The SEM-4 Transcription Factor Is Required for Regulation of the Oxidative Stress Response in Caenorhabditis elegans
Oxidative stress causes damage to cells by creating reactive oxygen species (ROS) and the overproduction of ROS have been linked to the onset of premature aging. We previously found that a brap-2 (BRCA1 associated protein 2) mutant significantly increases the expression of phase II detoxification enzymes in C. elegans. An RNAi suppression screen to identify transcription factors involved in the production of gst-4 mRNA in brap-2 worms identified SEM-4 as a potential candidate. Here, we show that knockdown of sem-4 suppresses the activation of gst-4 caused by the mutation in brap-2. We also demonstrate that sem-4 is require...
Source: G3: Genes Genomes Genetics - September 1, 2020 Category: Genetics & Stem Cells Authors: Rafikova, A., Hu, Q., Kubiseski, T. J. Tags: Investigations Source Type: research
Genome Resequencing, Improvement of Variant Calling, and Population Genomic Analyses Provide Insights into the Seedlessness in the Genus Vitis
This study provides fundamental insights relevant to variant calling from genome resequencing data of diverse interspecific hybrid germplasms such as grape and will accelerate future efforts aimed at crop improvement. (Source: G3: Genes Genomes Genetics)
Source: G3: Genes Genomes Genetics - September 1, 2020 Category: Genetics & Stem Cells Authors: Kim, M.-S., Hur, Y. Y., Kim, J. H., Jeong, S.-C. Tags: Investigations Source Type: research
High-Throughput Genome-Wide Genotyping To Optimize the Use of Natural Genetic Resources in the Grassland Species Perennial Ryegrass (Lolium perenne L.)
The natural genetic diversity of agricultural species is an essential genetic resource for breeding programs aiming to improve their ecosystem and production services. A large natural ecotype diversity is usually available for most grassland species. This could be used to recombine natural climatic adaptations and agronomic value to create improved populations of grassland species adapted to future regional climates. However describing natural genetic resources can be long and costly. Molecular markers may provide useful information to help this task. This opportunity was investigated for Lolium perenne L., using a set of ...
Source: G3: Genes Genomes Genetics - September 1, 2020 Category: Genetics & Stem Cells Authors: Keep, T., Sampoux, J.-P., Blanco-Pastor, J. L., Dehmer, K. J., Hegarty, M. J., Ledauphin, T., Litrico, I., Muylle, H., Roldan-Ruiz, I., Roschanski, A. M., Ruttink, T., Surault, F., Willner, E., Barre, P. Tags: Genomic Prediction Source Type: research
The Impact of DNA Methylation Dynamics on the Mutation Rate During Human Germline Development
In this study, we used whole genome bisulfite sequencing (WGBS) data of cells at 13 stages of human germline development and rare variants from the 1000 Genome Project as proxies for germline mutations to investigate the correlation between dynamic methylation levels and germline mutation rates at different scales. At the single-site level, we found a significant correlation between methylation and the germline point mutation rate at CpG sites during germline developmental stages. Then we explored the mutability of methylation dynamics in all stages. Our results also showed a broad correlation between the regional methylat...
Source: G3: Genes Genomes Genetics - September 1, 2020 Category: Genetics & Stem Cells Authors: Zhou, Y., He, F., Pu, W., Gu, X., Wang, J., Su, Z. Tags: Investigations Source Type: research
Identification of Hypoxia-Specific Biomarkers in Salmonids Using RNA-Sequencing and Validation Using High-Throughput qPCR
Identifying early gene expression responses to hypoxia (i.e., low dissolved oxygen) as a tool to assess the degree of exposure to this stressor is crucial for salmonids, because they are increasingly exposed to hypoxic stress due to anthropogenic habitat change, e.g., global warming, excessive nutrient loading, and persistent algal blooms. Our goal was to discover and validate gill gene expression biomarkers specific to the hypoxia response in salmonids across multi-stressor conditions. Gill tissue was collected from 24 freshwater juvenile Chinook salmon (Oncorhynchus tshawytscha), held in normoxia [dissolved oxygen (DO) &...
