MNase Profiling of Promoter Chromatin in Salmonella typhimurium-Stimulated GM12878 Cells Reveals Dynamic and Response-Specific Nucleosome Architecture
The nucleosome is the primary unit of chromatin structure and commonly imputed as a regulator of nuclear events, although the exact mechanisms remain unclear. Recent studies have shown that certain nucleosomes can have different sensitivities to micrococcal nuclease (MNase) digestion, resulting in the release of populations of nucleosomes dependent on the concentration of MNase. Mapping MNase sensitivity of nucleosomes at transcription start sites genome-wide reveals an important functional nucleosome organization that correlates with gene expression levels and transcription factor binding. In order to understand nucleosom...
Source: G3: Genes Genomes Genetics - July 6, 2020 Category: Genetics & Stem Cells Authors: Cole, L., Dennis, J. Tags: Genome Report Source Type: research
Whole-Genome Comparative and Pathogenicity Analysis of Salmonella enterica subsp. enterica Serovar Rissen
In this study, the pathogenicity and antibiotic resistance of a representative S. Rissen isolate were investigated. The cell model results showed that S. Rissen preferred to replicate in human macrophage cells U937 compared to murine macrophage cells RAW264.7, suggesting that it has a level of host adaptability. Genome sequencing and comparison analysis revealed that the distribution and nonsynonymous single nucleotide polymorphisms of virulence factors in S. Rissen were similar to those in S. Typhi rather than to those in S. Typhimurium. Taken together, our results suggest that although S. Rissen is a common serotype dist...
Source: G3: Genes Genomes Genetics - July 6, 2020 Category: Genetics & Stem Cells Authors: Zhou, A., Li, J., Xu, Z., Ni, J., Guo, J., Yao, Y.-F., Wu, W. Tags: Genome Report Source Type: research
Comparative RNAseq Analysis of the Insect-Pathogenic Fungus Metarhizium anisopliae Reveals Specific Transcriptome Signatures of Filamentous and Yeast-Like Development
The fungus Metarhizium anisopliae is a facultative insect pathogen used as biological control agent of several agricultural pests worldwide. It is a dimorphic fungus that is able to display two growth morphologies, a filamentous phase with formation of hyphae and a yeast-like phase with formation of single-celled blastospores. Blastospores play an important role for M. anisopliae pathogenicity during disease development. They are formed solely in the hemolymph of infected insects as a fungal strategy to quickly multiply and colonize the insect’s body. Here, we use comparative genome-wide transcriptome analyses to det...
Source: G3: Genes Genomes Genetics - July 6, 2020 Category: Genetics & Stem Cells Authors: Iwanicki, N. S., Junior, I. D., Eilenberg, J., De Fine Licht, H. H. Tags: Genome Report Source Type: research
Reference Genome Assembly for Australian Ascochyta rabiei Isolate ArME14
Ascochyta rabiei is the causal organism of ascochyta blight of chickpea and is present in chickpea crops worldwide. Here we report the release of a high-quality PacBio genome assembly for the Australian A. rabiei isolate ArME14. We compare the ArME14 genome assembly with an Illumina assembly for Indian A. rabiei isolate, ArD2. The ArME14 assembly has gapless sequences for nine chromosomes with telomere sequences at both ends and 13 large contig sequences that extend to one telomere. The total length of the ArME14 assembly was 40,927,385 bp, which was 6.26 Mb longer than the ArD2 assembly. Division of the genome by Occulter...
Source: G3: Genes Genomes Genetics - July 6, 2020 Category: Genetics & Stem Cells Authors: Shah, R. M., Williams, A. H., Hane, J. K., Lawrence, J. A., Farfan-Caceres, L. M., Debler, J. W., Oliver, R. P., Lee, R. C. Tags: Genome Report Source Type: research
Corrigendum
(Source: G3: Genes Genomes Genetics)
Source: G3: Genes Genomes Genetics - May 31, 2020 Category: Genetics & Stem Cells Tags: Corrigendum Source Type: research
Population Connectivity Predicts Vulnerability to White-Nose Syndrome in the Chilean Myotis (Myotis chiloensis) - A Genomics Approach
Despite its peculiar distribution, the biology of the southernmost bat species in the world, the Chilean myotis (Myotis chiloensis), has garnered little attention so far. The species has a north-south distribution of c. 2800 km, mostly on the eastern side of the Andes mountain range. Use of extended torpor occurs in the southernmost portion of the range, putting the species at risk of bat white-nose syndrome, a fungal disease responsible for massive population declines in North American bats. Here, we examined how geographic distance and topology would be reflected in the population structure of M. chiloensis along the maj...
