G3 Reviewer Index 2019
(Source: G3: Genes Genomes Genetics)
Source: G3: Genes Genomes Genetics - December 3, 2019 Category: Genetics & Stem Cells Tags: Reviewer Index Source Type: research

Corrigendum
(Source: G3: Genes Genomes Genetics)
Source: G3: Genes Genomes Genetics - December 3, 2019 Category: Genetics & Stem Cells Tags: Corrigendum Source Type: research

Machine Learning Enables High-Throughput Phenotyping for Analyses of the Genetic Architecture of Bulliform Cell Patterning in Maize
This study is the first to combine machine learning approaches, transcriptomics, and genomics to study bulliform cell patterning, and the first to utilize natural variation to investigate the genetic architecture of this microscopic trait. In addition, this study provides insight toward the improvement of macroscopic traits such as drought resistance and plant architecture in an agronomically important crop plant. (Source: G3: Genes Genomes Genetics)
Source: G3: Genes Genomes Genetics - December 3, 2019 Category: Genetics & Stem Cells Authors: Qiao, P., Lin, M., Vasquez, M., Matschi, S., Chamness, J., Baseggio, M., Smith, L. G., Sabuncu, M. R., Gore, M. A., Scanlon, M. J. Tags: Investigations Source Type: research

Network-Based Functional Prediction Augments Genetic Association To Predict Candidate Genes for Histamine Hypersensitivity in Mice
Genetic mapping is a primary tool of genetics in model organisms; however, many quantitative trait loci (QTL) contain tens or hundreds of positional candidate genes. Prioritizing these genes for validation is often ad hoc and biased by previous findings. Here we present a technique for prioritizing positional candidates based on computationally inferred gene function. Our method uses machine learning with functional genomic networks, whose links encode functional associations among genes, to identify network-based signatures of functional association to a trait of interest. We demonstrate the method by functionally ranking...
Source: G3: Genes Genomes Genetics - December 3, 2019 Category: Genetics & Stem Cells Authors: Tyler, A. L., Raza, A., Krementsov, D. N., Case, L. K., Huang, R., Ma, R. Z., Blankenhorn, E. P., Teuscher, C., Mahoney, J. M. Tags: Investigations Source Type: research

Marker-Trait Associations for Enhancing Agronomic Performance, Disease Resistance, and Grain Quality in Synthetic and Bread Wheat Accessions in Western Siberia
Exploiting genetically diverse lines to identify genes for improving crop performance is needed to ensure global food security. A genome-wide association study (GWAS) was conducted using 46,268 SNP markers on a diverse panel of 143 hexaploid bread and synthetic wheat to identify potential genes/genomic regions controlling agronomic performance (yield and 26 yield-related traits), disease resistance, and grain quality traits. From phenotypic evaluation, we found large genetic variation among the 35 traits and recommended five lines having a high yield, better quality, and multiple disease resistance for direct use in a bree...
Source: G3: Genes Genomes Genetics - December 3, 2019 Category: Genetics & Stem Cells Authors: Bhatta, M., Shamanin, V., Shepelev, S., Baenziger, P. S., Pozherukova, V., Pototskaya, I., Morgounov, A. Tags: Investigations Source Type: research

Expression of Heat Shock Protein 70 Is Insufficient To Extend Drosophila melanogaster Longevity
This study used the UAS/GAL4 system to determine whether hsp70 is sufficient to affect the longevity and the resistance to thermal, oxidative or desiccation stresses of the whole organism. We observed that HSP70 expression in the nervous system or muscles has no effect on longevity or stress resistance but ubiquitous expression reduces the life span of males. We also observed that the down-regulation of hsp70 using RNAi did not affect longevity. (Source: G3: Genes Genomes Genetics)
Source: G3: Genes Genomes Genetics - December 3, 2019 Category: Genetics & Stem Cells Authors: Xiao, C., Hull, D., Qiu, S., Yeung, J., Zheng, J., Barwell, T., Robertson, R. M., Seroude, L. Tags: Investigations Source Type: research

Classification-Based Inference of Dynamical Models of Gene Regulatory Networks
We present FIGR (Fast Inference of Gene Regulation), a novel classification-based inference approach to determining gene circuit parameters. We demonstrate FIGR’s effectiveness on synthetic data generated from random gene circuits of up to 50 genes as well as experimental data from the gap gene system of Drosophila melanogaster, a benchmark for inferring dynamical GRN models. FIGR is faster than global non-linear optimization by a factor of 600 and its computational complexity scales much better with GRN size. On a practical level, FIGR can accurately infer the biologically realistic gap gene network in under a minut...
Source: G3: Genes Genomes Genetics - December 3, 2019 Category: Genetics & Stem Cells Authors: Fehr, D. A., Handzlik, J. E., Manu, , Loh, Y. L. Tags: Investigations Source Type: research

Assessing by Modeling the Consequences of Increased Recombination in Recurrent Selection of Oryza sativa and Brassica rapa
Meiotic recombination generates genetic diversity but in most species the number of crossovers per meiosis is limited. Previous modeling studies showed that increasing recombination can enhance response to selection. However, such studies did not assume a specific method of modifying recombination. Our objective was to test whether two methods used to increase recombination in plants could increase genetic gain in a population undergoing recurrent selection such as in genomic selection programs. The first method, in Oryza sativa, used a mutant of anti-crossover genes, increasing global recombination without affecting the r...
Source: G3: Genes Genomes Genetics - December 3, 2019 Category: Genetics & Stem Cells Authors: Tourrette, E., Bernardo, R., Falque, M., Martin, O. C. Tags: Investigations Source Type: research