Source: G3: Genes Genomes Genetics - September 1, 2020 Category: Genetics & Stem Cells Authors: Akbarzadeh, A., Houde, A. L. S., Sutherland, B. J. G., Günther, O. P., Miller, K. M. Tags: Investigations Source Type: research
Loss of Heterozygosity and Base Mutation Rates Vary Among Saccharomyces cerevisiae Hybrid Strains
A growing body of evidence suggests that mutation rates exhibit intra-species specific variation. We estimated genome-wide loss of heterozygosity (LOH), gross chromosomal changes, and single nucleotide mutation rates to determine intra-species specific differences in hybrid and homozygous strains of Saccharomyces cerevisiae. The mutation accumulation lines of the S. cerevisiae hybrid backgrounds - S288c/YJM789 (S/Y) and S288c/RM11-1a (S/R) were analyzed along with the homozygous diploids RM11, S288c, and YJM145. LOH was extensive in both S/Y and S/R hybrid backgrounds. The S/Y background also showed longer LOH tracts, gros...
Source: G3: Genes Genomes Genetics - September 1, 2020 Category: Genetics & Stem Cells Authors: Pankajam, A. V., Dash, S., Saifudeen, A., Dutta, A., Nishant, K. T. Tags: Investigations Source Type: research
Inversion Genotyping in the Anopheles gambiae Complex Using High-Throughput Array and Sequencing Platforms
Chromosomal inversion polymorphisms have special importance in the Anopheles gambiae complex of malaria vector mosquitoes, due to their role in local adaptation and range expansion. The study of inversions in natural populations is reliant on polytene chromosome analysis by expert cytogeneticists, a process that is limited by the rarity of trained specialists, low throughput, and restrictive sampling requirements. To overcome this barrier, we ascertained tag single nucleotide polymorphisms (SNPs) that are highly correlated with inversion status (inverted or standard orientation). We compared the performance of the tag SNPs...
Source: G3: Genes Genomes Genetics - September 1, 2020 Category: Genetics & Stem Cells Authors: Love, R. R., Pombi, M., Guelbeogo, M. W., Campbell, N. R., Stephens, M. T., Dabire, R. K., Costantini, C., della Torre, A., Besansky, N. J. Tags: Investigations Source Type: research
Reconstruction of the Largest Pedigree Network for Pear Cultivars and Evaluation of the Genetic Diversity of the USDA-ARS National Pyrus Collection
In this study, we have analyzed this rich dataset to discover new synonyms and mutants, identify putative labeling errors in the collection, reconstruct the largest pear cultivar pedigree and further elucidate the genetic diversity of Pyrus. (Source: G3: Genes Genomes Genetics)
Source: G3: Genes Genomes Genetics - September 1, 2020 Category: Genetics & Stem Cells Authors: Montanari, S., Postman, J., Bassil, N. V., Neale, D. B. Tags: Investigations Source Type: research
Genome-Wide Association Analysis Identified ANXA1 Associated with Shoulder Impingement Syndrome in UK Biobank Samples
In this study, Genome-wide Association Study (GWAS) was conducted to identify the candidate loci associated with SIS by using the UK Biobank samples (including 3,626 SIS patients and 3,626 control subjects). Based on the GWAS results, gene set enrichment analysis was further performed to detect the candidate gene ontology and pathways associated with SIS. We identified multiple risk loci associated with SIS, such as rs750968 (P = 4.82 x 10–8), rs754832 (P = 4.83 x 10–8) and rs1873119 (P = 6.39 x 10–8) of ANXA1 gene. Some candidate pathways have been identified related to SIS, including those linked to inf...
Source: G3: Genes Genomes Genetics - September 1, 2020 Category: Genetics & Stem Cells Authors: Cheng, B., Ning, Y., Liang, C., Li, P., Liu, L., Cheng, S., Ma, M., Zhang, L., Qi, X., Wen, Y., Zhang, F. Tags: Investigations Source Type: research
Regulation of Gliogenesis by lin-32/Atoh1 in Caenorhabditis elegans
The regulation of gliogenesis is a fundamental process for nervous system development, as the appropriate glial number and identity is required for a functional nervous system. To investigate the molecular mechanisms involved in gliogenesis, we used C. elegans as a model and identified the function of the proneural gene lin-32/Atoh1 in gliogenesis. We found that lin-32 functions during embryonic development to negatively regulate the number of AMsh glia. The ectopic AMsh cells at least partially arise from cells originally fated to become CEPsh glia, suggesting that lin-32 is involved in the specification of specific glial...
