A Genetic Screen for Human Genes Suppressing FUS Induced Toxicity in Yeast
FUS is a nucleic acid binding protein that, when mutated, cause a subset of familial amyotrophic lateral sclerosis (ALS). Expression of FUS in yeast recapitulates several pathological features of the disease-causing mutant proteins, including nuclear to cytoplasmic translocation, formation of cytoplasmic inclusions, and cytotoxicity. Genetic screens using the yeast model of FUS have identified yeast genes and their corresponding human homologs suppressing FUS induced toxicity in yeast, neurons and animal models. To expand the search for human suppressor genes of FUS induced toxicity, we carried out a genome-scale genetic s...
Source: G3: Genes Genomes Genetics - May 31, 2020 Category: Genetics & Stem Cells Authors: Hayden, E., Chen, S., Chumley, A., Xia, C., Zhong, Q., Ju, S. Tags: Mutant Screen Report Source Type: research
The Rise of Fungi: A Report on the CIFAR Program Fungal Kingdom: Threats & Opportunities Inaugural Meeting
This report covers the research discussed during the meeting and the advancements made toward mitigating the devastating impact of fungi on plants, animals, and humans. (Source: G3: Genes Genomes Genetics)
Source: G3: Genes Genomes Genetics - May 31, 2020 Category: Genetics & Stem Cells Authors: Case, N. T., Heitman, J., Cowen, L. E. Tags: Meeting Report Source Type: research
A Highly Contiguous Genome for the Golden-Fronted Woodpecker (Melanerpes aurifrons) via Hybrid Oxford Nanopore and Short Read Assembly
Woodpeckers are found in nearly every part of the world and have been important for studies of biogeography, phylogeography, and macroecology. Woodpecker hybrid zones are often studied to understand the dynamics of introgression between bird species. Notably, woodpeckers are gaining attention for their enriched levels of transposable elements (TEs) relative to most other birds. This enrichment of TEs may have substantial effects on molecular evolution. However, comparative studies of woodpecker genomes are hindered by the fact that no high-contiguity genome exists for any woodpecker species. Using hybrid assembly methods c...
Source: G3: Genes Genomes Genetics - May 31, 2020 Category: Genetics & Stem Cells Authors: Wiley, G., Miller, M. J. Tags: Genome Report Source Type: research
A Genome Assembly of the Barley 'Transformation Reference Cultivar Golden Promise
Barley (Hordeum vulgare) is one of the most important crops worldwide and is also considered a research model for the large-genome small grain temperate cereals. Despite genomic resources improving all the time, they are limited for the cv. Golden Promise, the most efficient genotype for genetic transformation. We have developed a barley cv. Golden Promise reference assembly integrating Illumina paired-end reads, long mate-pair reads, Dovetail Chicago in vitro proximity ligation libraries and chromosome conformation capture sequencing (Hi-C) libraries into a contiguous reference assembly. The assembled genome of 7 chromoso...
Source: G3: Genes Genomes Genetics - May 31, 2020 Category: Genetics & Stem Cells Authors: Schreiber, M., Mascher, M., Wright, J., Padmarasu, S., Himmelbach, A., Heavens, D., Milne, L., Clavijo, B. J., Stein, N., Waugh, R. Tags: Genome Report Source Type: research
Genome Sequence of the Human Opportunistic Fungus Arthrocladium fulminans (CBS 136243)
The black yeast-like fungus Arthrocladium fulminans is known from strains that cause severe and eventually fatal disseminated infections in immunocompromised patients. Given the dramatic outcome of this clinical case, it is essential to understand the virulence potential of this species. The fungus is a member of the family Trichomeriaceae, at some phylogenetic distance from the Herpotrichiellaceae where most infectious fungi in the order Chaetothyriales are located. Main ecological preferences among Trichomeriaceae include colonization of exposed inert surfaces. Currently, black yeasts genomes that are available in public...