Accurate Allele Frequencies from Ultra-low Coverage Pool-Seq Samples in Evolve-and-Resequence Experiments
Evolve-and-resequence (E+R) experiments leverage next-generation sequencing technology to track the allele frequency dynamics of populations as they evolve. While previous work has shown that adaptive alleles can be detected by comparing frequency trajectories from many replicate populations, this power comes at the expense of high-coverage (>100x) sequencing of many pooled samples, which can be cost-prohibitive. Here, we show that accurate estimates of allele frequencies can be achieved with very shallow sequencing depths (
Source: G3: Genes Genomes Genetics - December 3, 2019 Category: Genetics & Stem Cells Authors: Tilk, S., Bergland, A., Goodman, A., Schmidt, P., Petrov, D., Greenblum, S. Tags: Investigations Source Type: research

Loss of rps9 in Zebrafish Leads to p53-Dependent Anemia
Ribosome is a vital molecular machine for protein translation in the cell. Defects in several ribosomal proteins including RPS19, RPL11 and RPS14 have been observed in two types of anemia: Diamond Blackfan Anemia and 5q- syndrome. In zebrafish, deficiency of these ribosomal proteins shows similar anemic phenotype. It remains to be determined if any other ribosome proteins are similarly involved in regulating erythropoiesis. Here we generated mutations in zebrafish rps9, a rarely studied ribosomal protein gene, and investigated its function. Analysis of this mutant demonstrates that rps9 disruption leads to impairment of er...
Source: G3: Genes Genomes Genetics - December 3, 2019 Category: Genetics & Stem Cells Authors: Chen, C., Huang, H., Yan, R., Lin, S., Qin, W. Tags: Investigations Source Type: research

Ectopic Expression of Litsea cubeba LcMADS20 Modifies Silique Architecture
This study systematically analyzed the MADS-box genes in L. cubeba at the transcriptional level and showed that LcMADS20 plays important roles in the regulation of fruit architecture. (Source: G3: Genes Genomes Genetics)
Source: G3: Genes Genomes Genetics - December 3, 2019 Category: Genetics & Stem Cells Authors: Jiao, Y., Yin, H., Chen, Y., Gao, M., Wu, L., Wang, Y. Tags: Investigations Source Type: research

Transcriptome Characterization of Reverse Development in Turritopsis dohrnii (Hydrozoa, Cnidaria)
Medusae of Turritopsis dohrnii undergo reverse development in response to physical damage, adverse environmental conditions, or aging. Senescent, weakened or damaged medusae transform into a cluster of poorly differentiated cells (known as the cyst stage), which metamorphose back into a preceding life cycle stage, the polyp. During the metamorphosis, cell transdifferentiation occurs. The cyst represents the intermediate stage between a reverting medusa and a healthy polyp, during which cell transdifferentiation and tissue reorganization take place. Here we characterize and compare the transcriptomes of the polyp and newbor...
Source: G3: Genes Genomes Genetics - December 3, 2019 Category: Genetics & Stem Cells Authors: Matsumoto, Y., Piraino, S., Miglietta, M. P. Tags: Investigations Source Type: research

Selecting Closely-Linked SNPs Based on Local Epistatic Effects for Haplotype Construction Improves Power of Association Mapping
Genome-wide association studies (GWAS) have gained central importance for the identification of candidate loci underlying complex traits. Single nucleotide polymorphism (SNP) markers are mostly used as genetic variants for the analysis of genotype-phenotype associations in populations, but closely linked SNPs that are grouped into haplotypes are also exploited. The benefit of haplotype-based GWAS approaches vs. SNP-based approaches is still under debate because SNPs in high linkage disequilibrium provide redundant information. To overcome some constraints of the commonly-used haplotype-based GWAS in which only consecutive ...
Source: G3: Genes Genomes Genetics - December 3, 2019 Category: Genetics & Stem Cells Authors: Liu, F., Schmidt, R. H., Reif, J. C., Jiang, Y. Tags: Investigations Source Type: research

OsSPL10, a SBP-Box Gene, Plays a Dual Role in Salt Tolerance and Trichome Formation in Rice (Oryza sativa L.)
In this study, OsSPL10-knockout and OsSPL10-overexpression mutants were created to check the function of the gene. The knockout mutants exhibited enhanced salt tolerance and glabrous leaves and glumes as expected, while the overexpression mutants showed opposite phenotypes, in which both salt sensitivity and trichome density on leaf and glume were increased. These results clearly confirmed that OsSPL10 is SST, and suggested that OsSPL10 controls the initiation rather than the elongation of trichomes. In addition, expression analysis indicated that OsSPL10 was preferentially expressed in young panicle and stem, and protein ...
Source: G3: Genes Genomes Genetics - December 3, 2019 Category: Genetics & Stem Cells Authors: Lan, T., Zheng, Y., Su, Z., Yu, S., Song, H., Zheng, X., Lin, G., Wu, W. Tags: Investigations Source Type: research

