Gametic selection favours polyandry and selfing
by Michael Francis Scott, Carl Mackintosh, Simone Immler
Competition among pollen or sperm (gametic selection) can cause evolution. Mating systems shape the intensity of gametic selection by determining the competitors involved, which can in turn cause the mating system itself to evolve. We model the bidirectional relationship between gametic selection and mating systems, focusing on variation in female mating frequency (monandry-polyandry) and self-fertilisation (selfing-outcrossing). First, we find that monandry and selfing both reduce the efficiency of gametic selection in removing deleterious alleles. This means that ...
Source: PLoS Genetics - February 16, 2024 Category: Genetics & Stem Cells Authors: Michael Francis Scott Source Type: research
CryptoCEN: A Co-Expression Network for < i > Cryptococcus neoformans < /i > reveals novel proteins involved in DNA damage repair
by Matthew J. O ’Meara, Jackson R. Rapala, Connie B. Nichols, A. Christina Alexandre, R. Blake Billmyre, Jacob L Steenwyk, J. Andrew Alspaugh, Teresa R. O’Meara
Elucidating gene function is a major goal in biology, especially among non-model organisms. However, doing so is complicated by the fact that molecular conservation does not always mirror functional conservation, and that complex relationships among genes are responsible for encoding pathways and higher-order biological processes. Co-expression, a promising approach for predicting gene function, relies on the general principal that genes with similar expressio...
Source: PLoS Genetics - February 15, 2024 Category: Genetics & Stem Cells Authors: Matthew J. O ’Meara Source Type: research
< i > het-B < /i > allorecognition in < i > Podospora anserina < /i > is determined by pseudo-allelic interaction of genes encoding a HET and lectin fold domain protein and a PII-like protein
by Corinne Clav é, Sonia Dheur, Sandra Lorena Ament-Velásquez, Alexandra Granger-Farbos, Sven J. Saupe
Filamentous fungi display allorecognition genes that trigger regulated cell death (RCD) when strains of unlike genotype fuse.Podospora anserina is one of several model species for the study of this allorecognition process termed heterokaryon or vegetative incompatibility. Incompatibility restricts transmission of mycoviruses between isolates. InP.anserina, genetic analyses have identified nine incompatibility loci, termedhet loci. Here we set out to clone the genes controllinghet-B incompatibility.het-B displays two in...
Source: PLoS Genetics - February 12, 2024 Category: Genetics & Stem Cells Authors: Corinne Clav é Source Type: research
High germline mutation rates, but not extreme population outbreaks, influence genetic diversity in a keystone coral predator
by Iva Popovic, Lucie A. Bergeron, Yves-Marie Bozec, Ann-Marie Waldvogel, Samantha M. Howitt, Katarina Damjanovic, Frances Patel, Maria G. Cabrera, Gert W örheide, Sven Uthicke, Cynthia Riginos
Lewontin ’s paradox, the observation that levels of genetic diversity (π) do not scale linearly with census population size (Nc) variation, is an evolutionary conundrum. The most extreme mismatches between π andNc are found for highly abundant marine invertebrates. Yet, the influences of new mutations on π relative to extrinsic processes such asNc fluctuations are unknown. Here, we provide the first germline mutation rate (μ...
Source: PLoS Genetics - February 12, 2024 Category: Genetics & Stem Cells Authors: Iva Popovic Source Type: research
Nazo, the < i > Drosophila < /i > homolog of the NBIA-mutated protein –c19orf12, is required for triglyceride homeostasis
by Perinthottathil Sreejith, Sara Lolo, Kristen R. Patten, Maduka Gunasinghe, Neya More, Leo J. Pallanck, Rajnish Bharadwaj
Lipid dyshomeostasis has been implicated in a variety of diseases ranging from obesity to neurodegenerative disorders such as Neurodegeneration with Brain Iron Accumulation (NBIA). Here, we uncover the physiological role of Nazo, theDrosophila melanogaster homolog of the NBIA-mutated protein –c19orf12, whose function has been elusive. Ablation ofDrosophila c19orf12 homologs leads to dysregulation of multiple lipid metabolism genes.nazo mutants exhibit markedly reduced gut lipid droplet and whole-bo...
