MutantHuntWGS: A Pipeline for Identifying Saccharomyces cerevisiae Mutations
MutantHuntWGS is a user-friendly pipeline for analyzing Saccharomyces cerevisiae whole-genome sequencing data. It uses available open-source programs to: (1) perform sequence alignments for paired and single-end reads, (2) call variants, and (3) predict variant effect and severity. MutantHuntWGS outputs a shortlist of variants while also enabling access to all intermediate files. To demonstrate its utility, we use MutantHuntWGS to assess multiple published datasets; in all cases, it detects the same causal variants reported in the literature. To encourage broad adoption and promote reproducibility, we distribute a containe...
Source: G3: Genes Genomes Genetics - September 1, 2020 Category: Genetics & Stem Cells Authors: Ellison, M. A., Walker, J. L., Ropp, P. J., Durrant, J. D., Arndt, K. M. Tags: Software and Data Resources Source Type: research
Genome-Wide Screen for Context-Dependent Tumor Suppressors Identified Using in Vivo Models for Neoplasia in Drosophila
Genetic approaches in Drosophila have successfully identified many genes involved in regulation of growth control as well as genetic interactions relevant to the initiation and progression of cancer in vivo. Here, we report on large-scale RNAi-based screens to identify potential tumor suppressor genes that interact with known cancer-drivers: the Epidermal Growth Factor Receptor and the Hippo pathway transcriptional cofactor Yorkie. These screens were designed to identify genes whose depletion drove tissue expressing EGFR or Yki from a state of benign overgrowth into neoplastic transformation in vivo. We also report on an i...
Source: G3: Genes Genomes Genetics - September 1, 2020 Category: Genetics & Stem Cells Authors: Groth, C., Vaid, P., Khatpe, A., Prashali, N., Ahiya, A., Andrejeva, D., Chakladar, M., Nagarkar, S., Paul, R., Kelkar, D., Eichenlaub, T., Herranz, H., Sridhar, T., Cohen, S. M., Shashidhara, L. Tags: Mutant Screen Report Source Type: research
Identification of New Regulators of the Oocyte-to-Embryo Transition in Drosophila
At the oocyte-to-embryo transition the highly differentiated oocyte arrested in meiosis becomes a totipotent embryo capable of embryogenesis. Oocyte maturation (release of the prophase I primary arrest) and egg activation (release from the secondary meiotic arrest and the trigger for the oocyte-to-embryo transition) serve as prerequisites for this transition, both events being controlled posttranscriptionally. Recently, we obtained a comprehensive list of proteins whose levels are developmentally regulated during these events via a high-throughput quantitative proteomic analysis of Drosophila melanogaster oocyte maturation...
Source: G3: Genes Genomes Genetics - September 1, 2020 Category: Genetics & Stem Cells Authors: Aviles-Pagan, E. E., Kang, A. S. W., Orr-Weaver, T. L. Tags: Mutant Screen Report Source Type: research
Genome-Wide Dynamic Evaluation of the UV-Induced DNA Damage Response
Genetic screens in Saccharomyces cerevisiae have allowed for the identification of many genes as sensors or effectors of DNA damage, typically by comparing the fitness of genetic mutants in the presence or absence of DNA-damaging treatments. However, these static screens overlook the dynamic nature of DNA damage response pathways, missing time-dependent or transient effects. Here, we examine gene dependencies in the dynamic response to ultraviolet radiation-induced DNA damage by integrating ultra-high-density arrays of 6144 diploid gene deletion mutants with high-frequency time-lapse imaging. We identify 494 ultraviolet ra...
Source: G3: Genes Genomes Genetics - September 1, 2020 Category: Genetics & Stem Cells Authors: Silva, E., Michaca, M., Munson, B., Bean, G. J., Jaeger, P. A., Licon, K., Winzeler, E. A., Ideker, T. Tags: Mutant Screen Report Source Type: research
The Complete Genome Sequence of the Staphylococcus Bacteriophage Metroid
Phages infecting bacteria of the genus Staphylococcus play an important role in their host’s ecology and evolution. On one hand, horizontal gene transfer from phage can encourage the rapid adaptation of pathogenic Staphylococcus enabling them to escape host immunity or access novel environments. On the other hand, lytic phages are promising agents for the treatment of bacterial infections, especially those resistant to antibiotics. As part of an ongoing effort to gain novel insights into bacteriophage diversity, we characterized the complete genome of the Staphylococcus bacteriophage Metroid, a cluster C phage with a...