Targeted Forward Genetics: Population-Scale Analyses of Allele Replacements Spanning Thousands of Base Pairs in Fission Yeast
Precise allele replacement (genome editing), without unwanted changes to the genome, provides a powerful tool to define the functions of DNA elements and encoded factors in their normal biological context. While CRISPR is now used extensively for gene targeting, its utility for precise allele replacement at population scale is limited because: (A) there is a strict requirement for a correctly positioned PAM motif to introduce recombinogenic dsDNA breaks (DSBs); (B) efficient replacements only occur very close to the DSBs; and (C) indels and off-target changes are frequently generated. Here we show, using a saturated mutati...
Source: G3: Genes Genomes Genetics - December 3, 2019 Category: Genetics & Stem Cells Authors: Storey, A. J., Wang, H.-P., Protacio, R. U., Davidson, M. K., Wahls, W. P. Tags: Investigations Source Type: research

rmtA-Dependent Transcriptome and Its Role in Secondary Metabolism, Environmental Stress, and Virulence in Aspergillus flavus
Aspergillus flavus colonizes numerous oil seed crops such as maize, peanuts, treenuts and cottonseed worldwide, contaminating them with aflatoxins and other harmful toxins. Previously our lab characterized the gene rmtA, which encodes an arginine methyltransferase in A. flavus, and demonstrated its role governing the expression of regulators in the aflatoxin gene cluster and subsequent synthesis of toxin. Furthermore, our studies revealed that rmtA also controls conidial and sclerotial development implicating it as an epigenetic regulator in A. flavus. To confirm this, we performed a RNA sequencing analysis to ascertain th...
Source: G3: Genes Genomes Genetics - December 3, 2019 Category: Genetics & Stem Cells Authors: Satterlee, T., Entwistle, S., Yin, Y., Cary, J. W., Lebar, M., Losada, L., Calvo, A. M. Tags: Investigations Source Type: research

Inference of Selection from Genetic Time Series Using Various Parametric Approximations to the Wright-Fisher Model
Detecting genomic regions under selection is an important objective of population genetics. Typical analyses for this goal are based on exploiting genetic diversity patterns in present time data but rapid advances in DNA sequencing have increased the availability of time series genomic data. A common approach to analyze such data is to model the temporal evolution of an allele frequency as a Markov chain. Based on this principle, several methods have been proposed to infer selection intensity. One of their differences lies in how they model the transition probabilities of the Markov chain. Using the Wright-Fisher model is ...
Source: G3: Genes Genomes Genetics - December 3, 2019 Category: Genetics & Stem Cells Authors: Paris, C., Servin, B., Boitard, S. Tags: Investigations Source Type: research

Investigating the Influence of Glycerol on the Utilization of Glucose in Yarrowia lipolytica Using RNA-Seq-Based Transcriptomics
This study provides an initial investigation on potentially novel carbon source regulation mechanisms in yeasts. (Source: G3: Genes Genomes Genetics)
Source: G3: Genes Genomes Genetics - December 3, 2019 Category: Genetics & Stem Cells Authors: Lubuta, P., Workman, M., Kerkhoven, E. J., Workman, C. T. Tags: Investigations Source Type: research

Genetic Architecture of Chilling Tolerance in Sorghum Dissected with a Nested Association Mapping Population
Dissecting the genetic architecture of stress tolerance in crops is critical to understand and improve adaptation. In temperate climates, early planting of chilling-tolerant varieties could provide longer growing seasons and drought escape, but chilling tolerance (75,000 data points from ~16,000 plots) in multi-environment field trials in Kansas under natural chilling stress (sown 30–45 days early) and normal growing conditions. Joint linkage mapping with early-planted field phenotypes revealed an oligogenic architecture, with 5–10 chilling tolerance loci explaining 20–41% of variation. Surprisingly, seve...
Source: G3: Genes Genomes Genetics - December 3, 2019 Category: Genetics & Stem Cells Authors: Marla, S. R., Burow, G., Chopra, R., Hayes, C., Olatoye, M. O., Felderhoff, T., Hu, Z., Raymundo, R., Perumal, R., Morris, G. P. Tags: Multiparental Populations Source Type: research

The Trithorax Group Factor ULTRAPETALA1 Regulates Developmental as Well as Biotic and Abiotic Stress Response Genes in Arabidopsis
In eukaryotes, Polycomb group (PcG) and trithorax group (trxG) factors oppositely regulate gene transcription during development through histone modifications, with PcG factors repressing and trxG factors activating the expression of their target genes. Although plant trxG factors regulate many developmental and physiological processes, their downstream targets are poorly characterized. Here we use transcriptomics to identify genome-wide targets of the Arabidopsis thaliana trxG factor ULTRAPETALA1 (ULT1) during vegetative and reproductive development and compare them with those of the PcG factor CURLY LEAF (CLF). We find t...
Source: G3: Genes Genomes Genetics - December 3, 2019 Category: Genetics & Stem Cells Authors: Tyler, L., Miller, M. J., Fletcher, J. C. Tags: Investigations Source Type: research

The Magnitude of Candida albicans Stress-Induced Genome Instability Results from an Interaction Between Ploidy and Antifungal Drugs
In this study, we compared the rates and types of genome perturbations in diploid and tetraploid C. albicans following exposure to two different classes of antifungal drugs; azoles and echinocandins. We measured mutations at three different scales: point mutation, loss-of-heterozygosity (LOH), and total DNA content for cells exposed to fluconazole and caspofungin. We found that caspofungin induced higher mutation rates than fluconazole, although this is likely an indirect consequence of stress-associated cell wall perturbations, rather than an inherent genotoxicity. Surprisingly, we found that antifungal drugs disproportio...
Source: G3: Genes Genomes Genetics - December 3, 2019 Category: Genetics & Stem Cells Authors: Avramovska, O., Hickman, M. A. Tags: Investigations Source Type: research