Source: G3: Genes Genomes Genetics - May 31, 2020 Category: Genetics & Stem Cells Authors: Lilley, T. M., Sävilammi, T., Ossa, G., Blomberg, A. S., Vasemägi, A., Yung, V., Vendrami, D. L. J., Johnson, J. S. Tags: Investigations Source Type: research
A Protamine Knockdown Mimics the Function of Sd in Drosophila melanogaster
Segregation Distorter (SD) is an autosomal meiotic drive system found worldwide in natural populations of Drosophila melanogaster. This gene complex induces the preferential and nearly exclusive transmission of the SD chromosome in SD/SD+ males. This selfish propagation occurs through the interplay of the Sd locus, its enhancers and the Rsps locus during spermatid development. The key distorter locus, Sd, encodes a truncated but enzymatically active RanGAP (RanGTPase-activating protein), a key nuclear transport factor in the Ran signaling pathway. When encoded by Sd, RanGAP is mislocalized to the nucleus interior, which th...
Source: G3: Genes Genomes Genetics - May 31, 2020 Category: Genetics & Stem Cells Authors: Gingell, L. F., McLean, J. R. Tags: Investigations Source Type: research
Levels of Heterochiasmy During Arabidopsis Development as Reported by Fluorescent Tagged Lines
Crossing over, the exchange of DNA between the chromosomes during meiosis, contributes significantly to genetic variation. The rate of crossovers (CO) varies depending upon the taxon, population, age, external conditions, and also, sometimes, between the sexes, a phenomenon called heterochiasmy. In the model plant Arabidopsis thaliana, the male rate of all crossover events (mCO) is typically nearly double the female rate (fCO). A previous, PCR-based genotyping study has reported that the disparity decreases with increasing parental age, because fCO rises while mCO remains stable. We revisited this topic using a fluorescent...
Source: G3: Genes Genomes Genetics - May 31, 2020 Category: Genetics & Stem Cells Authors: Saini, R., Singh, A. K., Hyde, G. J., Baskar, R. Tags: Investigations Source Type: research
Combined Multistage Linear Genomic Selection Indices To Predict the Net Genetic Merit in Plant Breeding
A combined multistage linear genomic selection index (CMLGSI) is a linear combination of phenotypic and genomic estimated breeding values useful for predicting the individual net genetic merit, which in turn is a linear combination of the true unobservable breeding values of the traits weighted by their respective economic values. The CMLGSI is a cost-saving strategy for improving multiple traits because the breeder does not need to measure all traits at each stage. The optimum (OCMLGSI) and decorrelated (DCMLGSI) indices are the main CMLGSIs. Whereas the OCMLGSI takes into consideration the index correlation values among ...
Source: G3: Genes Genomes Genetics - May 31, 2020 Category: Genetics & Stem Cells Authors: Ceron-Rojas, J. J., Crossa, J. Tags: Genomic Prediction Source Type: research
Divergence of Peroxisome Membrane Gene Sequence and Expression Between Yeast Species
Large population-genomic sequencing studies can enable highly-powered analyses of sequence signatures of natural selection. Genome repositories now available for Saccharomyces yeast make it a premier model for studies of the molecular mechanisms of adaptation. We mined the genomes of hundreds of isolates of the sister species S. cerevisiae and S. paradoxus to identify sequence hallmarks of adaptive divergence between the two. From the top hits we focused on a set of genes encoding membrane proteins of the peroxisome, an organelle devoted to lipid breakdown and other specialized metabolic pathways. In-depth population- and ...
