitrios Diamantidis, Wai-Tong Louis Fan, Matthias Birkner, John Wakeley
We consider a simple diploid population-genetic model with potentially high variability of offspring numbers among individuals. Specifically, against a backdrop of Wright-Fisher reproduction and no selection there is an additional probability that a big family occurs, meaning that a pair of individuals has a number of offspring on the order of the population size. We study how the pedigree of the population
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Interpreting Generative Adversarial Networks to Infer Natural Selection from Genetic Data. Genetics (IF 3.3) Pub Date : 2024-02-22 Rebecca Riley, Iain Mathieson, Sara Mathieson
Understanding natural selection and other forms of non-neutrality is a major focus for the use of machine learning in population genetics. Existing methods rely on computationally intensive simulated training data. Unlike efficient neutral coalescent simulations for demographic inference, realistic simulations of selection typically require slow forward simulations. Because there are many possible
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Genetic architecture of trait variance in craniofacial morphology. Genetics (IF 3.3) Pub Date : 2024-02-22 Fernando Andrade, Lisa Howell, Christopher J Percival, Joan T Richtsmeier, Ralph S Marcucio, Benedikt Hallgrímsson, James M Cheverud
The genetic architecture of trait variance has long been of interest in genetics and evolution. One of the earliest attempts to understand this architecture was presented in Lerner's Genetic Homeostasis (1954). Lerner proposed that heterozygotes should be better able to tolerate environmental perturbations because of functional differences between the alleles at a given locus, with each allele optimal
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Sall genes regulate hindlimb initiation in mouse embryos. Genetics (IF 3.3) Pub Date : 2024-02-22 Katherine Q Chen, Hiroko Kawakami, Aaron Anderson, Dylan Corcoran, Aditi Soni, Ryuichi Nishinakamura, Yasuhiko Kawakami
Vertebrate limbs start to develop as paired protrusions from the lateral plate mesoderm at specific locations of the body with forelimb buds developing anteriorly and hindlimb buds posteriorly. During the initiation process, limb progenitor cells maintain active proliferation to form protrusions and start to express Fgf10, which trigger molecular processes for outgrowth and patterning. Although both
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Characterization of adaptation mechanisms in sorghum using a multireference back-cross nested association mapping design and envirotyping. Genetics (IF 3.3) Pub Date : 2024-02-21 Vincent Garin, Chiaka Diallo, Mohamed Lamine Tékété, Korotimi Théra, Baptiste Guitton, Karim Dagno, Abdoulaye G Diallo, Mamoutou Kouressy, Willmar Leiser, Fred Rattunde, Ibrahima Sissoko, Aboubacar Touré, Baloua Nébié, Moussa Samaké, Jana Kholovà, Julien Frouin, David Pot, Michel Vaksmann, Eva Weltzien, Niaba Témé, Jean-François Rami
Identifying the genetic factors impacting the adaptation of crops to environmental conditions is of key interest for conservation and selection purposes. It can be achieved using population genomics, and evolutionary or quantitative genetics. Here we present a sorghum multireference back-cross nested association mapping population composed of 3,901 lines produced by crossing 24 diverse parents to 3
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PomBase: a Global Core Biodata Resource-growth, collaboration, and sustainability. Genetics (IF 3.3) Pub Date : 2024-02-20 Kim M Rutherford, Manuel Lera-Ramírez, Valerie Wood
PomBase (https://www.pombase.org), the model organism database (MOD) for fission yeast, was recently awarded Global Core Biodata Resource (GCBR) status by the Global Biodata Coalition (GBC; https://globalbiodata.org/) after a rigorous selection process. In this MOD review, we present PomBase's continuing growth and improvement over the last 2 years. We describe these improvements in the context of
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High-throughput genetic manipulation of multi-cellular organisms using a machine-vision guided embryonic microinjection robot. Genetics (IF 3.3) Pub Date : 2024-02-19 Andrew D Alegria, Amey S Joshi, Jorge Blanco Mendana, Kanav Khosla, Kieran T Smith, Benjamin Auch, Margaret Donovan, John Bischof, Daryl M Gohl, Suhasa B Kodandaramaiah
Microinjection is a technique used for transgenesis, mutagenesis, cell labeling, cryopreservation, and in vitro fertilization in multiple single and multicellular organisms. Microinjection requires specialized skills and involves rate limiting and labor-intensive preparatory steps. Here we constructed a machine vision guided generalized robot that fully automates the process of microinjection in fruit