Identification of Genes Required for Apical Protein Trafficking in Drosophila Photoreceptor Cells
Drosophila melanogaster photoreceptor cells are highly polarized epithelial cells. Their apical membrane is further subdivided into the stalk membrane and the light-sensing rhabdomere. The photo-pigment Rhodopsin1 (Rh1) localizes to the rhabdomere, whereas the apical determinant Crumbs (Crb) is enriched at the stalk membrane. The proteoglycan Eyes shut (Eys) is secreted through the apical membrane into an inter-rhabdomeral space. Rh1, Crb, and Eys are essential for the development of photoreceptor cells, normal vision, and photoreceptor cell survival. Human orthologs of all three proteins have been linked to retinal degene...
Source: G3: Genes Genomes Genetics - December 3, 2019 Category: Genetics & Stem Cells Authors: Laffafian, A., Tepass, U. Tags: Investigations Source Type: research

Natural Genetic Variation Screen in Drosophila Identifies Wnt Signaling, Mitochondrial Metabolism, and Redox Homeostasis Genes as Modifiers of Apoptosis
In this study, we examine the impact of the natural genetic variation in the Drosophila Genetic Reference Panel (DGRP) on two models of apoptosis-induced retinal degeneration: overexpression of p53 or reaper (rpr). We identify a number of known apoptotic, neural, and developmental genes as candidate modifiers of degeneration. We also use Gene Set Enrichment Analysis (GSEA) to identify pathways that harbor genetic variation that impact these apoptosis models, including Wnt signaling, mitochondrial metabolism, and redox homeostasis. Finally, we demonstrate that many of these candidates have a functional effect on apoptosis a...
Source: G3: Genes Genomes Genetics - December 3, 2019 Category: Genetics & Stem Cells Authors: Palu, R. A. S., Ong, E., Stevens, K., Chung, S., Owings, K. G., Goodman, A. G., Chow, C. Y. Tags: Investigations Source Type: research

Efficiency of a Constrained Linear Genomic Selection Index To Predict the Net Genetic Merit in Plants
The constrained linear genomic selection index (CLGSI) is a linear combination of genomic estimated breeding values useful for predicting the net genetic merit, which in turn is a linear combination of true unobservable breeding values of the traits weighted by their respective economic values. The CLGSI is the most general genomic index and allows imposing constraints on the expected genetic gain per trait to make some traits change their mean values based on a predetermined level, while the rest of them remain without restrictions. In addition, it includes the unconstrained linear genomic index as a particular case. Usin...
Source: G3: Genes Genomes Genetics - December 3, 2019 Category: Genetics & Stem Cells Authors: Ceron-Rojas, J. J., Crossa, J. Tags: Genomic Prediction Source Type: research

Genomics Analysis of L-DOPA Exposure in Drosophila sechellia
In this study, we aim to identify new genes important for host specialization by profiling gene expression response to 3,4-dihydroxyphenylalanine (L-DOPA). Recent work found it to be highly abundant in M. citrifolia, critical for reproductive success of D. sechellia, and supplementation of diet with the downstream pathway product dopamine can influence toxin resistance phenotypes in related species. Here we used a combination of functional genetics and genomics techniques to identify new genes that are important for D. sechellia ecological adaptation to this new niche. We show that L-DOPA exposure can affect toxin resistan...
Source: G3: Genes Genomes Genetics - December 3, 2019 Category: Genetics & Stem Cells Authors: Lanno, S. M., Lam, I., Drum, Z., Linde, S. C., Gregory, S. M., Shimshak, S. J., Becker, M. V., Brew, K. E., Budhiraja, A., Carter, E. A., Chigweshe, L., Collins, K. P., Earley, T., Einstein, H. L., Fan, A. A., Goss, S. S., Hagen, E. R., Hutcheon, S. B., K Tags: Investigations Source Type: research

An Atlas of Transcription Factors Expressed in Male Pupal Terminalia of Drosophila melanogaster
During development, transcription factors and signaling molecules govern gene regulatory networks to direct the formation of unique morphologies. As changes in gene regulatory networks are often implicated in morphological evolution, mapping transcription factor landscapes is important, especially in tissues that undergo rapid evolutionary change. The terminalia (genital and anal structures) of Drosophila melanogaster and its close relatives exhibit dramatic changes in morphology between species. While previous studies have identified network components important for patterning the larval genital disc, the networks governi...
Source: G3: Genes Genomes Genetics - December 3, 2019 Category: Genetics & Stem Cells Authors: Vincent, B. J., Rice, G. R., Wong, G. M., Glassford, W. J., Downs, K. I., Shastay, J. L., Charles-Obi, K., Natarajan, M., Gogol, M., Zeitlinger, J., Rebeiz, M. Tags: Software and Data Resources Source Type: research