Source: G3: Genes Genomes Genetics - September 1, 2020 Category: Genetics & Stem Cells Authors: Crane, A., Abaidoo, J., Beltran, G., Fry, D., Furey, C., Green, N., Johal, R., La Rosa, B., Jimenez, C. L., Luong, L., Maag, G., Porche, J., Reyes, L., Robinson, A., Sabbara, S., Herrera, L. S., Negrete, A. U., Wilson, P., Geiler-Samerotte, K., Pfeifer, S Tags: Genome Report Source Type: research
Improved Reference Genome for Cyclotella cryptica CCMP332, a Model for Cell Wall Morphogenesis, Salinity Adaptation, and Lipid Production in Diatoms (Bacillariophyta)
The diatom, Cyclotella cryptica, is a well-established model species for physiological studies and biotechnology applications of diatoms. To further facilitate its use as a model diatom, we report an improved reference genome assembly and annotation for C. cryptica strain CCMP332. We used a combination of long- and short-read sequencing to assemble a high-quality and contaminant-free genome. The genome is 171 Mb in size and consists of 662 scaffolds with a scaffold N50 of 494 kb. This represents a 176-fold decrease in scaffold number and 41-fold increase in scaffold N50 compared to the previous assembly. The genome contain...
Source: G3: Genes Genomes Genetics - September 1, 2020 Category: Genetics & Stem Cells Authors: Roberts, W. R., Downey, K. M., Ruck, E. C., Traller, J. C., Alverson, A. J. Tags: Genome Report Source Type: research
NetExtractor: Extracting a Cerebellar Tissue Gene Regulatory Network Using Differentially Expressed High Mutual Information Binary RNA Profiles
In this report, we address these problems via our NetExtractor algorithm. NetExtractor examines all pairwise gene expression profiles first with Gaussian mixture models (GMMs) to identify sample sub-populations followed by mutual information (MI) analysis that is capable of detecting non-linear differential bigenic expression relationships. We applied NetExtractor to brain tissue RNA profiles from the Genotype-Tissue Expression (GTEx) project to obtain a brain tissue specific gene expression relationship network centered on cerebellar and cerebellar hemisphere enriched edges. We leveraged the PsychENCODE pre-frontal cortex...
Source: G3: Genes Genomes Genetics - September 1, 2020 Category: Genetics & Stem Cells Authors: Husain, B., Hickman, A. R., Hang, Y., Shealy, B. T., Sapra, K., Feltus, F. A. Tags: Genome Report Source Type: research
The Genome Sequence of the Octocoral Paramuricea clavata - A Key Resource To Study the Impact of Climate Change in the Mediterranean
The octocoral, Paramuricea clavata, is a habitat-forming anthozoan with a key ecological role in rocky benthic and biodiversity-rich communities in the Mediterranean and Eastern Atlantic. Shallow populations of P. clavata in the North-Western Mediterranean are severely affected by warming-induced mass mortality events (MMEs). These MMEs have differentially impacted individuals and populations of P. clavata (i.e., varied levels of tissue necrosis and mortality rates) over thousands of kilometers of coastal areas. The eco-evolutionary processes, including genetic factors, contributing to these differential responses remain t...
Source: G3: Genes Genomes Genetics - September 1, 2020 Category: Genetics & Stem Cells Authors: Ledoux, J.-B., Cruz, F., Gomez-Garrido, J., Antoni, R., Blanc, J., Gomez-Gras, D., Kipson, S., Lopez-Sendino, P., Antunes, A., Linares, C., Gut, M., Alioto, T., Garrabou, J. Tags: Genome Report Source Type: research
Completed Genomic Sequence of Bacillus thuringiensis HER1410 Reveals a Cry-Containing Chromosome, Two Megaplasmids, and an Integrative Plasmidial Prophage
Bacillus thuringiensis is the most used biopesticide in agriculture. Its entomopathogenic capacity stems from the possession of plasmid-borne insecticidal crystal genes (cry), traditionally used as discriminant taxonomic feature for that species. As such, crystal and plasmid identification are key to the characterization of this species. To date, about 600 B. thuringiensis genomes have been reported, but less than 5% have been completed, while the other draft genomes are incomplete, hindering full plasmid delineation. Here we present the complete genome of Bacillus thuringiensis HER1410, a strain closely related to B. thur...
Source: G3: Genes Genomes Genetics - September 1, 2020 Category: Genetics & Stem Cells Authors: Lechuga, A., Lood, C., Salas, M., van Noort, V., Lavigne, R., Redrejo-Rodriguez, M. Tags: Genome Report Source Type: research
Fully Phased Sequence of a Diploid Human Genome Determined de Novo from the DNA of a Single Individual
In recent years, improved sequencing technology and computational tools have made de novo genome assembly more accessible. Many approaches, however, generate either an unphased or only partially resolved representation of a diploid genome, in which polymorphisms are detected but not assigned to one or the other of the homologous chromosomes. Yet chromosomal phase information is invaluable for the understanding of phenotypic trait inheritance in the cases of compound heterozygosity, allele-specific expression or cis-acting variants. Here we use a combination of tools and sequencing technologies to generate a de novo diploid...