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Enrichment of hard sweeps on the X chromosome compared to autosomes in six Drosophila species. Genetics (IF 3.3) Pub Date : 2024-02-16 Mariana Harris, Bernard Kim, Nandita Garud
The X chromosome, being hemizygous in males, is exposed one third of the time increasing the visibility of new mutations to natural selection, potentially leading to different evolutionary dynamics than autosomes. Recently, we found an enrichment of hard selective sweeps over soft selective sweeps on the X chromosome relative to the autosomes in a North American population of Drosophila melanogaster
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Histone Variant H2A.Z and Linker Histone H1 Influence Chromosome Condensation in Saccharomyces cerevisiae. Genetics (IF 3.3) Pub Date : 2024-02-14 Anna M Rogers, Nola R Neri, Lorencia Chigweshe, Scott G Holmes
Chromosome condensation is essential for the fidelity of chromosome segregation during mitosis and meiosis. Condensation is associated both with local changes in nucleosome structure and larger scale alterations in chromosome topology mediated by the condensin complex. We examined the influence of linker histone H1 and variant histone H2A.Z on chromosome condensation in budding yeast cells. Linker
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To be or not to be: orb, the fusome and oocyte specification in Drosophila. Genetics (IF 3.3) Pub Date : 2024-02-12 Justinn Barr, Rocky Diegmiller, Megan M Colonnetta, Wenfan Ke, Jasmin Imran Alsous, Tomer Stern, Stanislav Y Shvartsman, Paul Schedl
In the fruit fly Drosophila melanogaster, two cells in a cyst of 16 interconnected cells have the potential to become the oocyte, but only one of these will assume an oocyte fate as the cysts transition through regions 2a and 2b of the germarium. The mechanism of specification depends on a polarized microtubule network, a dynein dependent Egl:BicD mRNA cargo complex, a special membranous structure
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An expression-directed linear mixed model (edLMM) discovering low-effect genetic variants. Genetics (IF 3.3) Pub Date : 2024-02-05 Qing Li, Jiayi Bian, Yanzhao Qian, Pathum Kossinna, Copper Gau, Paul M K Gordon, Xiang Zhou, Xingyi Guo, Jun Yan, Jingjing Wu, Quan Long
Detecting genetic variants with low effect sizes using a moderate sample size is difficult, hindering downstream efforts to learn pathology and estimating heritability. In this work, by utilizing informative weights learned from training genetically predicted gene expression models, we formed an alternative approach to estimate the polygenic term in a linear mixed model (LMM). Our LMM estimates the
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FlyBase: updates to the Drosophila genes and genomes database. Genetics (IF 3.3) Pub Date : 2024-02-01 Arzu Öztürk-Çolak, Steven J Marygold, Giulia Antonazzo, Helen Attrill, Damien Goutte-Gattat, Victoria K Jenkins, Beverley B Matthews, Gillian Millburn, Gilberto Dos Santos, Christopher J Tabone
FlyBase (flybase.org) is a model organism database and knowledge base about Drosophila melanogaster, commonly known as the fruit fly. Researchers from around the world rely on the genetic, genomic, and functional information available in FlyBase, as well as its tools to view and interrogate these data. In this article, we describe the latest developments and updates to FlyBase. These include the introduction
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Premature endocycling of Drosophila follicle cells causes pleiotropic defects in oogenesis. Genetics (IF 3.3) Pub Date : 2024-02-01 Hunter C Herriage, Brian R Calvi
Endocycling cells grow and repeatedly duplicate their genome without dividing. Cells switch from mitotic cycles to endocycles in response to developmental signals during the growth of specific tissues in a wide range of organisms. The purpose of switching to endocycles, however, remains unclear in many tissues. Additionally, cells can switch to endocycles in response to conditional signals, which can
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Role of the San1 ubiquitin ligase in the heat stress-induced degradation of non-native Nup1 in the nuclear pore complex. Genetics (IF 3.3) Pub Date : 2024-02-01 Takanari Ikeda, Kenji Yamazaki, Fumihiko Okumura, Takumi Kamura, Kunio Nakatsukasa