Regeneration Rosetta: An Interactive Web Application To Explore Regeneration-Associated Gene Expression and Chromatin Accessibility
Time-course high-throughput assays of gene expression and enhancer usage in zebrafish provide a valuable characterization of the dynamic mechanisms governing gene regulatory programs during CNS axon regeneration. To facilitate the exploration and functional interpretation of a set of fully-processed data on regeneration-associated temporal transcription networks, we have created an interactive web application called Regeneration Rosetta. Using either built-in or user-provided lists of genes in one of dozens of supported organisms, our web application facilitates the (1) visualization of clustered temporal expression trends...
Source: G3: Genes Genomes Genetics - December 3, 2019 Category: Genetics & Stem Cells Authors: Rau, A., Dhara, S. P., Udvadia, A. J., Auer, P. L. Tags: Software and Data Resources Source Type: research

The Genome Sequence of the Eastern Woodchuck (Marmota monax) - A Preclinical Animal Model for Chronic Hepatitis B
The Eastern woodchuck (Marmota monax) has been extensively used in research of chronic hepatitis B and liver cancer because its infection with the woodchuck hepatitis virus closely resembles a human hepatitis B virus infection. Development of novel immunotherapeutic approaches requires genetic information on immune pathway genes in this animal model. The woodchuck genome was assembled with a combination of high-coverage whole-genome shotgun sequencing of Illumina paired-end, mate-pair libraries and fosmid pool sequencing. The result is a 2.63 Gigabase (Gb) assembly with a contig N50 of 74.5 kilobases (kb), scaffold N50 of ...
Source: G3: Genes Genomes Genetics - December 3, 2019 Category: Genetics & Stem Cells Authors: Alioto, T. S., Cruz, F., Gomez-Garrido, J., Triyatni, M., Gut, M., Frias, L., Esteve-Codina, A., Menne, S., Kiialainen, A., Kumpesa, N., Birzele, F., Schmucki, R., Gut, I. G., Spleiss, O. Tags: Genome Report Source Type: research

The de Novo Reference Genome and Transcriptome Assemblies of the Wild Tomato Species Solanum chilense Highlights Birth and Death of NLR Genes Between Tomato Species
Wild tomato species, like Solanum chilense, are important germplasm resources for enhanced biotic and abiotic stress resistance in tomato breeding. S. chilense also serves as a model to study adaptation of plants to drought and the evolution of seed banks. The absence of a well-annotated reference genome in this compulsory outcrossing, very diverse species limits in-depth studies on the genes involved. We generated ~134 Gb of DNA and 157 Gb of RNA sequence data for S chilense, which yielded a draft genome with an estimated length of 914 Mb, encoding 25,885 high-confidence predicted gene models, which show homology to known...
Source: G3: Genes Genomes Genetics - December 3, 2019 Category: Genetics & Stem Cells Authors: Stam, R., Nosenko, T., Hörger, A. C., Stephan, W., Seidel, M., Kuhn, J. M. M., Haberer, G., Tellier, A. Tags: Genome Report Source Type: research

A Highly Contiguous Reference Genome for Northern Bobwhite (Colinus virginianus)
Northern bobwhites (Colinus virginianus) are small quails in the New World Quail family (Odontophoridae) and are one of the most phenotypically diverse avian species. Despite extensive research on bobwhite ecology, genomic studies investigating the evolution of phenotypic diversity in this species are lacking. Here, we present a new, highly contiguous assembly for bobwhites using tissue samples from a vouchered, wild, female bird collected in Louisiana. By performing a de novo assembly and scaffolding the assembly with Dovetail Chicago and HiC libraries and the HiRise pipeline, we produced an 866.8 Mb assembly including 1,...
Source: G3: Genes Genomes Genetics - December 3, 2019 Category: Genetics & Stem Cells Authors: Salter, J. F., Johnson, O., Stafford, N. J., Herrin, W. F., Schilling, D., Cedotal, C., Brumfield, R. T., Faircloth, B. C. Tags: Genome Report Source Type: research

Genome Assemblies of Two Rare Opportunistic Yeast Pathogens: Diutina rugosa (syn. Candida rugosa) and Trichomonascus ciferrii (syn. Candida ciferrii)
Infections caused by opportunistic yeast pathogens have increased over the last years. These infections can be originated by a large number of diverse yeast species of varying incidence, and with distinct clinically relevant phenotypic traits, such as different susceptibility profiles to antifungal drugs, which challenge diagnosis and treatment. Diutina rugosa (syn. Candida rugosa) and Trichomonascus ciferrii (syn. Candida ciferrii) are two opportunistic rare yeast pathogens, which low incidence (
Source: G3: Genes Genomes Genetics - December 3, 2019 Category: Genetics & Stem Cells Authors: Mixao, V., Saus, E., Hansen, A. P., Lass-Florl, C., Gabaldon, T. Tags: Genome Report Source Type: research

Genome of Spea multiplicata, a Rapidly Developing, Phenotypically Plastic, and Desert-Adapted Spadefoot Toad
Frogs and toads (anurans) are widely used to study many biological processes. Yet, few anuran genomes have been sequenced, limiting research on these organisms. Here, we produce a draft genome for the Mexican spadefoot toad, Spea multiplicata, which is a member of an unsequenced anuran clade. Atypically for amphibians, spadefoots inhabit deserts. Consequently, they possess many unique adaptations, including rapid growth and development, prolonged dormancy, phenotypic (developmental) plasticity, and adaptive, interspecies hybridization. We assembled and annotated a 1.07 Gb Sp. multiplicata genome containing 19,639 genes. By...
Source: G3: Genes Genomes Genetics - December 3, 2019 Category: Genetics & Stem Cells Authors: Seidl, F., Levis, N. A., Schell, R., Pfennig, D. W., Pfennig, K. S., Ehrenreich, I. M. Tags: Genome Report Source Type: research