Source: PLoS Genetics - February 9, 2024 Category: Genetics & Stem Cells Authors: Perinthottathil Sreejith Source Type: research
Estimating the health impact of nicotine exposure by dissecting the effects of nicotine versus non-nicotine constituents of tobacco smoke: A multivariable Mendelian randomisation study
by Jasmine N. Khouja, Eleanor Sanderson, Robyn E. Wootton, Amy E. Taylor, Billy A. Church, Rebecca C. Richmond, Marcus R. Munaf ò
The detrimental health effects of smoking are well-known, but the impact of regular nicotine use without exposure to the other constituents of tobacco is less clear. Given the increasing daily use of alternative nicotine delivery systems, such as e-cigarettes, it is increasingly important to understand and separate the effects of nicotine use from the impact of tobacco smoke exposure. Using a multivariable Mendelian randomisation framework, we explored the direct effects of nicotine compared w...
Source: PLoS Genetics - February 9, 2024 Category: Genetics & Stem Cells Authors: Jasmine N. Khouja Source Type: research
TRAILS: Tree reconstruction of ancestry using incomplete lineage sorting
by Iker Rivas-Gonz ález, Mikkel H. Schierup, John Wakeley, Asger Hobolth
Genome-wide genealogies of multiple species carry detailed information about demographic and selection processes on individual branches of the phylogeny. Here, we introduce TRAILS, a hidden Markov model that accurately infers time-resolved population genetics parameters, such as ancestral effective population sizes and speciation times, for ancestral branches using a multi-species alignment of three species and an outgroup. TRAILS leverages the information contained in incomplete lineage sorting fragments by modelling genealogies along the genome as...
Source: PLoS Genetics - February 8, 2024 Category: Genetics & Stem Cells Authors: Iker Rivas-Gonz ález Source Type: research
Nonhomologous tails direct heteroduplex rejection and mismatch correction during single-strand annealing in < i > Saccharomyces cerevisiae < /i >
by Elena Sap ède, Neal Sugawara, Randall G. Tyers, Yuko Nakajima, Mosammat Faria Afreen, Jesselin Romero Escobar, James E. Haber
Single-strand annealing (SSA) is initiated when a double strand break (DSB) occurs between two flanking repeated sequences, resulting in a deletion that leaves a single copy of the repeat. We studied budding yeast strains carrying two 200-bpURA3 sequences separated by 2.6 kb of spacer DNA (phage lambda) in which a site-specific DSB can be created by HO or Cas9 endonucleases. Repeat-mediated deletion requires removal of long 3 ’-ended single-stranded tails (flaps) by Rad1-Rad10 with the assist...
Source: PLoS Genetics - February 5, 2024 Category: Genetics & Stem Cells Authors: Elena Sap ède Source Type: research
ZmARF1 positively regulates low phosphorus stress tolerance via modulating lateral root development in maize
In this study, we found that the transcription factorZmARF1 was associated with low inorganic phosphate (Pi) stress-related traits in maize. This superior root morphology and greater phosphate stress tolerance could be ascribed to the overexpression ofZmARF1. The knock out mutantzmarf1 had shorter primary roots, fewer root tip number, and lower root volume and surface area. Transcriptomic data indicate thatZmLBD1, a direct downstream target gene, is involved in lateral root development, which enhances phosphate starvation tolerance. A transcriptional activation assay revealed thatZmARF1 specifically binds to the GC-box mot...
Source: PLoS Genetics - February 5, 2024 Category: Genetics & Stem Cells Authors: Fengkai Wu Source Type: research
CRISPR screen for protein inclusion formation uncovers a role for SRRD in the regulation of intermediate filament dynamics and aggresome assembly
by Katelyn M. Sweeney, Sapanna Chantarawong, Edward M. Barbieri, Greg Cajka, Matthew Liu, Lynn Spruce, Hossein Fazelinia, Bede Portz, Katie Copley, Tomer Lapidot, Lauren Duhamel, Phoebe Greenwald, Naseeb Saida, Reut Shalgi, James Shorter, Ophir Shalem
The presence of large protein inclusions is a hallmark of neurodegeneration, and yet the precise molecular factors that contribute to their formation remain poorly understood. Screens using aggregation-prone proteins have commonly relied on downstream toxicity as a readout rather than the direct formation of aggregates. Here, we combined a genome-wide CRISPR knockout screen ...