The nuclear pore complex (NPC) mediates the selective exchange of macromolecules between the nucleus and the cytoplasm. Neurodegenerative diseases such as amyotrophic lateral sclerosis are characterized by mislocalization of nucleoporins (Nups), transport receptors, and Ras-related nuclear proteins into nucleoplasmic or cytosolic aggregates, underscoring the importance of precise assembly of the NPC
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Effects of parental age and polymer composition on short tandem repeat de novo mutation rates. Genetics (IF 3.3) Pub Date : 2024-01-31 Michael E Goldberg, Michelle D Noyes, Evan E Eichler, Aaron R Quinlan, Kelley Harris
Short tandem repeats (STRs) are hotspots of genomic variability in the human germline because of their high mutation rates, which have long been attributed largely to polymerase slippage during DNA replication. This model suggests that STR mutation rates should scale linearly with a father's age, as progenitor cells continually divide after puberty. In contrast, it suggests that STR mutation rates
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Counting the genetic ancestors from source populations in members of an admixed population. Genetics (IF 3.3) Pub Date : 2024-01-30 Lily Agranat-Tamir, Jazlyn A Mooney, Noah A Rosenberg
In a genetically admixed population, admixed individuals possess genealogical and genetic ancestry from multiple source groups. Under a mechanistic model of admixture, we study the number of distinct ancestors from the source populations that the admixture represents. Combining a mechanistic admixture model with a recombination model that describes the probability that a genealogical ancestor is a
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Maternal mitochondrial function affects paternal mitochondrial inheritance in Drosophila. Genetics (IF 3.3) Pub Date : 2024-01-30 Jinguo Cao, Yuying Luo, Yonghe Chen, Zhaoqi Wu, Jiting Zhang, Yi Wu, Wen Hu
The maternal inheritance of mitochondria is a widely accepted paradigm, and mechanisms that prevent paternal mitochondria transmission to offspring during spermatogenesis and post-fertilization have been described. Although certain species do retain paternal mitochondria, the factors affecting paternal mitochondria inheritance in these cases are unclear. More importantly, the evolutionary benefit of
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A missense SNP in the tumor suppressor SETD2 reduces H3K36me3 and mitotic spindle integrity in Drosophila. Genetics (IF 3.3) Pub Date : 2024-01-30 Jovan S Brockett, Tad Manalo, Hala Zein-Sabatto, Jina Lee, Junnan Fang, Philip Chu, Harry Feng, Dattatraya Patil, Priscilla Davidson, Kenneth Ogan, Viraj A Master, John G Pattaras, David L Roberts, Sharon H Bergquist, Matthew A Reyna, John A Petros, Dorothy A Lerit, Rebecca S Arnold
Mutations in SETD2 are among the most prevalent drivers of renal cell carcinoma (RCC). We identified a novel single nucleotide polymorphism (SNP) in SETD2, E902Q, within a subset of RCC patients, which manifests as both an inherited or tumor-associated somatic mutation. To determine if the SNP is biologically functional, we used CRISPR-based genome editing to generate the orthologous mutation within
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Distinct genomic contexts predict gene presence-absence variation in different pathotypes of Magnaporthe oryzae. Genetics (IF 3.3) Pub Date : 2024-01-30 Pierre M Joubert, Ksenia V Krasileva
Fungi use the accessory gene content of their pangenomes to adapt to their environments. While gene presence-absence variation (PAV) contributes to shaping accessory gene reservoirs, the genomic contexts that shape these events remain unclear. Since pangenome studies are typically species-wide and do not analyze different populations separately, it is yet to be uncovered whether PAV patterns and mechanisms
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Calcineurin contributes to RNAi-mediated transgene silencing and small interfering RNA production in the human fungal pathogen Cryptococcus neoformans. Genetics (IF 3.3) Pub Date : 2024-01-27 Vikas Yadav, Riya Mohan, Sheng Sun, Joseph Heitman
Adaptation to external environmental challenges at the cellular level requires rapid responses and involves relay of information to the nucleus to drive key gene expression changes through downstream transcription factors. Here, we describe an alternative route of adaptation through a direct role for cellular signaling components in governing gene expression via RNA interference-mediated small RNA
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Gene loss and cis-regulatory novelty shaped core histone gene evolution in the apiculate yeast Hanseniaspora uvarum. Genetics (IF 3.3) Pub Date : 2024-01-25 Max A B Haase, Jacob L Steenwyk, Jef D Boeke