Source: G3: Genes Genomes Genetics - September 1, 2020 Category: Genetics & Stem Cells Authors: Soifer, l., Fong, N. L., Yi, N., Ireland, A. T., Lam, I., Sooknah, M., Paw, J. S., Peluso, P., Concepcion, G. T., Rank, D., Hastie, A. R., Jojic, V., Ruby, J. G., Botstein, D., Roy, M. A. Tags: Genome Report Source Type: research
A Nanopore Based Chromosome-Level Assembly Representing Atlantic Cod from the Celtic Sea
Currently available genome assemblies for Atlantic cod (Gadus morhua) have been constructed from fish belonging to the Northeast Arctic Cod (NEAC) population; a migratory population feeding in the Barents Sea. These assemblies have been crucial for the development of genetic markers which have been used to study population differentiation and adaptive evolution in Atlantic cod, pinpointing four discrete islands of genomic divergence located on linkage groups 1, 2, 7 and 12. In this paper, we present a high-quality reference genome from a male Atlantic cod representing a southern population inhabiting the Celtic sea. The ge...
Source: G3: Genes Genomes Genetics - September 1, 2020 Category: Genetics & Stem Cells Authors: Kirubakaran, T. G., Andersen, O., Moser, M., Arnyasi, M., McGinnity, P., Lien, S., Kent, M. Tags: Genome Report Source Type: research
Human-Genetic Ancestry Inference and False Positives in Forensic Familial Searching
In forensic familial search methods, a query DNA profile is tested against a database to determine if the query profile represents a close relative of a database entrant. One challenge for familial search is that the calculations may require specification of allele frequencies for the unknown population from which the query profile has originated. The choice of allele frequencies affects the rate at which non-relatives are erroneously classified as relatives, and allele-frequency misspecification can substantially inflate false positive rates compared to use of allele frequencies drawn from the same population as the query...
Source: G3: Genes Genomes Genetics - August 4, 2020 Category: Genetics & Stem Cells Authors: Fortier, A. L., Kim, J., Rosenberg, N. A. Tags: Investigations Source Type: research
Conservation and Divergence in Duplicated Fiber Coexpression Networks Accompanying Domestication of the Polyploid Gossypium hirsutum L
Gossypium hirsutum L. (Upland cotton) has an evolutionary history involving inter-genomic hybridization, polyploidization, and subsequent domestication. We analyzed the developmental dynamics of the cotton fiber transcriptome accompanying domestication using gene coexpression networks for both joint and homoeologous networks. Remarkably, most genes exhibited expression for at least one homoeolog, confirming previous reports of widespread gene usage in cotton fibers. Most coexpression modules comprising the joint network are preserved in each subgenomic network and are enriched for similar biological processes, showing a ge...
Source: G3: Genes Genomes Genetics - August 4, 2020 Category: Genetics & Stem Cells Authors: Gallagher, J. P., Grover, C. E., Hu, G., Jareczek, J. J., Wendel, J. F. Tags: Investigations Source Type: research
Comparative Genomic Analyses and a Novel Linkage Map for Cisco (Coregonus artedi) Provide Insights into Chromosomal Evolution and Rediploidization Across Salmonids
In this study, we generate a novel linkage map for cisco (Coregonus artedi), an economically and culturally important fish in North America and a member of the subfamily Coregoninae, which previously lacked a high-density haploid linkage map. We also conduct comparative genomic analyses to refine our understanding of chromosomal fusion/fission history across salmonids. To facilitate this comparative approach, we use the naming strategy of protokaryotype identifiers (PKs) to associate duplicated chromosomes to their putative ancestral state. The female linkage map for cisco contains 20,292 loci, 3,225 of which are likely wi...
Source: G3: Genes Genomes Genetics - August 4, 2020 Category: Genetics & Stem Cells Authors: Blumstein, D. M., Campbell, M. A., Hale, M. C., Sutherland, B. J. G., McKinney, G. J., Stott, W., Larson, W. A. Tags: Investigations Source Type: research
APP-Induced Patterned Neurodegeneration Is Exacerbated by APOE4 in Caenorhabditis elegans
Genetic and epidemiological studies have found that variations in the amyloid precursor protein (APP) and the apoliopoprotein E (APOE) genes represent major modifiers of the progressive neurodegeneration in Alzheimer’s disease (AD). An extra copy of or gain-of-function mutations in APP correlate with early onset AD. Compared to the other variants (APOE2 and APOE3), the 4 allele of APOE (APOE4) hastens and exacerbates early and late onset forms of AD. Convenient in vivo models to study how APP and APOE4 interact at the cellular and molecular level to influence neurodegeneration are lacking. Here, we show that the nema...
Source: G3: Genes Genomes Genetics - August 4, 2020 Category: Genetics & Stem Cells Authors: Sae-Lee, W., Scott, L. L., Brose, L., Encarnacion, A. J., Shi, T., Kore, P., Oyibo, L. O., Ye, C., Rozmiarek, S. K., Pierce, J. T. Tags: Investigations Source Type: research
