Corrigendum
(Source: G3: Genes Genomes Genetics)
Source: G3: Genes Genomes Genetics - July 7, 2020 Category: Genetics & Stem Cells Tags: Corrigendum Source Type: research

The Gut Microbial Architecture of Efficiency Traits in the Domestic Poultry Model Species Japanese Quail (Coturnix japonica) Assessed by Mixed Linear Models
It is well known that mammals and avian gut microbiota compositions are shaped by the host genomes and affect quantitative traits. The microbial architecture describes the impact of the microbiota composition on quantitative trait variation and the number and effect distribution of microbiota features. In the present study the gut microbial architecture of feed-related traits phosphorus and calcium utilization, daily gain, feed intake and feed per gain ratio in the domestic poultry model species Japanese quail were assessed by mixed linear models. The ileum microbiota composition was characterized by 16S rRNA amplicon sequ...
Source: G3: Genes Genomes Genetics - July 7, 2020 Category: Genetics & Stem Cells Authors: Vollmar, S., Wellmann, R., Borda-Molina, D., Rodehutscord, M., Camarinha-Silva, A., Bennewitz, J. Tags: Investigations Source Type: research

Contractions of the C-Terminal Domain of Saccharomyces cerevisiae Rpb1p Are Mediated by Rad5p
We report that contractions require the post-replication repair factor Rad5p but, unlike expansions, not the homologous recombination factors Rad51p and Rad52p. Sequence analysis of contraction events reveals that deleted regions are flanked by microhomologies. We also find that G-quadruplex forming sequences predicted by the QGRS Mapper are enriched on the noncoding strand of the CTD compared to the body of RPB1. Formation of G-quadruplexes in the CTD coding region could block the replication fork, necessitating post-replication repair. We propose that contractions of the CTD result when microhomologies misalign during Ra...
Source: G3: Genes Genomes Genetics - July 7, 2020 Category: Genetics & Stem Cells Authors: Stewart, T., Exner, A. E., Patnaik, P., Fuchs, S. M. Tags: Investigations Source Type: research

Dissecting the Genetic Architecture of Cystatin C in Diversity Outbred Mice
Plasma concentration of Cystatin C (CysC) level is a biomarker of glomerular filtration rate in the kidney. We use a Systems Genetics approach to investigate the genetic determinants of plasma CysC concentration. To do so we perform Quantitative Trait Loci (QTL) and expression QTL (eQTL) analysis of 120 Diversity Outbred (DO) female mice, 56 weeks of age. We performed network analysis of kidney gene expression to determine if the gene modules with common functions are associated with kidney biomarkers of chronic kidney diseases. Our data demonstrates that plasma concentrations and kidney mRNA levels of CysC are associated ...
Source: G3: Genes Genomes Genetics - July 7, 2020 Category: Genetics & Stem Cells Authors: Huda, M. N., VerHague, M., Albright, J., Smallwood, T., Bell, T. A., Que, E., Miller, D. R., Roshanravan, B., Allayee, H., Manuel de Villena, F. P., Bennett, B. J. Tags: Multiparental Populations Source Type: research

An Investigation into the Genetic History of Japanese Populations of Three Starfish, Acanthaster planci, Linckia laevigata, and Asterias amurensis, Based on Complete Mitochondrial DNA Sequences
Crown-of-thorns starfish, Acanthaster planci (COTS), are common in coral reefs of Indo-Pacific Ocean. Since they are highly fecund predators of corals, periodic outbreaks of COTS cause substantial loss of healthy coral reefs. Using complete mitochondrial DNA sequences, we here examined how COTS outbreaks in the Ryukyu Archipelago, Japan are reflected by the profile of their population genetics. Population genetics of the blue starfish, Linckia laevigata, which lives in the Ryukyu Archipelago, but not break out and the northern Pacific sea star, Asterias amurensis, which lives in colder seawater around the main Islands of J...
Source: G3: Genes Genomes Genetics - July 7, 2020 Category: Genetics & Stem Cells Authors: Inoue, J., Hisata, K., Yasuda, N., Satoh, N. Tags: Investigations Source Type: research