Source: PLoS Genetics - February 5, 2024 Category: Genetics & Stem Cells Authors: Katelyn M. Sweeney Source Type: research
Endolysosomal trafficking controls yolk granule biogenesis in vitellogenic < i > Drosophila < /i > oocytes
by Yue Yu, Dongsheng Chen, Stephen M. Farmer, Shiyu Xu, Beatriz Rios, Amanda Solbach, Xin Ye, Lili Ye, Sheng Zhang
Endocytosis and endolysosomal trafficking are essential for almost all aspects of physiological functions of eukaryotic cells. As our understanding on these membrane trafficking events are mostly from studies in yeast and cultured mammalian cells, one challenge is to systematically evaluate the findings from these cell-based studies in multicellular organisms under physiological settings. One potentially valuablein vivo system to address this challenge is the vitellogenic oocyte inDrosophila, which undergoes ...
Source: PLoS Genetics - February 5, 2024 Category: Genetics & Stem Cells Authors: Yue Yu Source Type: research
Tissue-specific and < i > cis < /i > -regulatory changes underlie parallel, adaptive gene expression evolution in house mice
by Sylvia M. Durkin, Mallory A. Ballinger, Michael W. Nachman
Changes in gene regulation have long been appreciated as a driving force of adaptive evolution, however the relative contributions ofcis- andtrans-acting changes to gene regulation over short evolutionary timescales remain unclear. Instances of recent, parallel phenotypic evolution provide an opportunity to assess whether parallel patterns are seen at the level of gene expression, and to assess the relative contribution ofcis- andtrans- changes to gene regulation in the early stages of divergence. Here, we studied gene expression in liver and brown adipose tiss...
Source: PLoS Genetics - February 2, 2024 Category: Genetics & Stem Cells Authors: Sylvia M. Durkin Source Type: research
Transposon dynamics in the emerging oilseed crop < i > Thlaspi arvense < /i >
by Adri án Contreras-Garrido, Dario Galanti, Andrea Movilli, Claude Becker, Oliver Bossdorf, Hajk-Georg Drost, Detlef Weigel
Genome evolution is partly driven by the mobility of transposable elements (TEs) which often leads to deleterious effects, but their activity can also facilitate genetic novelty and catalyze local adaptation. We explored how the intraspecific diversity of TE polymorphisms might contribute to the broad geographic success and adaptive capacity of the emerging oil cropThlaspi arvense (field pennycress). We classified the TE inventory based on a high-quality genome assembly, estimated the age of retrot...
Source: PLoS Genetics - January 31, 2024 Category: Genetics & Stem Cells Authors: Adri án Contreras-Garrido Source Type: research
A connection between the ribosome and two < i > S < /i > . < i > pombe < /i > tRNA modification mutants subject to rapid tRNA decay
by Thareendra De Zoysa, Alayna C. Hauke, Nivedita R. Iyer, Erin Marcus, Sarah M. Ostrowski, Franziska Stegemann, Dmitri N. Ermolenko, Justin C. Fay, Eric M. Phizicky
tRNA modifications are crucial in all organisms to ensure tRNA folding and stability, and accurate translation. In both the yeastSaccharomyces cerevisiae and the evolutionarily distant yeastSchizosaccharomyces pombe, mutants lacking certain tRNA body modifications (outside the anticodon loop) are temperature sensitive due to rapid tRNA decay (RTD) of a subset of hypomodified tRNAs. Here we show that for each of twoS.pombe mutants subject to RTD, mutations in ...
Source: PLoS Genetics - January 31, 2024 Category: Genetics & Stem Cells Authors: Thareendra De Zoysa Source Type: research
Emergence and spread of the barley net blotch pathogen coincided with crop domestication and cultivation history
In this study, we have used 104P.teres f.teres genomes from four continents to explore the population structure and demographic history of the fungal pathogen. We showed thatP.teres f.teres is structured into populations that tend to be geographically restricted to different regions. Using Multiple Sequentially Markovian Coalescent and machine learning approaches we demonstrated that the demographic history of the pathogen correlates with the history of barley, highlighting the importance of human migration and trade in spreading the pathogen. Exploring signatures of natural selection, we identified several population-spec...
Source: PLoS Genetics - January 29, 2024 Category: Genetics & Stem Cells Authors: Demetris Taliadoros Source Type: research
