GWideCodeML: A Python Package for Testing Evolutionary Hypotheses at the Genome-Wide Level
One of the most widely used programs for detecting positive selection, at the molecular level, is the program codeml, which is implemented in the Phylogenetic Analysis by Maximum Likelihood (PAML) package. However, it has a limitation when it comes to genome-wide studies, as it runs on a gene-by-gene basis. Furthermore, the size of such studies will depend on the number of orthologous genes the genomes have income and these are often restricted to only account for instances where a one-to-one relationship is observed between the genomes. In this work, we present GWideCodeML, a Python package, which runs a genome-wide codem...
Source: G3: Genes Genomes Genetics - December 3, 2020 Category: Genetics & Stem Cells Authors: Macias, L. G., Barrio, E., Toft, C. Tags: Software and Data Resources Source Type: research
Comprehensive Synthetic Genetic Array Analysis of Alleles That Interact with Mutation of the Saccharomyces cerevisiae RecQ Helicases Hrq1 and Sgs1
Most eukaryotic genomes encode multiple RecQ family helicases, including five such enzymes in humans. For many years, the yeast Saccharomyces cerevisiae was considered unusual in that it only contained a single RecQ helicase, named Sgs1. However, it has recently been discovered that a second RecQ helicase, called Hrq1, resides in yeast. Both Hrq1 and Sgs1 are involved in genome integrity, functioning in processes such as DNA inter-strand crosslink repair, double-strand break repair, and telomere maintenance. However, it is unknown if these enzymes interact at a genetic, physical, or functional level as demonstrated for the...
Source: G3: Genes Genomes Genetics - December 3, 2020 Category: Genetics & Stem Cells Authors: Sanders, E., Nguyen, P. A., Rogers, C. M., Bochman, M. L. Tags: Mutant Screen Report Source Type: research
The Genetic and Physical Interactomes of the Saccharomyces cerevisiae Hrq1 Helicase
The human genome encodes five RecQ helicases (RECQL1, BLM, WRN, RECQL4, and RECQL5) that participate in various processes underpinning genomic stability. Of these enzymes, the disease-associated RECQL4 is comparatively understudied due to a variety of technical challenges. However, Saccharomyces cerevisiae encodes a functional homolog of RECQL4 called Hrq1, which is more amenable to experimentation and has recently been shown to be involved in DNA inter-strand crosslink (ICL) repair and telomere maintenance. To expand our understanding of Hrq1 and the RecQ4 subfamily of helicases in general, we took a multi-omics approach ...
Source: G3: Genes Genomes Genetics - December 3, 2020 Category: Genetics & Stem Cells Authors: Rogers, C. M., Sanders, E., Nguyen, P. A., Smith-Kinnaman, W., Mosley, A. L., Bochman, M. L. Tags: Mutant Screen Report Source Type: research
Chemical-Genetic Interactions with the Proline Analog L-Azetidine-2-Carboxylic Acid in Saccharomyces cerevisiae
Non-proteinogenic amino acids, such as the proline analog L-azetidine-2-carboxylic acid (AZC), are detrimental to cells because they are mis-incorporated into proteins and lead to proteotoxic stress. Our goal was to identify genes that show chemical-genetic interactions with AZC in Saccharomyces cerevisiae and thus also potentially define the pathways cells use to cope with amino acid mis-incorporation. Screening the yeast deletion and temperature sensitive collections, we found 72 alleles with negative chemical-genetic interactions with AZC treatment and 12 alleles that suppress AZC toxicity. Many of the genes with negati...
Source: G3: Genes Genomes Genetics - December 3, 2020 Category: Genetics & Stem Cells Authors: Berg, M. D., Zhu, Y., Isaacson, J., Genereaux, J., Loll-Krippleber, R., Brown, G. W., Brandl, C. J. Tags: Mutant Screen Report Source Type: research
A Genome-Wide RNAi Screen for Enhancers of a Germline Tumor Phenotype Caused by Elevated GLP-1/Notch Signaling in Caenorhabditis elegans
Stem cells are tightly controlled in vivo. Both the balance between self-renewal and differentiation and the rate of proliferation are often regulated by multiple factors. The Caenorhabditis elegans hermaphrodite germ line provides a simple and accessible system for studying stem cells in vivo. In this system, GLP-1/Notch activity prevents the differentiation of distal germ cells in response to ligand production from the nearby distal tip cell, thereby supporting a stem cell pool. However, a delay in germline development relative to somatic gonad development can cause a pool of undifferentiated germ cells to persist in res...