RSU-1 Maintains Integrity of Caenorhabditis elegans Vulval Muscles by Regulating {alpha}-Actinin
Egg-laying behavior in Caenorhabditis elegans is a well-known model for investigating fundamental cellular processes. In egg-laying, muscle contraction is the relaxation of the vulval muscle to extrude eggs from the vulva. Unlike skeletal muscle, vulval muscle lacks visible striations of the sarcomere. Therefore, vulval muscle must counteract the mechanical stress, caused by egg extrusion and body movement, from inducing cell-shape distortion by maintaining its cytoskeletal integrity. However, the underlying mechanisms that regulate the cellular integrity in vulval muscles remain unclear. Here, we demonstrate that C. elega...
Source: G3: Genes Genomes Genetics - July 7, 2020 Category: Genetics & Stem Cells Authors: Wang, X., Huang, S., Zheng, C., Ge, W., Wu, C., Tse, Y. C. Tags: Investigations Source Type: research

Selective Loss of Diversity in Doubled-Haploid Lines from European Maize Landraces
Maize landraces are well adapted to their local environments and present valuable sources of genetic diversity for breeding and conservation. But the maintenance of open-pollinated landraces in ex-situ programs is challenging, as regeneration of seed can often lead to inbreeding depression and the loss of diversity due to genetic drift. Recent reports suggest that the production of doubled-haploid (DH) lines from landraces may serve as a convenient means to preserve genetic diversity in a homozygous form that is immediately useful for modern breeding. The production of doubled-haploid (DH) lines presents an extreme case of...
Source: G3: Genes Genomes Genetics - July 7, 2020 Category: Genetics & Stem Cells Authors: Zeitler, L., Ross-Ibarra, J., Stetter, M. G. Tags: Investigations Source Type: research

Evidence That Runt Acts as a Counter-Repressor of Groucho During Drosophila melanogaster Primary Sex Determination
Runx proteins are bifunctional transcription factors that both repress and activate transcription in animal cells. Typically, Runx proteins work in concert with other transcriptional regulators, including co-activators and co-repressors to mediate their biological effects. In Drosophila melanogaster the archetypal Runx protein, Runt, functions in numerous processes including segmentation, neurogenesis and sex determination. During primary sex determination Runt acts as one of four X-linked signal element (XSE) proteins that direct female-specific activation of the establishment promoter (Pe) of the master regulatory gene S...
Source: G3: Genes Genomes Genetics - July 7, 2020 Category: Genetics & Stem Cells Authors: Mahadeveraju, S., Jung, Y.-H., Erickson, J. W. Tags: Genetics of Sex Source Type: research

An Unusual Amino Acid Substitution Within Hummingbird Cytochrome c Oxidase Alters a Key Proton-Conducting Channel
Hummingbirds in flight exhibit the highest mass-specific metabolic rate of all vertebrates. The bioenergetic requirements associated with sustained hovering flight raise the possibility of unique amino acid substitutions that would enhance aerobic metabolism. Here, we have identified a non-conservative substitution within the mitochondria-encoded cytochrome c oxidase subunit I (COI) that is fixed within hummingbirds, but not among other vertebrates. This unusual change is also rare among metazoans, but can be identified in several clades with diverse life histories. We performed atomistic molecular dynamics simulations usi...
Source: G3: Genes Genomes Genetics - July 7, 2020 Category: Genetics & Stem Cells Authors: Dunn, C. D., Akpınar, B. A., Sharma, V. Tags: Investigations Source Type: research

Training Population Optimization for Genomic Selection in Miscanthus
Miscanthus is a perennial grass with potential for lignocellulosic ethanol production. To ensure its utility for this purpose, breeding efforts should focus on increasing genetic diversity of the nothospecies Miscanthus x giganteus (Mxg) beyond the single clone used in many programs. Germplasm from the corresponding parental species M. sinensis (Msi) and M. sacchariflorus (Msa) could theoretically be used as training sets for genomic prediction of Mxg clones with optimal genomic estimated breeding values for biofuel traits. To this end, we first showed that subpopulation structure makes a substantial contribution to the ge...
Source: G3: Genes Genomes Genetics - July 7, 2020 Category: Genetics & Stem Cells Authors: Olatoye, M. O., Clark, L. V., Labonte, N. R., Dong, H., Dwiyanti, M. S., Anzoua, K. G., Brummer, J. E., Ghimire, B. K., Dzyubenko, E., Dzyubenko, N., Bagmet, L., Sabitov, A., Chebukin, P., Głowacka, K., Heo, K., Jin, X., Nagano, H., Peng, J., Yu, C Tags: Genomic Prediction Source Type: research

qRf8-1, a Novel QTL for the Fertility Restoration of Maize CMS-C Identified by QTL-seq
This study not only expands the original fertility restoration system but also provides valuable insights into the complex genetic mechanisms underlying the fertility restoration of CMS-C. (Source: G3: Genes Genomes Genetics)
Source: G3: Genes Genomes Genetics - July 7, 2020 Category: Genetics & Stem Cells Authors: Zheng, M., Yang, T., Liu, X., Lü, G., Zhang, P., Jiang, B., Zhou, S., Lu, Y., Lan, H., Zhang, S., Li, C., Rong, T., Cao, M. Tags: Investigations Source Type: research