Source: G3: Genes Genomes Genetics - May 31, 2020 Category: Genetics & Stem Cells Authors: Moreno, L. F., Menezes da Silva, N., Weiss, V. A., de Fatima Costa, F., Bittencourt, J. V., Macedo, L. M., Gomes, R. R., Souza, E. M., Vicente, V. A., Stielow, B., de Hoog, S. Tags: Genome Report Source Type: research
Identifying Small Molecules That Promote Quasipalindrome-Associated Template-Switch Mutations in Escherichia coli
DNA can assemble into non-B form structures that stall replication and cause genomic instability. One such secondary structure results from an inverted DNA repeat that can assemble into hairpin and cruciform structures during DNA replication. Quasipalindromes (QP), imperfect inverted repeats, are sites of mutational hotspots. Quasipalindrome-associated mutations (QPMs) occur through a template-switch mechanism in which the replicative polymerase stalls at a QP site and uses the nascent strand as a template instead of the correct template strand. This mutational event causes the QP to become a perfect or more perfect invert...
Source: G3: Genes Genomes Genetics - May 3, 2020 Category: Genetics & Stem Cells Authors: Klaric, J. A., Perr, E. L., Lovett, S. T. Tags: Investigations Source Type: research
MYCs and PIFs Act Independently in Arabidopsis Growth Regulation
Plants have a variety of strategies to avoid canopy shade and compete with their neighbors for light, collectively called the shade avoidance syndrome (SAS). Plants also have extensive systems to defend themselves against pathogens and herbivores. Defense and shade avoidance are two fundamental components of plant survival and productivity, and there are often tradeoffs between growth and defense. Recently, MYC2, a major positive regulator of defense, was reported to inhibit elongation during shade avoidance. Here, we further investigate the role of MYC2 and the related MYC3 and MYC4 in shade avoidance, and we examine the ...
Source: G3: Genes Genomes Genetics - May 3, 2020 Category: Genetics & Stem Cells Authors: Li, C., Nozue, K., Maloof, J. N. Tags: Investigations Source Type: research
Dissecting Adaptive Traits with Nested Association Mapping: Genetic Architecture of Inflorescence Morphology in Sorghum
In the cereal crop sorghum (Sorghum bicolor) inflorescence morphology variation underlies yield variation and confers adaptation across precipitation gradients, but its genetic basis is poorly understood. We characterized the genetic architecture of sorghum inflorescence morphology using a global nested association mapping (NAM) population (2200 recombinant inbred lines) and 198,000 phenotypic observations from multi-environment trials for four inflorescence morphology traits (upper branch length, lower branch length, rachis length, and rachis diameter). Trait correlations suggest that lower and upper branch length are und...
Source: G3: Genes Genomes Genetics - May 3, 2020 Category: Genetics & Stem Cells Authors: Olatoye, M. O., Marla, S. R., Hu, Z., Bouchet, S., Perumal, R., Morris, G. P. Tags: Multiparental Populations Source Type: research
Evaluation of STAR and Kallisto on Single Cell RNA-Seq Data Alignment
Alignment of scRNA-Seq data are the first and one of the most critical steps of the scRNA-Seq analysis workflow, and thus the choice of proper aligners is of paramount importance. Recently, STAR an alignment method and Kallisto a pseudoalignment method have both gained a vast amount of popularity in the single cell sequencing field. However, an unbiased third-party comparison of these two methods in scRNA-Seq is lacking. Here we conduct a systematic comparison of them on a variety of Drop-seq, Fluidigm and 10x genomics data, from the aspects of gene abundance, alignment accuracy, as well as computational speed and memory u...
Source: G3: Genes Genomes Genetics - May 3, 2020 Category: Genetics & Stem Cells Authors: Du, Y., Huang, Q., Arisdakessian, C., Garmire, L. X. Tags: Investigations Source Type: research
Comparative Cytology of Female Meiosis I Among Drosophila Species
The physical connections established by recombination are normally sufficient to ensure proper chromosome segregation during female Meiosis I. However, nonexchange chromosomes (such as the Muller F element or "dot" chromosome in D. melanogaster) can still segregate accurately because they remain connected by heterochromatic tethers. A recent study examined female meiosis in the closely related species D. melanogaster and D. simulans, and found a nearly twofold difference in the mean distance the obligately nonexchange dot chromosomes were separated during Prometaphase. That study proposed two speculative hypotheses for thi...
Source: G3: Genes Genomes Genetics - May 3, 2020 Category: Genetics & Stem Cells Authors: Majekodunmi, A., Bowen, A. O., Gilliland, W. D. Tags: Investigations Source Type: research
Genes Encoding Recognition of the Cladosporium fulvum Effector Protein Ecp5 Are Encoded at Several Loci in the Tomato Genome
The molecular interactions between tomato and Cladosporium fulvum have been an important model for molecular plant pathology. Complex genetic loci on tomato chromosomes 1 and 6 harbor genes for resistance to Cladosporium fulvum, encoding receptor like-proteins that perceive distinct Cladosporium fulvum effectors and trigger plant defenses. Here, we report classical mapping strategies for loci in tomato accessions that respond to Cladosporium fulvum effector Ecp5, which is very sequence-monomorphic. We screened 139 wild tomato accessions for an Ecp5-induced hypersensitive response, and in five accessions, the Ecp5-induced h...