Core histone genes display a remarkable diversity of cis-regulatory mechanisms despite their protein sequence conservation. However, the dynamics and significance of this regulatory turnover are not well understood. Here we describe the evolutionary history of core histone gene regulation across 400 million years in budding yeasts. We find that canonical mode of core histone regulation - mediated by
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Echinobase: a resource to support the echinoderm research community. Genetics (IF 3.3) Pub Date : 2024-01-23 Cheryl A Telmer, Kamran Karimi, Macie M Chess, Sergei Agalakov, Bradley I Arshinoff, Vaneet Lotay, Dong Zhuo Wang, Stanley Chu, Troy J Pells, Peter D Vize, Veronica F Hinman, Charles A Ettensohn
Echinobase (www.echinobase.org) is a model organism knowledgebase serving as a resource for the community that studies echinoderms, a phylum of marine invertebrates that includes sea urchins and sea stars. Echinoderms have been important experimental models for over 100 years and continue to make important contributions to environmental, evolutionary, and developmental studies, including research on
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Shared evolutionary processes shape landscapes of genomic variation in the great apes. Genetics (IF 3.3) Pub Date : 2024-01-18 Murillo F Rodrigues, Andrew D Kern, Peter L Ralph
For at least the past five decades population genetics, as a field, has worked to describe the precise balance of forces that shape patterns of variation in genomes. The problem is challenging because modelling the interactions between evolutionary processes is difficult, and different processes can impact genetic variation in similar ways. In this paper, we describe how diversity and divergence between
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Natural variation in the zinc-finger-encoding exon of Prdm9 affects hybrid sterility phenotypes in mice. Genetics (IF 3.3) Pub Date : 2024-01-13 Khawla F N AbuAlia, Elena Damm, Kristian K Ullrich, Amisa Mukaj, Emil Parvanov, Jiri Forejt, Linda Odenthal-Hesse
PRDM9-mediated reproductive isolation was first described in the progeny of Mus musculus musculus (MUS) PWD/Ph and Mus musculus domesticus (DOM) C57BL/6J inbred strains. These male F1-hybrids fail to complete chromosome synapsis and arrest meiosis at prophase I, due to incompatibilities between the Prdm9 gene and hybrid sterility locus Hstx2. We identified fourteen alleles of Prdm9 in exon 12, encoding
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Dynein directs prophase centrosome migration to control the stem cell division axis in the developing C. elegans epidermis. Genetics (IF 3.3) Pub Date : 2024-01-12 Cátia Carvalho, Daniel J Barbosa, Ricardo Celestino, Esther Zanin, Ana Xavier Carvalho, Reto Gassmann
The microtubule motor dynein is critical for the assembly and positioning of mitotic spindles. In C. elegans, these dynein functions have been extensively studied in the early embryo but remain poorly explored in other developmental contexts. Here we use a hypomorphic dynein mutant to investigate the motor's contribution to asymmetric stem cell-like divisions in the larval epidermis. Live imaging of
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Transcribed enhancer sequences are required for maize p1 paramutation. Genetics (IF 3.3) Pub Date : 2024-1-4 Lyudmila V Sidorenko, Vicki L Chandler, Xiujuan Wang, Thomas Peterson
Paramutation is a transfer of heritable silencing states between interacting endogenous alleles or between endogenous alleles and homologous transgenes. Prior results demonstrated that paramutation occurs at the P1-rr (red pericarp and red cob) allele of the maize p1 (pericarp color 1) gene when exposed to a transgene containing a 1.2-kb enhancer fragment (P1.2) of P1-rr. The paramutable P1-rr allele
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Centromere-Proximal Suppression of Meiotic Crossovers in Drosophila is Robust to Changes in Centromere Number, Repetitive DNA Content, and Centromere-Clustering. Genetics (IF 3.3) Pub Date : 2023-12-27 Nila M Pazhayam, Leah K Frazier, Jeff Sekelsky
Accurate segregation of homologous chromosomes during meiosis depends on both the presence and regulated placement of crossovers (COs). The centromere effect, or CO exclusion in pericentromeric regions of the chromosome, is a meiotic CO patterning phenomenon that helps prevent nondisjunction (NDJ), thereby protecting against chromosomal disorders and other meiotic defects. Despite being identified
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The fitness consequences of genetic divergence between polymorphic gene arrangements. Genetics (IF 3.3) Pub Date : 2023-12-26 Brian Charlesworth