Source: G3: Genes Genomes Genetics - September 1, 2020 Category: Genetics & Stem Cells Authors: Zhang, A., Noma, K., Yan, D. Tags: Investigations Source Type: research
Genetic Diversity and Population Structure of Races of Fusarium oxysporum Causing Cotton Wilt
To better understand the evolution of virulence we are interested in identifying the genetic basis of this trait in pathogenic fungi and in developing tools for the rapid characterization of variation in virulence among populations associated with epidemics. Fusarium oxysporum f. sp. vasinfectum (FOV) is a haploid fungus that causes devastating outbreaks of Fusarium wilt of cotton wherever it is grown. In the United States, six nominal races and eleven genotypes of FOV have been characterized based on the translation elongation factor (EF-1α) gene and intergenic spacer region (IGS), but it is unclear how race or geno...
Source: G3: Genes Genomes Genetics - September 1, 2020 Category: Genetics & Stem Cells Authors: Halpern, H. C., Qi, P., Kemerait, R. C., Brewer, M. T. Tags: Investigations Source Type: research
A Meta-Analysis of Wolbachia Transcriptomics Reveals a Stage-Specific Wolbachia Transcriptional Response Shared Across Different Hosts
Wolbachia is a genus containing obligate, intracellular endosymbionts with arthropod and nematode hosts. Numerous studies have identified differentially expressed transcripts in Wolbachia endosymbionts that potentially inform the biological interplay between these endosymbionts and their hosts, albeit with discordant results. Here, we re-analyze previously published Wolbachia RNA-Seq transcriptomics data sets using a single workflow consisting of the most up-to-date algorithms and techniques, with the aim of identifying trends or patterns in the pan-Wolbachia transcriptional response. We find that data from one of the earl...
Source: G3: Genes Genomes Genetics - September 1, 2020 Category: Genetics & Stem Cells Authors: Chung, M., Basting, P. J., Patkus, R. S., Grote, A., Luck, A. N., Ghedin, E., Slatko, B. E., Michalski, M., Foster, J. M., Bergman, C. M., Hotopp, J. C. D. Tags: Investigations Source Type: research
Gene Transcription as a Limiting Factor in Protein Production and Cell Growth
Cell growth is driven by the synthesis of proteins, genes, and other cellular components. Defining processes that limit biosynthesis rates is fundamental for understanding the determinants of cell physiology. Here, we analyze the consequences of engineering cells to express extremely high levels of mCherry proteins, as a tool to define limiting processes that fail to adapt upon increasing biosynthetic demands. Protein-burdened cells were transcriptionally and phenotypically similar to mutants of the Mediator, a transcription coactivator complex. However, our binding data suggest that the Mediator was not depleted from endo...
Source: G3: Genes Genomes Genetics - September 1, 2020 Category: Genetics & Stem Cells Authors: Metzl-Raz, E., Kafri, M., Yaakov, G., Barkai, N. Tags: Investigations Source Type: research
The Effects of Quantitative Trait Architecture on Detection Power in Short-Term Artificial Selection Experiments
In this study, we use forward simulation to build a more realistic model of an E&R experiment in which a quantitative polygenic trait experiences a short, but strong, episode of truncation selection. We study the expected power for QTL detection in such an experiment and how this power is influenced by different aspects of trait architecture, including the number of QTL affecting the trait, their starting frequencies, effect sizes, clustering along a chromosome, dominance, and epistasis patterns. We show that all of these parameters can affect allele frequency dynamics at the QTL and linked loci in complex and often un...
Source: G3: Genes Genomes Genetics - September 1, 2020 Category: Genetics & Stem Cells Authors: Lou, R. N., Therkildsen, N. O., Messer, P. W. Tags: Investigations Source Type: research
Characterization and Fine Mapping of a Yellow-Virescent Gene Regulating Chlorophyll Biosynthesis and Early Stage Chloroplast Development in Brassica napus
Chlorophyll biosynthesis and chloroplast development are crucial to photosynthesis and plant growth, but their regulatory mechanism remains elusive in many crop species. We isolated a Brassica napus yellow-virescent leaf (yvl) mutant, which exhibited yellow-younger-leaf and virescent-older-leaf with decreased chlorophyll accumulation and delayed chloroplast development. We mapped yvl locus to a 70-kb interval between molecular markers yvl-O10 and InDel-O6 on chromosome A03 in BC2F2 population using whole genome re-sequencing and bulked segregant analysis. The mutant had a ‘C’ to ‘T’ substitution in ...
Source: G3: Genes Genomes Genetics - September 1, 2020 Category: Genetics & Stem Cells Authors: Zhao, C., Liu, L., Safdar, L. B., Xie, M., Cheng, X., Liu, Y., Xiang, Y., Tong, C., Tu, J., Huang, J., Liu, S. Tags: Investigations Source Type: research