Source: G3: Genes Genomes Genetics - May 3, 2020 Category: Genetics & Stem Cells Authors: Iakovidis, M., Soumpourou, E., Anderson, E., Etherington, G., Yourstone, S., Thomas, C. Tags: Genetics of Immunity Source Type: research
Anchor Away - A Fast, Reliable and Reversible Technique To Inhibit Proteins in Drosophila melanogaster
Several techniques have been developed to study specific gene function in loss-of-function situations. In Drosophila melanogaster, RNAi and the generation of mutant clones are widely used. However, both techniques have the limitation that there is a significant time lag before gene function is abolished. Given the relatively rapid development of Drosophila, such perdurance is a serious impediment to study gene function. Here we describe the adaptation of the anchor-away technique for use in Drosophila. Anchor-away was originally developed in yeast to quickly and efficiently abrogate the function of nuclear proteins by sequ...
Source: G3: Genes Genomes Genetics - May 3, 2020 Category: Genetics & Stem Cells Authors: Bosch, P. S., Pepperl, J., Basler, K. Tags: Investigations Source Type: research
Epigenetic Regulation of ABA-Induced Transcriptional Responses in Maize
Plants are subjected to extreme environmental conditions and must adapt rapidly. The phytohormone abscisic acid (ABA) accumulates during abiotic stress, signaling transcriptional changes that trigger physiological responses. Epigenetic modifications often facilitate transcription, particularly at genes exhibiting temporal, tissue-specific and environmentally-induced expression. In maize (Zea mays), MEDIATOR OF PARAMUTATION 1 (MOP1) is required for progression of an RNA-dependent epigenetic pathway that regulates transcriptional silencing of loci genomewide. MOP1 function has been previously correlated with genomic regions ...
Source: G3: Genes Genomes Genetics - May 3, 2020 Category: Genetics & Stem Cells Authors: Vendramin, S., Huang, J., Crisp, P. A., Madzima, T. F., McGinnis, K. M. Tags: Investigations Source Type: research
Genome-Wide Association Study Reveals Novel Candidate Genes Associated with Productivity and Disease Resistance to Moniliophthora spp. in Cacao (Theobroma cacao L.)
Cacao (Theobroma cacao L.), the source of chocolate, is one of the most important commodity products worldwide that helps improve the economic livelihood of farmers. Diseases like frosty pod rot caused by Moniliophthora roreri and witches’ broom caused by Moniliophthora perniciosa limit the cacao productivity, this can be solved by using resistant varieties. In the current study, we sequenced 229 cacao accessions using genotyping-by-sequencing to examine the genetic diversity and population structure employing 9,003 and 8,131 single nucleotide polymorphisms recovered by mapping against two cacao genomes (Criollo B97-...
Source: G3: Genes Genomes Genetics - May 3, 2020 Category: Genetics & Stem Cells Authors: Osorio-Guarin, J. A., Berdugo-Cely, J. A., Coronado-Silva, R. A., Baez, E., Jaimes, Y., Yockteng, R. Tags: Investigations Source Type: research
SKN-1 Is a Negative Regulator of DAF-16 and Somatic Stress Resistance in Caenorhabditis elegans
The transcription factor SKN-1, the C. elegans ortholog of mammalian Nrf protein, is a well-known longevity factor, and its activation is observed in several long-lived models. SKN-1 also plays essential roles in xenobiotic and oxidative stress responses. Here, we report deleterious functions of SKN-1 in somatic stress resistance that may impair lifespan. Constitutive SKN-1 activation impairs animal resistance to several stresses, including heat, ER stress and mitochondrial stress, which result from the suppression of DAF-16, another master regulator of longevity. SKN-1 activation abrogates DAF-16 nuclear import and downre...
Source: G3: Genes Genomes Genetics - May 3, 2020 Category: Genetics & Stem Cells Authors: Deng, J., Dai, Y., Tang, H., Pang, S. Tags: Investigations Source Type: research