Source: G3: Genes Genomes Genetics - December 3, 2020 Category: Genetics & Stem Cells Authors: Dalfo, D., Ding, Y., Liang, Q., Fong, A., Cipriani, P. G., Piano, F., Zheng, J. C., Qin, Z., Hubbard, E. J. A. Tags: Mutant Screen Report Source Type: research
Genome Sequence of the Banana Aphid, Pentalonia nigronervosa Coquerel (Hemiptera: Aphididae) and Its Symbionts
The banana aphid, Pentalonia nigronervosa Coquerel (Hemiptera: Aphididae), is a major pest of cultivated bananas (Musa spp., order Zingiberales), primarily due to its role as a vector of Banana bunchy top virus (BBTV), the most severe viral disease of banana worldwide. Here, we generated a highly complete genome assembly of P. nigronervosa using a single PCR-free Illumina sequencing library. Using the same sequence data, we also generated complete genome assemblies of the P. nigronervosa symbiotic bacteria Buchnera aphidicola and Wolbachia. To improve our initial assembly of P. nigronervosa we developed a k-mer based dedup...
Source: G3: Genes Genomes Genetics - December 3, 2020 Category: Genetics & Stem Cells Authors: Mathers, T. C., Mugford, S. T., Hogenhout, S. A., Tripathi, L. Tags: GENOME REPORT Source Type: research
Draft Genome of the Common Snapping Turtle, Chelydra serpentina, a Model for Phenotypic Plasticity in Reptiles
Turtles are iconic reptiles that inhabit a range of ecosystems from oceans to deserts and climates from the tropics to northern temperate regions. Yet, we have little understanding of the genetic adaptations that allow turtles to survive and reproduce in such diverse environments. Common snapping turtles, Chelydra serpentina, are an ideal model species for studying adaptation to climate because they are widely distributed from tropical to northern temperate zones in North America. They are also easy to maintain and breed in captivity and produce large clutch sizes, which makes them amenable to quantitative genetic and mole...
Source: G3: Genes Genomes Genetics - December 3, 2020 Category: Genetics & Stem Cells Authors: Das, D., Singh, S. K., Bierstedt, J., Erickson, A., Galli, G. L. J., Crossley, D. A., Rhen, T. Tags: Genome Report Source Type: research
Neurogenetics: A Call for Papers
(Source: G3: Genes Genomes Genetics)
Source: G3: Genes Genomes Genetics - December 3, 2020 Category: Genetics & Stem Cells Tags: Call For Papers Source Type: research
Corrigendum
(Source: G3: Genes Genomes Genetics)
Source: G3: Genes Genomes Genetics - November 5, 2020 Category: Genetics & Stem Cells Tags: Corrigendum Source Type: research
CRISpy-Pop: A Web Tool for Designing CRISPR/Cas9-Driven Genetic Modifications in Diverse Populations
CRISPR/Cas9 is a powerful tool for editing genomes, but design decisions are generally made with respect to a single reference genome. With population genomic data becoming available for an increasing number of model organisms, researchers are interested in manipulating multiple strains and lines. CRISpy-pop is a web application that generates and filters guide RNA sequences for CRISPR/Cas9 genome editing for diverse yeast and bacterial strains. The current implementation designs and predicts the activity of guide RNAs against more than 1000 Saccharomyces cerevisiae genomes, including 167 strains frequently used in bioener...
Source: G3: Genes Genomes Genetics - November 5, 2020 Category: Genetics & Stem Cells Authors: Stoneman, H. R., Wrobel, R. L., Place, M., Graham, M., Krause, D. J., De Chiara, M., Liti, G., Schacherer, J., Landick, R., Gasch, A. P., Sato, T. K., Hittinger, C. T. Tags: Investigations Source Type: research
Identification and Characterization of Breakpoints and Mutations on Drosophila melanogaster Balancer Chromosomes
Balancers are rearranged chromosomes used in Drosophila melanogaster to maintain deleterious mutations in stable populations, preserve sets of linked genetic elements and construct complex experimental stocks. Here, we assess the phenotypes associated with breakpoint-induced mutations on commonly used third chromosome balancers and show remarkably few deleterious effects. We demonstrate that a breakpoint in p53 causes loss of radiation-induced apoptosis and a breakpoint in Fucosyltransferase A causes loss of fucosylation in nervous and intestinal tissue—the latter study providing new markers for intestinal cell ident...
