Phenotypic Associations Among Cell Cycle Genes in Saccharomyces cerevisiae
A long-standing effort in biology is to precisely define and group phenotypes that characterize a biological process, and the genes that underpin them. In Saccharomyces cerevisiae and other organisms, functional screens have generated rich lists of phenotypes associated with individual genes. However, it is often challenging to identify sets of phenotypes and genes that are most closely associated with a given biological process. Here, we focused on the 166 phenotypes arising from loss-of-function and the 86 phenotypes from gain-of-function mutations in 571 genes currently assigned to cell cycle-related ontologies in S. ce...
Source: G3: Genes Genomes Genetics - July 6, 2020 Category: Genetics & Stem Cells Authors: Bermudez, R. M., Wu, P. I.-F., Callerame, D., Hammer, S., Hu, J. C., Polymenis, M. Tags: Investigations Source Type: research
Linkage Disequilibrium-Based Inference of Genome Homology and Chromosomal Rearrangements Between Species
The aim of this study was to analyze the genomic homology between cattle (Bos taurus) and buffaloes (Bubalus bubalis) and to propose a rearrangement of the buffalo genome through linkage disequilibrium analyses of buffalo SNP markers referenced in the cattle genome assembly and also compare it to the buffalo genome assembly. A panel of bovine SNPs (single nucleotide polymorphisms) was used for hierarchical, non-hierarchical and admixture cluster analyses. Thus, the linkage disequilibrium information between markers of a specific panel of buffalo was used to infer chromosomal rearrangement. Haplotype diversity and imputatio...
Source: G3: Genes Genomes Genetics - July 6, 2020 Category: Genetics & Stem Cells Authors: de Abreu Santos, D. J., Ferreira de Camargo, G. M., Cardoso, D. F., Buzanskas, M. E., Aspilcueta-Borquis, R. R., Hurtado-Lugo, N. A., de Araujo Neto, F. R., Galvao de Albuquerque, L., Ma, L., Tonhati, H. Tags: Investigations Source Type: research
Inferring Parameters of the Distribution of Fitness Effects of New Mutations When Beneficial Mutations Are Strongly Advantageous and Rare
In this study, I analyze uSFS data from simulated populations subject to advantageous mutations with effects on fitness ranging from mildly to strongly beneficial. As expected, frequent, mildly beneficial mutations contribute substantially to standing genetic variation and parameters are accurately recovered from the uSFS. However, when advantageous mutations are strongly selected and rare, there are very few segregating in populations at any one time. Fitting the uSFS in such cases leads to underestimates of the strength of positive selection and may lead researchers to false conclusions regarding the relative contributio...
Source: G3: Genes Genomes Genetics - July 6, 2020 Category: Genetics & Stem Cells Authors: Booker, T. R. Tags: Investigations Source Type: research
Pod and Seed Trait QTL Identification To Assist Breeding for Peanut Market Preferences
Although seed and pod traits are important for peanut breeding, little is known about the inheritance of these traits. A recombinant inbred line (RIL) population of 156 lines from a cross of Tifrunner x NC 3033 was genotyped with the Axiom_Arachis1 SNP array and SSRs to generate a genetic map composed of 1524 markers in 29 linkage groups (LG). The genetic positions of markers were compared with their physical positions on the peanut genome to confirm the validity of the linkage map and explore the distribution of recombination and potential chromosomal rearrangements. This linkage map was then used to identify Quantitative...
Source: G3: Genes Genomes Genetics - July 6, 2020 Category: Genetics & Stem Cells Authors: Chavarro, C., Chu, Y., Holbrook, C., Isleib, T., Bertioli, D., Hovav, R., Butts, C., Lamb, M., Sorensen, R., A. Jackson, S., Ozias-Akins, P. Tags: Investigations Source Type: research
Genetic Underpinnings of Host Manipulation by Ophiocordyceps as Revealed by Comparative Transcriptomics
Ant-infecting Ophiocordyceps fungi are globally distributed, host manipulating, specialist parasites that drive aberrant behaviors in infected ants, at a lethal cost to the host. An apparent increase in activity and wandering behaviors precedes a final summiting and biting behavior onto vegetation, which positions the manipulated ant in a site beneficial for fungal growth and transmission. We investigated the genetic underpinnings of host manipulation by: (i) producing a high-quality hybrid assembly and annotation of the Ophiocordyceps camponoti-floridani genome, (ii) conducting laboratory infections coupled with RNAseq of...