Inversions restrict recombination when heterozygous with standard arrangements, but often have few noticeable phenotypic effects. Nevertheless, there are several examples of inversions that can be maintained polymorphic by strong selection under laboratory conditions. A long-standing model for the source of such selection is divergence between arrangements with respect to recessive or partially recessive
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Dissecting the major genetic components underlying cotton lint development. Genetics (IF 3.3) Pub Date : 2023-12-26 Yali Sun, Yuman Yuan, Shoupu He, Warwick Stiller, Iain Wilson, Xiongming Du, Qian-Hao Zhu
Numerous genetic loci and several functionally characterised genes have been linked to determination of lint percentage (lint%), one of the most important cotton yield components, but we still know little about the major genetic components underlying lint%. Here, we first linked the genetic loci containing MYB25-like_At and HD1_At to the fibreless seed trait of SL1-7-1 and found that MYB25-like_At
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Complex epistatic interactions between ELF3, PRR9, and PRR7 regulates the circadian clock and plant physiology. Genetics (IF 3.3) Pub Date : 2023-12-24 Li Yuan, Paula Avello, Zihao Zhu, Sarah C L Lock, Kayla McCarthy, Ethan J Redmond, Amanda M Davis, Yang Song, Daphne Ezer, Jonathan W Pitchford, Marcel Quint, Qiguang Xie, Xiaodong Xu, Seth J Davis, James Ronald
Circadian clocks are endogenous timekeeping mechanisms that coordinate internal physiological responses with the external environment. EARLY FLOWERING3 (ELF3), PSEUDO RESPONSE REGULATOR (PRR9), and PRR7 are essential components of the plant circadian clock and facilitate entrainment of the clock to internal and external stimuli. Previous studies have highlighted a critical role for ELF3 in repressing
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Bone morphogenetic protein signaling: the pathway and its regulation. Genetics (IF 3.3) Pub Date : 2023-12-20 Takuya Akiyama, Laurel A Raftery, Kristi A Wharton
In the mid-1960s, bone morphogenetic proteins (BMPs) were first identified in the extracts of bone to have the remarkable ability to induce heterotopic bone. When the Drosophila gene decapentaplegic (dpp) was first identified to share sequence similarity with mammalian BMP2/BMP4 in the late-1980s, it became clear that secreted BMP ligands can mediate processes other than bone formation. Following this
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Recombination hotspots in Neurospora crassa controlled by idiomorphic sequences and meiotic silencing. Genetics (IF 3.3) Pub Date : 2023-12-20 P Jane Yeadon, Frederick J Bowring, David E A Catcheside
Genes regulating recombination in specific chromosomal intervals of Neurospora crassa were described in the 1960s but the mechanism is still unknown. For each of the rec-1, rec-2 and rec-3 genes, a single copy of the putative dominant allele, for example rec-2SL found in St Lawrence OR74 A wild type, reduces recombination in chromosomal regions specific to that gene. However, when we sequenced the
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Heterozygosity alters Msh5 binding to meiotic chromosomes in the baker's yeast. Genetics (IF 3.3) Pub Date : 2023-12-20 Suman Dash, Sameer Joshi, Ajith V Pankajam, Akira Shinohara, Koodali T Nishant
Meiotic crossovers are initiated from programmed DNA Double Strand Breaks (DSBs). The Msh4-Msh5 heterodimer is an evolutionarily conserved mismatch repair related protein complex that promotes meiotic crossovers by stabilizing strand invasion intermediates and joint molecule structures such as Holliday junctions. In vivo studies using homozygous strains of the baker's yeast Saccharomyces cerevisiae
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A pair of RNA binding proteins inhibit ion transporter expression to maintain lifespan. Genetics (IF 3.3) Pub Date : 2023-12-19 Rebekah Napier-Jameson, Olivia Marx, Adam Norris
Regulation of lifespan by transcription factors has been well established. More recently a role for RNA binding proteins (RBPs) in regulating lifespan has also emerged. In both cases, a major challenge is to determine which regulatory targets are functionally responsible for the observed lifespan phenotype. We recently identified a pair of neuronal RBPs, exc-7/ELAVL and mbl-1/Muscleblind, which in
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Using encrypted genotypes and phenotypes for collaborative genomic analyses to maintain data confidentiality. Genetics (IF 3.3) Pub Date : 2023-12-12 Tianjing Zhao, Fangyi Wang, Richard Mott, Jack Dekkers, Hao Cheng