Source: G3: Genes Genomes Genetics - November 5, 2020 Category: Genetics & Stem Cells Authors: Miller, D. E., Kahsai, L., Buddika, K., Dixon, M. J., Kim, B. Y., Calvi, B. R., Sokol, N. S., Hawley, R. S., Cook, K. R. Tags: Investigations Source Type: research
Identifying Key Genetic Regions for Cell Sheet Morphogenesis on Chromosome 2L Using a Drosophila Deficiency Screen in Dorsal Closure
Cell sheet morphogenesis is essential for metazoan development and homeostasis of animal form – it contributes to developmental milestones including gastrulation, neural tube closure, heart and palate formation and to tissue maintenance during wound healing. Dorsal closure, a well-characterized stage in Drosophila embryogenesis and a model for cell sheet morphogenesis, is a remarkably robust process during which coordination of conserved gene expression patterns and signaling cascades regulate the cellular shape changes and movements. New ‘dorsal closure genes’ continue to be discovered due to advances in...
Source: G3: Genes Genomes Genetics - November 5, 2020 Category: Genetics & Stem Cells Authors: Fogerson, S. M., Mortensen, R. D., Moore, R. P., Chiou, H. Y., Prabhu, N. K., Wei, A. H., Tsai, D., Jadi, O., Andoh-Baidoo, K., Crawford, J., Mudziviri, M., Kiehart, D. P. Tags: Investigations Source Type: research
Strain-Dependent Modifier Genes Determine Survival in Zfp423 Mice
Zfp423 encodes a transcriptional regulatory protein that interacts with canonical signaling and lineage pathways. Mutations in mouse Zfp423 or its human ortholog ZNF423 are associated with a range of developmental abnormalities reminiscent of ciliopathies, including cerebellar vermis hypoplasia and other midline brain defects. Null mice have reduced viability in most strain backgrounds. Here we show complete lethality on a C57BL/6J background, dominant rescue in backcrosses to any of 13 partner strains, with strain-dependent survival frequencies, and evidence for a BALB/c-derived survival modifier locus on chromosome 5. Su...
Source: G3: Genes Genomes Genetics - November 5, 2020 Category: Genetics & Stem Cells Authors: Alcaraz, W. A., Liu, Z., Valdes, P., Chen, E., Valdovino Gonzalez, A. G., Wade, S., Wong, C., Kim, E., Chen, H.-H. M., Ponn, A., Concepcion, D., Hamilton, B. A. Tags: Investigations Source Type: research
Genomic Prediction Informed by Biological Processes Expands Our Understanding of the Genetic Architecture Underlying Free Amino Acid Traits in Dry Arabidopsis Seeds
Plant growth, development, and nutritional quality depends upon amino acid homeostasis, especially in seeds. However, our understanding of the underlying genetics influencing amino acid content and composition remains limited, with only a few candidate genes and quantitative trait loci identified to date. Improved knowledge of the genetics and biological processes that determine amino acid levels will enable researchers to use this information for plant breeding and biological discovery. Toward this goal, we used genomic prediction to identify biological processes that are associated with, and therefore potentially influen...
Source: G3: Genes Genomes Genetics - November 5, 2020 Category: Genetics & Stem Cells Authors: Turner-Hissong, S. D., Bird, K. A., Lipka, A. E., King, E. G., Beissinger, T. M., Angelovici, R. Tags: Genomic Prediction Source Type: research
Network Analysis Prioritizes DEWAX and ICE1 as the Candidate Genes for Major eQTL Hotspots in Seed Germination of Arabidopsis thaliana
Seed germination is characterized by a constant change of gene expression across different time points. These changes are related to specific processes, which eventually determine the onset of seed germination. To get a better understanding on the regulation of gene expression during seed germination, we performed a quantitative trait locus mapping of gene expression (eQTL) at four important seed germination stages (primary dormant, after-ripened, six-hour after imbibition, and radicle protrusion stage) using Arabidopsis thaliana Bay x Sha recombinant inbred lines (RILs). The mapping displayed the distinctness of the eQTL ...
Source: G3: Genes Genomes Genetics - November 5, 2020 Category: Genetics & Stem Cells Authors: Hartanto, M., Joosen, R. V. L., Snoek, B. L., Willems, L. A. J., Sterken, M. G., de Ridder, D., Hilhorst, H. W. M., Ligterink, W., Nijveen, H. Tags: Investigations Source Type: research