Source: G3: Genes Genomes Genetics - July 6, 2020 Category: Genetics & Stem Cells Authors: Will, I., Das, B., Trinh, T., Brachmann, A., Ohm, R. A., de Bekker, C. Tags: Investigations Source Type: research
Improving Prediction Accuracy Using Multi-allelic Haplotype Prediction and Training Population Optimization in Wheat
The use of haplotypes may improve the accuracy of genomic prediction over single SNPs because haplotypes can better capture linkage disequilibrium and genomic similarity in different lines and may capture local high-order allelic interactions. Additionally, prediction accuracy could be improved by portraying population structure in the calibration set. A set of 383 advanced lines and cultivars that represent the diversity of the University of Minnesota wheat breeding program was phenotyped for yield, test weight, and protein content and genotyped using the Illumina 90K SNP Assay. Population structure was confirmed using si...
Source: G3: Genes Genomes Genetics - July 6, 2020 Category: Genetics & Stem Cells Authors: Sallam, A. H., Conley, E., Prakapenka, D., Da, Y., Anderson, J. A. Tags: Genomic Prediction Source Type: research
Population Differentiation at the PVT1 Gene Locus: Implications for Prostate Cancer
Genetic variation in susceptibility to complex diseases, such as cancer, is well-established. Enrichment of disease associated alleles in specific populations could have implications for disease incidence and prevalence. Prostate cancer (PCa) is a disease with well-established higher incidence, prevalence, and worse outcomes among men of African ancestry in comparison to other populations. PCa is a multi-factorial, complex disease, but the exact mechanisms for its development and progression are unclear. The gene desert located on chromosome 8q24 is associated with aggressiveness of PCa. Interestingly, the non-protein codi...
Source: G3: Genes Genomes Genetics - July 6, 2020 Category: Genetics & Stem Cells Authors: Pal, G., Di, L., Orunmuyi, A., Olapade-Olaopa, E. O., Qiu, W., Ogunwobi, O. O. Tags: Investigations Source Type: research
Independent Whole-Genome Duplications Define the Architecture of the Genomes of the Devastating West African Cacao Black Pod Pathogen Phytophthora megakarya and Its Close Relative Phytophthora palmivora
In this study, we reconstructed the complete diploid genomes of multiple isolates of both species using single-molecule real-time sequencing. Thirty-one additional genotypes were sequenced to analyze inter- and intra-species genomic diversity. The P. megakarya genome is exceptionally large (222 Mbp) and nearly twice the size of P. palmivora (135 Mbp) and most known Phytophthora species (~100 Mbp on average). Previous reports pointed toward a whole-genome duplication (WGD) in P. palmivora. In this study, we demonstrate that both species underwent independent and relatively recent WGD events. In P. megakarya we identified a ...
Source: G3: Genes Genomes Genetics - July 6, 2020 Category: Genetics & Stem Cells Authors: Morales-Cruz, A., Ali, S. S., Minio, A., Figueroa-Balderas, R., Garcia, J. F., Kasuga, T., Puig, A. S., Marelli, J.-P., Bailey, B. A., Cantu, D. Tags: Investigations Source Type: research
Genetic Characterization of a Wheat Association Mapping Panel Relevant to Brazilian Breeding Using a High-Density Single Nucleotide Polymorphism Array
Bread wheat (Triticum aestivum L.) is one of the world’s most important crops. Maintaining wheat yield gains across all of its major production areas is a key target toward underpinning global food security. Brazil is a major wheat producer in South America, generating grain yields of around 6.8 million tons per year. Here, we establish and genotype a wheat association mapping resource relevant to contemporary Brazilian wheat breeding programs. The panel of 558 wheat accessions was genotyped using an Illumina iSelect 90,000 single nucleotide polymorphism array. Following quality control, the final data matrix consist...
Source: G3: Genes Genomes Genetics - July 6, 2020 Category: Genetics & Stem Cells Authors: Mellers, G., Aguilera, J. G., Bird, N., Variani Bonato, A. L., Bonow, S., Caierao, E., Consoli, L., Santana, F. M., Simmonds, J., Steed, A., Montan Torres, G. A., Uauy, C., Wright, T. I. C., Scheeren, P. L., Nicholson, P., Cockram, J. Tags: Investigations Source Type: research
Genomic Heritabilities and Correlations of 17 Traits Related to Obesity and Associated Conditions in the Japanese Population
Over the past few decades, obesity has become a public health issue of global concern. Even though disparities exist between human populations, e.g., the higher liver fat content of the Japanese despite a lower body mass index (BMI), studies on the genetics of obesity still largely focus on populations of European descent, leading to a dearth of genetic data on non-European populations. In this context, this study aimed to establish a broad picture of the genetic attributes of the Japanese population, by examining a representative sample of 18,889 individuals participating in the Tohoku Medical Megabank Project cohort. We ...