To adhere to and capitalize on the benefits of the FAIR (Findable, Accessible, Interoperable and Reusable) principles in agricultural genome-to-phenome studies, it is crucial to address privacy and intellectual property issues that prevent sharing and reuse of data in research and industry. Direct sharing of genotype and phenotype data is often prohibited due to intellectual property and privacy concerns
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Molecular identification of a peroxidase gene controlling body size in the entomopathogenic nematode Steinernema hermaphroditum. Genetics (IF 3.3) Pub Date : 2023-12-11 Hillel T Schwartz, Chieh-Hsiang Tan, Jackeline Peraza, Krystal Louise T Raymundo, Paul W Sternberg
The entomopathogenic nematode Steinernema hermaphroditum was recently rediscovered and is being developed as a genetically tractable experimental system for the study of previously unexplored biology, including parasitism of its insect hosts and mutualism with its bacterial endosymbiont Xenorhabdus griffiniae. Through whole-genome re-sequencing and genetic mapping we have for the first time molecularly
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Bradysia (Sciara) coprophila larvae up-regulate DNA repair pathways and down-regulate developmental regulators in response to ionizing radiation. Genetics (IF 3.3) Pub Date : 2023-12-08 John M Urban, Jack R Bateman, Kodie R Garza, Julia Borden, Jaison Jain, Alexia Brown, Bethany J Thach, Jacob E Bliss, Susan A Gerbi
The level of resistance to radiation and the developmental and molecular responses can vary between species, and even between developmental stages of one species. For flies (Order: Diptera), prior studies concluded that the fungus gnat Bradysia (Sciara) coprophila (sub-order: Nematocera) is more resistant to irradiation-induced mutations that cause visible phenotypes than the fruit fly Drosophila melanogaster
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A cosmopolitan inversion facilitates seasonal adaptation in overwintering Drosophila. Genetics (IF 3.3) Pub Date : 2023-12-05 Joaquin C B Nunez, Benedict A Lenhart, Alyssa Bangerter, Connor S Murray, Giovanni R Mazzeo, Yang Yu, Taylor L Nystrom, Courtney Tern, Priscilla A Erickson, Alan O Bergland
Fluctuations in the strength and direction of natural selection through time are a ubiquitous feature of life on Earth. One evolutionary outcome of such fluctuations is adaptive tracking, wherein populations rapidly adapt from standing genetic variation. In certain circumstances, adaptive tracking can lead to the long-term maintenance of functional polymorphism despite allele frequency change due to
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rvTWAS: identifying gene-trait association using sequences by utilizing transcriptome-directed feature selection. Genetics (IF 3.3) Pub Date : 2023-11-24 Jingni He, Qing Li, Qingrun Zhang
Towards the identification of genetic basis of complex traits, transcriptome-wide association study (TWAS) is successful in integrating transcriptome data. However, TWAS is only applicable for common variants, excluding rare variants in exome or whole genome sequences. This is partly because of the inherent limitation of TWAS protocols that rely on predicting gene expressions. Our previous research
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Finishing the egg. Genetics (IF 3.3) Pub Date : 2023-11-24 Celeste Berg, Matthew Sieber, Jianjun Sun
Gamete development is a fundamental process that is highly conserved from early eukaryotes to mammals. As germ cells develop, they must coordinate a dynamic series of cellular processes that support growth, cell specification, patterning, the loading of maternal factors (RNAs, proteins, and nutrients), differentiation of structures to enable fertilization and ensure embryonic survival, and other processes
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rec-1 loss of function increases recombination in the central gene clusters at the expense of autosomal pairing centers. Genetics (IF 3.3) Pub Date : 2023-11-24 Tom Parée, Luke Noble, João Ferreira Gonçalves, Henrique Teotónio
Meiotic control of crossover (CO) number and position is critical for homologous chromosome segregation and organismal fertility, recombination of parental genotypes, and the generation of novel genetic combinations. We here characterize the recombination rate landscape of a rec-1 loss of function modifier of CO position in Caenorhabditis elegans, one of the first ever modifiers discovered. By averaging
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Comparison of transcriptome-wide N6-methyladenosine profiles from healthy trio families reveals regulator-mediated methylation alterations. Genetics (IF 3.3) Pub Date : 2023-11-24 Yini Li, Hang Liu, Chuan He, Lijia Ma