Corrigendum
(Source: G3: Genes Genomes Genetics)
Source: G3: Genes Genomes Genetics - November 5, 2019 Category: Genetics & Stem Cells Tags: Corrigendum Source Type: research

A Mouse Mutation That Dysregulates Neighboring Galnt17 and Auts2 Genes Is Associated with Phenotypes Related to the Human AUTS2 Syndrome
AUTS2 was originally discovered as the gene disrupted by a translocation in human twins with Autism spectrum disorder, intellectual disability, and epilepsy. Since that initial finding, AUTS2-linked mutations and variants have been associated with a very broad array of neuropsychiatric disorders, sugg esting that AUTS2 is required for fundamental steps of neurodevelopment. However, genotype-phenotype correlations in this region are complicated, because most mutations could also involve neighboring genes. Of particular interest is the nearest downstream neighbor of AUTS2, GALNT17, which encodes a brain-expressed N-acetylgal...
Source: G3: Genes Genomes Genetics - November 5, 2019 Category: Genetics & Stem Cells Authors: Weisner, P. A., Chen, C.-Y., Sun, Y., Yoo, J., Kao, W.-C., Zhang, H., Baltz, E. T., Troy, J. M., Stubbs, L. Tags: Investigations Source Type: research

Unpredictable Effects of the Genetic Background of Transgenic Lines in Physiological Quantitative Traits
Physiology, fitness and disease phenotypes are complex traits exhibiting continuous variation in natural populations. To understand complex trait gene functions transgenic lines of undefined genetic background are often combined to assess quantitative phenotypes ignoring the impact of genetic polymorphisms. Here, we used inbred wild-type strains of the Drosophila Genetics Reference Panel to assess the phenotypic variation of six physiological and fitness traits, namely, female fecundity, survival and intestinal mitosis upon oral infection, defecation rate and fecal pH upon oral infection, and terminal tracheal cell branchi...
Source: G3: Genes Genomes Genetics - November 5, 2019 Category: Genetics & Stem Cells Authors: Evangelou, A., Ignatiou, A., Antoniou, C., Kalanidou, S., Chatzimatthaiou, S., Shianiou, G., Ellina, S., Athanasiou, R., Panagi, M., Apidianakis, Y., Pitsouli, C. Tags: Investigations Source Type: research

Mapping of the Sex Determining Region on Linkage Group 12 of Guppy (Poecilia reticulata)
The objectives of this study were mapping of the sex-determining (SD) region on linkage group 12 of guppy, and identification of a sex specific marker. We generated eight polymorphic microsatellite markers distributed along the distal 5.4 Mbp sequence of the previously identified SD region on linkage group (LG) 12. The markers were tested for association with sex in 156 individuals of the Red Blonde and Flame strains, and 126 progeny of four full-sibs Red Blonde families. A male-specific allele was found for microsatellite gu1066 at position of 25.3 Mbp on LG12 for both strains, and gu832 at position 24.4 Mbp for the Flame...
Source: G3: Genes Genomes Genetics - November 5, 2019 Category: Genetics & Stem Cells Authors: Dor, L., Shirak, A., Kohn, Y. Y., Gur, T., Weller, J. I., Zilberg, D., Seroussi, E., Ron, M. Tags: Genetics of Sex Source Type: research

Efficient Estimation of Marker Effects in Plant Breeding
This study introduces two methods designed to couple high prediction accuracy with efficient computational performance: 1) a non-MCMC method to estimate marker effects with a Laplace prior; and 2) an iterative framework that allows solving whole-genome regression within mixed models with replicated observations in a single-stage. The investigation provides insights on predictive ability and marker effect estimates. Various genomic prediction techniques are compared based on cross-validation, assessing predictions across and within family. Properties of quantitative trait loci detection and single-stage method were evaluate...
Source: G3: Genes Genomes Genetics - November 5, 2019 Category: Genetics & Stem Cells Authors: Xavier, A. Tags: Genomic Prediction Source Type: research

Genome-Wide Analysis of Cell Cycle-Regulating Genes in the Symbiotic Dinoflagellate Breviolum minutum
A delicate relationship exists between reef-building corals and their photosynthetic endosymbionts. Unfortunately, this relationship can be disrupted, with corals expelling these algae when temperatures rise even marginally above the average summer maximum. Interestingly, several studies indicate that failure of corals to regulate symbiont cell divisions at high temperatures may underlie this disruption; increased proliferation of symbionts may stress host cells by over-production of reactive oxygen species or by disrupting the flow of nutrients. This needs to be further investigated, so to begin deciphering the molecular ...
Source: G3: Genes Genomes Genetics - November 5, 2019 Category: Genetics & Stem Cells Authors: Cato, M. L., Jester, H. D., Lavertu, A., Lyman, A., Tallent, L. M., Mitchell, G. C. Tags: Investigations Source Type: research