Origin Specific Genomic Selection: A Simple Process To Optimize the Favorable Contribution of Parents to Progeny
Modern crop breeding is in constant demand for new genetic diversity as part of the arms race with genetic gain. The elite gene pool has limited genetic variation and breeders are trying to introduce novelty from unadapted germplasm, landraces and wild relatives. For polygenic traits, currently available approaches to introgression are not ideal, as there is a demonstrable bias against exotic alleles during selection. Here, we propose a partitioned form of genomic selection, called Origin Specific Genomic Selection (OSGS), where we identify and target selection on favorable exotic alleles. Briefly, within a population deri...
Source: G3: Genes Genomes Genetics - July 7, 2020 Category: Genetics & Stem Cells Authors: Yang, C. J., Sharma, R., Gorjanc, G., Hearne, S., Powell, W., Mackay, I. Tags: Genomic Prediction Source Type: research

Low Additive Genetic Variation in a Trait Under Selection in Domesticated Rice
Quantitative traits are important targets of both natural and artificial selection. The genetic architecture of these traits and its change during the adaptive process is thus of fundamental interest. The fate of the additive effects of variants underlying a trait receives particular attention because they constitute the genetic variation component that is transferred from parents to offspring and thus governs the response to selection. While estimation of this component of phenotypic variation is challenging, the increasing availability of dense molecular markers puts it within reach. Inbred plant species offer an additio...
Source: G3: Genes Genomes Genetics - July 7, 2020 Category: Genetics & Stem Cells Authors: Karavolias, N. G., Greenberg, A. J., Barrero, L. S., Maron, L. G., Shi, Y., Monteverde, E., Pineros, M. A., McCouch, S. R. Tags: Investigations Source Type: research

Support Vector Machine for Lung Adenocarcinoma Staging Through Variant Pathways
Lung adenocarcinoma (LUAD) is one of the most common malignant tumors. How to effectively diagnose LUAD at an early stage and make an accurate judgement of the occurrence and progression of LUAD are still the focus of current research. Support vector machine (SVM) is one of the most effective methods for diagnosing LUAD of different stages. The study aimed to explore the dynamic change of differentially expressed genes (DEGs) in different stages of LUAD, and to assess the risk of LUAD through DEGs enriched pathways and establish a diagnostic model based on SVM method. Based on TMN stages and gene expression profiles of 517...
Source: G3: Genes Genomes Genetics - July 7, 2020 Category: Genetics & Stem Cells Authors: Di, F., He, C., Pu, G., Zhang, C. Tags: Investigations Source Type: research

QTG-Finder2: A Generalized Machine-Learning Algorithm for Prioritizing QTL Causal Genes in Plants
Linkage mapping has been widely used to identify quantitative trait loci (QTL) in many plants and usually requires a time-consuming and labor-intensive fine mapping process to find the causal gene underlying the QTL. Previously, we described QTG-Finder, a machine-learning algorithm to rationally prioritize candidate causal genes in QTLs. While it showed good performance, QTG-Finder could only be used in Arabidopsis and rice because of the limited number of known causal genes in other species. Here we tested the feasibility of enabling QTG-Finder to work on species that have few or no known causal genes by using orthologs o...
Source: G3: Genes Genomes Genetics - July 7, 2020 Category: Genetics & Stem Cells Authors: Lin, F., Lazarus, E. Z., Rhee, S. Y. Tags: Investigations Source Type: research

Systematic Identification and Analysis of Light-Responsive Circular RNA and Co-expression Networks in Lettuce (Lactuca sativa)
Circular RNA (circRNA) is a covalently-closed single-stranded RNA molecule that plays an important role in transcriptional regulation of gene expression in a variety of species. Light intensity is a pivotal environmental factor affecting plant growth and development. However, little is known regarding photoresponsive plant circRNAs. Here, we aimed to investigate the expression and function of circRNAs in lettuce leaves in response to different light intensity treatments. We performed RNA sequencing (RNA-Seq) on leaves of lettuce (Lactuca sativa) to determine circRNA expression profiles and reverse-transcription polymerase ...
Source: G3: Genes Genomes Genetics - July 7, 2020 Category: Genetics & Stem Cells Authors: Yang, Z., Yang, Z., Xie, Y., Liu, Q., Mei, Y., Wu, Y. Tags: Investigations Source Type: research