The N6-methyladenosine (m6A) modification is a highly conserved RNA modification found in eukaryotic messenger RNAs (mRNAs). It plays a vital role in regulating various biological processes. Dysregulation of m6A modifications has been linked to a range of complex genetic diseases in humans. However, there has been a lack of comprehensive characterization and comparison of m6A modifications at the transcriptome-wide
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Lipophorin Receptors Genetically Modulate Neurodegeneration Caused by Reduction of Psn Expression in the Aging Drosophila Brain. Genetics (IF 3.3) Pub Date : 2023-11-23 Jongkyun Kang, Chen Zhang, Yuhao Wang, Jian Feng, Bonnie Berger, Norbert Perrimon, Jie Shen
Mutations in the Presenilin (PSEN) genes are the most common cause of early-onset familial Alzheimer's disease (FAD). Studies in cell culture, in vitro biochemical systems, and knockin mice showed that PSEN mutations are loss-of-function mutations, impairing γ-secretase activity. Mouse genetic analysis highlighted the importance of Presenilin (PS) in learning and memory, synaptic plasticity and neurotransmitter
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Fourth Chromosome Resource Project: a comprehensive resource for genetic analysis in Drosophila that includes humanized stocks. Genetics (IF 3.3) Pub Date : 2023-11-20 Michael J Stinchfield,Brandon P Weasner,Bonnie M Weasner,David Zhitomersky,Justin P Kumar,Michael B O'Connor,Stuart J Newfeld
The 4th chromosome is the final frontier for genetic analysis in Drosophila. Small, heterochromatic and devoid of recombination the 4th has long been ignored. Nevertheless, its long arm contains 79 protein coding genes. The Fourth Chromosome Resource Project (FCRP) has a goal of facilitating the investigation of genes on this neglected chromosome. The project has 446 stocks publicly available at the
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Genetic models of fibrillinopathies. Genetics (IF 3.3) Pub Date : 2023-11-16 Kim M Summers
The fibrillinopathies represent a group of diseases in which the 10-12 nm extracellular microfibrils are disrupted by genetic variants in one of the genes encoding fibrillin molecules, large glycoproteins of the extracellular matrix. The best-known fibrillinopathy is Marfan syndrome, an autosomal dominant condition affecting the cardiovascular, ocular, skeletal, and other systems, with a prevalence
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Mutations in yeast Pcf11, a conserved protein essential for mRNA 3' end processing and transcription termination, elicit the Environmental Stress Response. Genetics (IF 3.3) Pub Date : 2023-11-15 Joel H Graber,Derick Hoskinson,Huiyun Liu,Katarzyna Kaczmarek Michaels,Peter S Benson,Nathaniel J Maki,Christian L Wilson,Caleb McGrath,Franco Puleo,Erika Pearson,Jason N Kuehner,Claire Moore
The Pcf11 protein is an essential subunit of the large complex that cleaves and polyadenylates eukaryotic mRNA precursor. It has also been functionally linked to gene-looping, termination of RNA Polymerase II (Pol II) transcripts, and mRNA export. We have examined a poorly characterized but conserved domain (amino acids 142-225) of the Saccharomyces cerevisiae Pcf11 and found that while it is not needed
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Germline mitotic quiescence and cell death are induced in Caenorhabditis elegans by exposure to pathogenic Pseudomonas aeruginosa. Genetics (IF 3.3) Pub Date : 2023-11-13 Daniel P Bollen,Kirthi C Reddy,Laura I Lascarez-Lagunas,Dennis H Kim,Monica P Colaiácovo
The impact of exposure to microbial pathogens on animal reproductive capacity and germline physiology is not well understood. The nematode Caenorhabditis elegans is a bacterivore that encounters pathogenic microbes in its natural environment. How pathogenic bacteria affect host reproductive capacity of C. elegans is not well understood. Here, we show that exposure of C. elegans hermaphrodites to the
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A role for β-1,6- and β-1,3-Glucans in Kinetochore Function in Saccharomyces cerevisiae. Genetics (IF 3.3) Pub Date : 2023-11-10 Rucha Kshirsagar, Arno Munhoven, Tra My Tran Nguyen, Ann E Ehrenhofer-Murray
Chromosome segregation is crucial for the faithful inheritance of DNA to the daughter cells after DNA replication. For this, the kinetochore, a megadalton protein complex, assembles on centromeric chromatin containing the histone H3 variant CENP-A and provides a physical connection to the microtubules. Here, we report an unanticipated role for enzymes required for β-1,6- and β-1,3 glucan biosynthesis