Single-Step Genome-Wide Association Study for Resistance to Piscirickettsia salmonis in Rainbow Trout (Oncorhynchus mykiss)
The objectives of this study were to i) identify the genomic regions associated with resistance to P. salmonis; and ii) identify candidate genes associated with the trait in rainbow trout. We experimentally challenged 2,130 rainbow trout with P. salmonis and genotyped them with a 57 K single nucleotide polymorphism (SNP) array. Resistance to P. salmonis was defined as time to death (TD) and as binary survival (BS). Significant heritabilities were estimated for TD and BS (0.48 ± 0.04 and 0.34 ± 0.04, respectively). A total of 2,047 fish and 26,068 SNPs passed quality control for samples and genotypes. Using a ...
Source: G3: Genes Genomes Genetics - November 5, 2019 Category: Genetics & Stem Cells Authors: Barria, A., Marin-Nahuelpi, R., Caceres, P., Lopez, M. E., Bassini, L. N., Lhorente, J. P., Yanez, J. M. Tags: Investigations Source Type: research

Visualization and Quantification of Transposon Activity in Caenorhabditis elegans RNAi Pathway Mutants
RNA silencing pathways play critical roles in maintaining quiescence of transposons in germ cells to promote genome integrity. However the precise mechanism by which different types of transposons are recognized by these pathways is not fully understood. Furthermore, the location in the germline where this transposition occurs after disruption of transposon silencing was previously unknown. Here we utilize the spatial and temporal organization of the Caenorhabditis elegans germline to demonstrate that transposition of DNA transposons in RNA silencing pathway mutants occur in all stages of adult germ cells. We further demon...
Source: G3: Genes Genomes Genetics - November 5, 2019 Category: Genetics & Stem Cells Authors: Wallis, D. C., Nguyen, D. A. H., Uebel, C. J., Phillips, C. M. Tags: Investigations Source Type: research

Limits to Genomic Divergence Under Sexually Antagonistic Selection
Since the autosomal genome is shared between the sexes, sex-specific fitness optima present an evolutionary challenge. While sexually antagonistic selection might favor different alleles within females and males, segregation randomly reassorts alleles at autosomal loci between sexes each generation. This process of homogenization during transmission thus prevents between-sex allelic divergence generated by sexually antagonistic selection from accumulating across multiple generations. However, recent empirical studies have reported high male-female FST statistics. Here, we use a population genetic model to evaluate whether ...
Source: G3: Genes Genomes Genetics - November 5, 2019 Category: Genetics & Stem Cells Authors: Kasimatis, K. R., Ralph, P. L., Phillips, P. C. Tags: Investigations Source Type: research

Genetic Dissection Reveals the Role of Ash1 Domains in Counteracting Polycomb Repression
Antagonistic functions of Polycomb and Trithorax proteins are essential for proper development of all metazoans. While the Polycomb proteins maintain the repressed state of many key developmental genes, the Trithorax proteins ensure that these genes stay active in cells where they have to be expressed. Ash1 is the Trithorax protein that was proposed to counteract Polycomb repression by methylating lysine 36 of histone H3. However, it was recently shown that genetic replacement of Drosophila histone H3 with the variant that carried Arginine instead of Lysine at position 36 did not impair the ability of Ash1 to counteract Po...
Source: G3: Genes Genomes Genetics - November 5, 2019 Category: Genetics & Stem Cells Authors: Dorafshan, E., Kahn, T. G., Glotov, A., Savitsky, M., Schwartz, Y. B. Tags: Investigations Source Type: research

Expression-Based Cell Lineage Analysis in Drosophila Through a Course-Based Research Experience for Early Undergraduates
A variety of genetic techniques have been devised to determine cell lineage relationships during tissue development. Some of these systems monitor cell lineages spatially and/or temporally without regard to gene expression by the cells, whereas others correlate gene expression with the lineage under study. The GAL4 Technique for Real-time and Clonal Expression (G-TRACE) system allows for rapid, fluorescent protein-based visualization of both current and past GAL4 expression patterns and is therefore amenable to genome-wide expression-based lineage screens. Here we describe the results from such a screen, performed by under...
Source: G3: Genes Genomes Genetics - November 5, 2019 Category: Genetics & Stem Cells Authors: Olson, J. M., Evans, C. J., Ngo, K. T., Kim, H. J., Nguyen, J. D., Gurley, K. G. H., Ta, T., Patel, V., Han, L., Truong-N, K. T., Liang, L., Chu, M. K., Lam, H., Ahn, H. G., Banerjee, A. K., Choi, I. Y., Kelley, R. G., Moridzadeh, N., Khan, A. M., Khan, O Tags: Investigations Source Type: research

Transgenic Analyses in Drosophila Reveal That mCORL1 Is Functionally Distinct from mCORL2 and dCORL
Uncovering how new members of multigene families acquire new functions is an important topic in evolutionary and developmental genetics. CORL proteins (SKOR in mice, Fussel in humans and fussel in Flybase) are a family of CNS specific proteins related to mammalian Sno/Ski oncogenes. Drosophila CORL (dCORL) participates in TGF-β and insulin signaling during development and in adult homeostasis but roles for the two mouse CORL proteins (mCORL) are essentially unknown. A series of studies were conducted to test the hypothesis based on previous results that mCORL1 is more similar to dCORL than mCORL2. Neither an updated a...
Source: G3: Genes Genomes Genetics - November 5, 2019 Category: Genetics & Stem Cells Authors: Stinchfield, M. J., Miyazawa, K., Newfeld, S. J. Tags: Investigations Source Type: research