Source: G3: Genes Genomes Genetics - July 6, 2020 Category: Genetics & Stem Cells Authors: Gervais, O., Ueno, K., Kawai, Y., Hitomi, Y., Misawa, K., Teraguchi, S., Wang, Y.-Y., Tokunaga, K., Nagasaki, M. Tags: Investigations Source Type: research
Insulin-Like Signalling Influences the Coordination of Larval Hemocyte Number with Body Size in Drosophila melanogaster
Blood cells, known as hemocytes in invertebrates, play important and conserved roles in immunity, wound healing and tissue remodelling. The control of hemocyte number is therefore critical to ensure these functions are not compromised, and studies using Drosophila melanogaster are proving useful for understanding how this occurs. Recently, the embryonic patterning gene, torso-like (tsl), was identified as being required both for normal hemocyte development and for providing immunity against certain pathogens. Here, we report that Tsl is required specifically during the larval phase of hematopoiesis, and that tsl mutant lar...
Source: G3: Genes Genomes Genetics - July 6, 2020 Category: Genetics & Stem Cells Authors: Bakopoulos, D., Beadle, L. F., Esposito, K. M., Mirth, C. K., Warr, C. G., Johnson, T. K. Tags: Investigations Source Type: research
Meta-analysis of Diets Used in Drosophila Microbiome Research and Introduction of the Drosophila Dietary Composition Calculator (DDCC)
Nutrition is a major factor influencing many aspects of Drosophila melanogaster physiology. However, a wide range of diets, many of which are termed "standard" in the literature, are utilized for D. melanogaster research, leading to inconsistencies in reporting of nutrition-dependent phenotypes across the field. This is especially evident in microbiome studies, as diet has a pivotal role in microbiome composition and resulting host-microbe interactions. Here, we performed a meta-analysis of diets used in fly microbiome research and provide a web-based tool for researchers to determine the nutritional content of diets of in...
Source: G3: Genes Genomes Genetics - July 6, 2020 Category: Genetics & Stem Cells Authors: Lesperance, D. N. A., Broderick, N. A. Tags: Software and Data Resources Source Type: research
Adapting Genotyping-by-Sequencing and Variant Calling for Heterogeneous Stock Rats
The heterogeneous stock (HS) is an outbred rat population derived from eight inbred rat strains. HS rats are ideally suited for genome wide association studies; however, only a few genotyping microarrays have ever been designed for rats and none of them are currently in production. To address the need for an efficient and cost effective method of genotyping HS rats, we have adapted genotype-by-sequencing (GBS) to obtain genotype information at large numbers of single nucleotide polymorphisms (SNPs). In this paper, we have outlined the laboratory and computational steps we took to optimize double digest genotype-by-sequenci...
Source: G3: Genes Genomes Genetics - July 6, 2020 Category: Genetics & Stem Cells Authors: Gileta, A. F., Gao, J., Chitre, A. S., Bimschleger, H. V., St. Pierre, C. L., Gopalakrishnan, S., Palmer, A. A. Tags: Software and Data Resources Source Type: research
Genomic Variant Analyses in Pyrethroid Resistant and Susceptible Malaria Vector, Anopheles sinensis
In this study, we tested the hypothesis that other genomic variants are associated with the resistance phenotype. Using paired-end whole genome sequencing (DNA-seq), we generated 108 Gb of DNA sequence from deltamethrin -resistant and -susceptible mosquito pools with an average coverage of 83.3x depth. Using a stringent filtering method, we identified a total of 916,926 single nucleotide variants (SNVs), including 32,240 non-synonymous mutations. A total of 958 SNVs differed significantly in allele frequency between deltamethrin -resistant and -susceptible mosquitoes. Of these, 43 SNVs were present within 37 genes that cod...
Source: G3: Genes Genomes Genetics - July 6, 2020 Category: Genetics & Stem Cells Authors: Chang, X., Zhong, D., Wang, X., Bonizzoni, M., Li, Y., Zhou, G., Cui, L., Wei, X., Yan, G. Tags: Genome Report Source Type: research
Improving the Chromosome-Level Genome Assembly of the Siamese Fighting Fish (Betta splendens) in a University Masters Course
We present an improved full chromosome-level assembly of the Siamese fighting fish generated during a university master’s course. The use of ~35x long-read nanopore data drastically improved the baseline assembly in terms of continuity. We show that relatively in-expensive high-throughput sequencing technologies such as the long-read MinION sequencing platform can be used in educational settings allowing the students to gain practical skills in modern genomics and generate high quality results that benefit downstream research projects. (Source: G3: Genes Genomes Genetics)
Source: G3: Genes Genomes Genetics - July 6, 2020 Category: Genetics & Stem Cells Authors: Prost, S., Petersen, M., Grethlein, M., Hahn, S. J., Kuschik-Maczollek, N., Olesiuk, M. E., Reschke, J.-O., Schmey, T. E., Zimmer, C., Gupta, D. K., Schell, T., Coimbra, R., De Raad, J., Lammers, F., Winter, S., Janke, A. Tags: Genome Report Source Type: research