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The SWI/SNF nucleosome remodeler constrains enhancer activity during Drosophila wing development. Genetics (IF 3.3) Pub Date : 2023-11-09 Matthew J Niederhuber, Mary Leatham-Jensen, Daniel J McKay
Chromatin remodeling is central to the dynamic changes in gene expression that drive cell fate determination. During development, the sets of enhancers that are accessible for use change globally as cells transition between stages. While transcription factors and nucleosome remodelers are known to work together to control enhancer accessibility, it is unclear how the short stretches of DNA that they
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Crossover shortage in potato is caused by StMSH4 mutant alleles and leads to either highly uniform unreduced pollen or sterility. Genetics (IF 3.3) Pub Date : 2023-11-07 Corentin R Clot, Dennis Klein, Joey Koopman, Cees Schuit, Christel J M Engelen, Ronald C B Hutten, Matthijs Brouwer, Richard G F Visser, Martina Juranić, Herman J van Eck
The balanced segregation of homologous chromosomes during meiosis is essential for fertility and is mediated by crossovers. A strong reduction of crossover (CO) number leads to the unpairing of homologous chromosomes after the withdrawal of the synaptonemal complex. This results in the random segregation of univalents during meiosis I and ultimately to the production of unbalanced and sterile gametes
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Finding information about uncharacterized Drosophila melanogaster genes. Genetics (IF 3.3) Pub Date : 2023-11-02 Stephanie E Mohr,Ah-Ram Kim,Yanhui Hu,Norbert Perrimon
Genes that have been identified in the genome but remain uncharacterized with regards to function offer an opportunity to uncover novel biological information. Novelty is exciting but can also be a barrier. If nothing is known, how does one start planning and executing experiments? Here, we provide a recommended information-mining workflow and a corresponding guide to accessing information about uncharacterized
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Centromere structure and function: lessons from Drosophila. Genetics (IF 3.3) Pub Date : 2023-11-01 Eftychia Kyriacou,Patrick Heun
The fruit fly Drosophila melanogaster serves as a powerful model organism for advancing our understanding of biological processes, not just by studying its similarities with other organisms including ourselves but also by investigating its differences to unravel the underlying strategies that evolved to achieve a common goal. This is particularly true for centromeres, specialized genomic regions present
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Hedgehog signaling guides migration of primordial germ cells to the Drosophila somatic gonad. Genetics (IF 3.3) Pub Date : 2023-11-01 Girish Deshpande,Chris Ng,Nicholas Jourjine,Joy Wan Chiew,Juliana Dasilva,Paul Schedl
In addition to inducing nonautonomous specification of cell fate in both Drosophila and vertebrates, the Hedgehog pathway guides cell migration in a variety of different tissues. Although its role in axon guidance in the vertebrate nervous system is widely recognized, its role in guiding the migratory path of primordial germ cells (PGCs) from the outside surface of the Drosophila embryo through the
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E2F1, DIAP1, and the presence of a homologous chromosome promote while JNK inhibits radiation-induced Loss of Heterozygosity in Drosophila melanogaster. Genetics (IF 3.3) Pub Date : 2023-10-24 Jeremy Brown,Tin Tin Su
Loss of Heterozygosity (LOH) can occur when a heterozygous mutant cell loses the remaining wild type allele to become a homozygous mutant. LOH can have physiological consequences if, for example, the affected gene encodes a tumor suppressor. We used fluorescent reporters to study mechanisms of LOH induction by X-rays, a type of ionizing radiation (IR), in Drosophila melanogaster larval wing discs.
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Diversification of small RNA pathways underlies germline RNAi incompetence in wild C. elegans strains. Genetics (IF 3.3) Pub Date : 2023-10-22 Han Ting Chou, Francisco Valencia, Jacqueline C Alexander, Avery Davis Bell, Diptodip Deb, Daniel A Pollard, Annalise B Paaby
The discovery that experimental delivery of dsRNA can induce gene silencing at target genes revolutionized genetics research, by both uncovering essential biological processes and creating new tools for developmental geneticists. However, the efficacy of exogenous RNAi varies dramatically within the C. elegans natural population, raising questions about our understanding of RNAi in the lab relative