The Ancestral Caenorhabditis elegans Cuticle Suppresses rol-1
Genetic background commonly modifies the effects of mutations. We discovered that worms mutant for the canonical rol-1 gene, identified by Brenner in 1974, do not roll in the genetic background of the wild strain CB4856. Using linkage mapping, association analysis and gene editing, we determined that N2 carries an insertion in the collagen gene col-182 that acts as a recessive enhancer of rol-1 rolling. From population and comparative genomics, we infer the insertion is derived in N2 and related laboratory lines, likely arising during the domestication of Caenorhabditis elegans, and breaking a conserved protein. The ancest...
Source: G3: Genes Genomes Genetics - July 7, 2020 Category: Genetics & Stem Cells Authors: Noble, L. M., Miah, A., Kaur, T., Rockman, M. V. Tags: Investigations Source Type: research

Validation of QTLs for Fiber Quality Introgressed from Gossypium mustelinum by Selective Genotyping
Gene introgression from wild species has been shown to be a feasible approach for fiber quality improvement in Upland cotton. Previously, we developed an interspecific G. mustelinum x G. hirsutum advanced-backcross population and mapped over one hundred QTL for fiber quality traits. In the current study, a trait-based selective genotyping approach was utilized to prioritize a small subset of introgression lines with high phenotypic values for different fiber quality traits, to simultaneously validate multiple fiber quality QTL in a single experiment. A total of 75 QTL were detected by CIM and/or single-marker analysis, inc...
Source: G3: Genes Genomes Genetics - July 7, 2020 Category: Genetics & Stem Cells Authors: Chen, Q., Wang, W., Wang, C., Zhang, M., Yu, J., Zhang, Y., Yuan, B., Ding, Y., Jones, D. C., Paterson, A. H., Chee, P. W., Wang, B. Tags: Investigations Source Type: research

The Predicted RNA-Binding Protein ETR-1/CELF1 Acts in Muscles To Regulate Neuroblast Migration in Caenorhabditis elegans
Neuroblast migration is a critical aspect of nervous system development (e.g., neural crest migration). In an unbiased forward genetic screen, we identified a novel player in neuroblast migration, the ETR-1/CELF1 RNA binding protein. CELF1 RNA binding proteins are involved in multiple aspects of RNA processing including alternative splicing, stability, and translation. We find that a specific mutation in alternatively-spliced exon 8 results in migration defects of the AQR and PQR neurons, and not the embryonic lethality and body wall muscle defects of complete knockdown of the locus. Surprisingly, ETR-1 was required in bod...
Source: G3: Genes Genomes Genetics - July 7, 2020 Category: Genetics & Stem Cells Authors: Ochs, M. E., Josephson, M. P., Lundquist, E. A. Tags: Investigations Source Type: research

The Gene scb-1 Underlies Variation in Caenorhabditis elegans Chemotherapeutic Responses
Pleiotropy, the concept that a single gene controls multiple distinct traits, is prevalent in most organisms and has broad implications for medicine and agriculture. The identification of the molecular mechanisms underlying pleiotropy has the power to reveal previously unknown biological connections between seemingly unrelated traits. Additionally, the discovery of pleiotropic genes increases our understanding of both genetic and phenotypic complexity by characterizing novel gene functions. Quantitative trait locus (QTL) mapping has been used to identify several pleiotropic regions in many organisms. However, gene knockout...
Source: G3: Genes Genomes Genetics - July 7, 2020 Category: Genetics & Stem Cells Authors: Evans, K. S., Andersen, E. C. Tags: Investigations Source Type: research

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 7, 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 7, 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 7, 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 7, 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 7, 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 7, 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 7, 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 7, 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 7, 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 7, 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 7, 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 d...
Source: G3: Genes Genomes Genetics - July 7, 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 7, 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 7, 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 7, 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

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 7, 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 7, 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 7, 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 7, 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 - June 1, 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 - June 1, 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 - June 1, 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 - June 1, 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 - June 1, 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 - June 1, 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 - June 1, 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 - June 1, 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 - June 1, 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 - June 1, 2020 Category: Genetics & Stem Cells Authors: Li, R., Vavrik, C., Danna, C. H. Tags: Investigations Source Type: research