Source: G3: Genes Genomes Genetics - May 31, 2020 Category: Genetics & Stem Cells Authors: Dubin, C. A., Roop, J. I., Brem, R. B. Tags: Investigations Source Type: research
Application of Low Coverage Genotyping by Sequencing in Selectively Bred Arctic Charr (Salvelinus alpinus)
Arctic charr (Salvelinus alpinus) is a species of high economic value for the aquaculture industry, and of high ecological value due to its Holarctic distribution in both marine and freshwater environments. Novel genome sequencing approaches enable the study of population and quantitative genetic parameters even on species with limited or no prior genomic resources. Low coverage genotyping by sequencing (GBS) was applied in a selected strain of Arctic charr in Sweden originating from a landlocked freshwater population. For the needs of the current study, animals from year classes 2013 (171 animals, parental population) and...
Source: G3: Genes Genomes Genetics - May 31, 2020 Category: Genetics & Stem Cells Authors: Palaiokostas, C., Clarke, S. M., Jeuthe, H., Brauning, R., Bilton, T. P., Dodds, K. G., McEwan, J. C., De Koning, D.-J. Tags: Genomic Prediction Source Type: research
Dbf4-Dependent Kinase (DDK)-Mediated Proteolysis of CENP-A Prevents Mislocalization of CENP-A in Saccharomyces cerevisiae
The evolutionarily conserved centromeric histone H3 variant (Cse4 in budding yeast, CENP-A in humans) is essential for faithful chromosome segregation. Mislocalization of CENP-A to non-centromeric chromatin contributes to chromosomal instability (CIN) in yeast, fly, and human cells and CENP-A is highly expressed and mislocalized in cancers. Defining mechanisms that prevent mislocalization of CENP-A is an area of active investigation. Ubiquitin-mediated proteolysis of overexpressed Cse4 (GALCSE4) by E3 ubiquitin ligases such as Psh1 prevents mislocalization of Cse4, and psh1 strains display synthetic dosage lethality (SDL) ...
Source: G3: Genes Genomes Genetics - May 31, 2020 Category: Genetics & Stem Cells Authors: Eisenstatt, J. R., Boeckmann, L., Au, W.-C., Garcia, V., Bursch, L., Ocampo, J., Costanzo, M., Weinreich, M., Sclafani, R. A., Baryshnikova, A., Myers, C. L., Boone, C., Clark, D. J., Baker, R., Basrai, M. A. Tags: Investigations Source Type: research
Resistance Mechanisms of Saccharomyces cerevisiae to Commercial Formulations of Glyphosate Involve DNA Damage Repair, the Cell Cycle, and the Cell Wall Structure
The use of glyphosate-based herbicides is widespread and despite their extensive use, their effects are yet to be deciphered completely. The additives in commercial formulations of glyphosate, though labeled inert when used individually, have adverse effects when used in combination with other additives along with the active ingredient. As a species, Saccharomyces cerevisiae has a wide range of resistance to glyphosate-based herbicides. To investigate the underlying genetic differences between sensitive and resistant strains, global changes in gene expression were measured, when yeast were exposed to a glyphosate-based her...
Source: G3: Genes Genomes Genetics - May 31, 2020 Category: Genetics & Stem Cells Authors: Ravishankar, A., Pupo, A., Gallagher, J. E. G. Tags: Investigations Source Type: research
Proxies of CRISPR/Cas9 Activity To Aid in the Identification of Mutagenized Arabidopsis Plants
CRISPR/Cas9 has become the preferred gene-editing technology to obtain loss-of-function mutants in plants, and hence a valuable tool to study gene function. This is mainly due to the easy reprogramming of Cas9 specificity using customizable small non-coding RNAs, and to the possibility of editing several independent genes simultaneously. Despite these advances, the identification of CRISPR-edited plants remains time and resource-intensive. Here, based on the premise that one editing event in one locus is a good predictor of editing event/s in other locus/loci, we developed a CRISPR co-editing selection strategy that greatl...
Source: G3: Genes Genomes Genetics - May 31, 2020 Category: Genetics & Stem Cells Authors: Li, R., Vavrik, C., Danna, C. H. Tags: Investigations Source Type: research