Chromosome Preference During Homologous Recombination Repair of DNA Double-Strand Breaks in Drosophila melanogaster
DNA double-strand breaks (DSBs) are especially toxic DNA lesions that, if left unrepaired, can lead to wide-ranging genomic instability. Of the pathways available to repair DSBs, the most accurate is homologous recombination (HR), where a homologous sequence is used as a donor template to restore genetic information at the break site. While much of the biochemical aspects of HR repair have been characterized, how the repair machinery locates and discriminates between potential homologous donor templates throughout the genome remains elusive. We use Drosophila melanogaster to investigate whether there is a preference betwee...
Source: G3: Genes Genomes Genetics - November 5, 2019 Category: Genetics & Stem Cells Authors: Fernandez, J., Bloomer, H., Kellam, N., LaRocque, J. R. Tags: Investigations Source Type: research

Molecular Profiling of the Drosophila Antenna Reveals Conserved Genes Underlying Olfaction in Insects
Repellent odors are widely used to prevent insect-borne diseases, making it imperative to identify the conserved molecular underpinnings of their olfactory systems. Currently, little is known about the molecules supporting odor signaling beyond the odor receptors themselves. Most known molecules function in one of two classes of olfactory sensilla, single-walled or double-walled, which have differing morphology and odor response profiles. Here, we took two approaches to discover novel genes that contribute to insect olfaction in the periphery. We transcriptionally profiled Drosophila melanogaster amos mutants that lack tri...
Source: G3: Genes Genomes Genetics - November 5, 2019 Category: Genetics & Stem Cells Authors: Mohapatra, P., Menuz, K. Tags: Investigations Source Type: research

Comparison and Characterization of Mutations Induced by Gamma-Ray and Carbon-Ion Irradiation in Rice (Oryza sativa L.) Using Whole-Genome Resequencing
In this study, we characterized mutations induced by gamma rays and carbon(C)-ion beams in rice (Oryza sativa L.) mutant lines at M5 generation using whole-genome resequencing. On average, 57.0 single base substitutions (SBS), 17.7 deletions, and 5.9 insertions were detected in each gamma-ray-irradiated mutant, whereas 43.7 single SBS, 13.6 deletions, and 5.3 insertions were detected in each C-ion-irradiated mutant. The structural variation (SV) analysis detected 2.0 SVs (including large deletions or insertions, inversions, duplications, and reciprocal translocations) on average in each C-ion-irradiated mutant, while 0.6 S...
Source: G3: Genes Genomes Genetics - November 5, 2019 Category: Genetics & Stem Cells Authors: Li, F., Shimizu, A., Nishio, T., Tsutsumi, N., Kato, H. Tags: Investigations Source Type: research

Pitfalls and Remedies for Cross Validation with Multi-trait Genomic Prediction Methods
Incorporating measurements on correlated traits into genomic prediction models can increase prediction accuracy and selection gain. However, multi-trait genomic prediction models are complex and prone to overfitting which may result in a loss of prediction accuracy relative to single-trait genomic prediction. Cross-validation is considered the gold standard method for selecting and tuning models for genomic prediction in both plant and animal breeding. When used appropriately, cross-validation gives an accurate estimate of the prediction accuracy of a genomic prediction model, and can effectively choose among disparate mod...
Source: G3: Genes Genomes Genetics - November 5, 2019 Category: Genetics & Stem Cells Authors: Runcie, D., Cheng, H. Tags: Genomic Prediction Source Type: research

Three Quantitative Trait Loci Explain More than 60% of Variation for Chill Coma Recovery Time in a Natural Population of Drosophila ananassae
Ectothermic species such as insects are particularly vulnerable to climatic fluctuations. Nevertheless, many insects that evolved and diversified in the tropics have successfully colonized temperate regions all over the globe. To shed light on the genetic basis of cold tolerance in such species, we conducted a quantitative trait locus (QTL) mapping experiment for chill coma recovery time (CCRT) in Drosophila ananassae, a cosmopolitan species that has expanded its range from tropical to temperate regions. We created a mapping population of recombinant inbred advanced intercross lines (RIAILs) from two founder strains with d...
Source: G3: Genes Genomes Genetics - November 5, 2019 Category: Genetics & Stem Cells Authors: Königer, A., Arif, S., Grath, S. Tags: Investigations Source Type: research

Activity-Dependent Regulation of the Proapoptotic BH3-Only Gene egl-1 in a Living Neuron Pair in Caenorhabditis elegans
The BH3-only family of proteins is key for initiating apoptosis in a variety of contexts, and may also contribute to non-apoptotic cellular processes. Historically, the nematode Caenorhabditis elegans has provided a powerful system for studying and identifying conserved regulators of BH3-only proteins. In C. elegans, the BH3-only protein egl-1 is expressed during development to cell-autonomously trigger most developmental cell deaths. Here we provide evidence that egl-1 is also transcribed after development in the sensory neuron pair URX without inducing apoptosis. We used genetic screening and epistasis analysis to determ...
Source: G3: Genes Genomes Genetics - November 5, 2019 Category: Genetics & Stem Cells Authors: Cohn, J., Dwivedi, V., Valperga, G., Zarate, N., de Bono, M., Horvitz, H. R., Pierce, J. T. Tags: Investigations Source Type: research