An Essential Regulatory System Originating from Polygenic Transcriptional Rewiring of PhoP-PhoQ of Xanthomonas campestris [Genome and Systems Biology]
How essential, regulatory genes originate and evolve is intriguing because mutations of these genes not only lead to lethality in organisms, but also have pleiotropic effects since they control the expression of multiple downstream genes. Therefore, the evolution of essential, regulatory genes is not only determined by genetic variations of their own sequences, but also by the biological function of downstream genes and molecular mechanisms of regulation. To understand the origin of essential, regulatory genes, experimental dissection of the complete regulatory cascade is needed. Here, we provide genetic evidences to revea...
Source: Genetics - August 4, 2017 Category: Genetics & Stem Cells Authors: Peng, B.-Y., Pan, Y., Li, R.-J., Wei, J.-W., Liang, F., Wang, L., Wang, F.-F., Qian, W. Tags: Genome and Systems Biology Source Type: research
Causal Genetic Variation Underlying Metabolome Differences [Genetics of Complex Traits]
An ongoing challenge in biology is to predict the phenotypes of individuals from their genotypes. Genetic variants that cause disease often change an individual’s total metabolite profile, or metabolome. In light of our extensive knowledge of metabolic pathways, genetic variants that alter the metabolome may help predict novel phenotypes. To link genetic variants to changes in the metabolome, we studied natural variation in the yeast Saccharomyces cerevisiae. We used an untargeted mass spectrometry method to identify dozens of metabolite Quantitative Trait Loci (mQTL), genomic regions containing genetic variation tha...
Source: Genetics - August 4, 2017 Category: Genetics & Stem Cells Authors: Swain-Lenz, D., Nikolskiy, I., Cheng, J., Sudarsanam, P., Nayler, D., Staller, M. V., Cohen, B. A. Tags: Genetics of Complex Traits Source Type: research
Heritable Micro-environmental Variance Covaries with Fitness in an Outbred Population of Drosophila serrata [Genetics of Complex Traits]
The genetic basis of stochastic variation within a defined environment, and the consequences of such micro-environmental variance for fitness are poorly understood. Using a multigenerational breeding design in Drosophila serrata, we demonstrated that the micro-environmental variance in a set of morphological wing traits in a randomly mating population had significant additive genetic variance in most single wing traits. Although heritability was generally low (<1%), coefficients of additive genetic variance were of a magnitude typical of other morphological traits, indicating that the micro-environmental variance is an ...
Source: Genetics - August 4, 2017 Category: Genetics & Stem Cells Authors: Sztepanacz, J. L., McGuigan, K., Blows, M. W. Tags: Genetics of Complex Traits Source Type: research
Networks Underpinning Symbiosis Revealed Through Cross-Species eQTL Mapping [Genetics of Complex Traits]
Organisms engage in extensive cross-species molecular dialog, yet the underlying molecular actors are known for only a few interactions. Many techniques have been designed to uncover genes involved in signaling between organisms. Typically, these focus on only one of the partners. We developed an expression quantitative trait locus (eQTL) mapping-based approach to identify cause-and-effect relationships between genes from two partners engaged in an interspecific interaction. We demonstrated the approach by assaying expression of 98 isogenic plants (Medicago truncatula), each inoculated with a genetically distinct line of t...
Source: Genetics - August 4, 2017 Category: Genetics & Stem Cells Authors: Guo, Y., Fudali, S., Gimeno, J., DiGennaro, P., Chang, S., Williamson, V. M., Bird, D. M., Nielsen, D. M. Tags: Genetics of Complex Traits Source Type: research
Complex Coding and Regulatory Polymorphisms in a Restriction Factor Determine the Susceptibility of Drosophila to Viral Infection [Population and Evolutionary Genetics]
It is common to find that major-effect genes are an important cause of variation in susceptibility to infection. Here we have characterized natural variation in a gene called pastrel that explains over half of the genetic variance in susceptibility to the Drosophila C virus (DCV) in populations of Drosophila melanogaster. We found extensive allelic heterogeneity, with a sample of seven alleles of pastrel from around the world conferring four phenotypically distinct levels of resistance. By modifying candidate SNPs in transgenic flies, we show that the largest effect is caused by an amino acid polymorphism that arose when a...
Source: Genetics - August 4, 2017 Category: Genetics & Stem Cells Authors: Cao, C., Cogni, R., Barbier, V., Jiggins, F. M. Tags: Population and Evolutionary Genetics Source Type: research
Discovering Complete Quasispecies in Bacterial Genomes [Population and Evolutionary Genetics]
Mobile genetic elements can be found in almost all genomes. Possibly the most common nonautonomous mobile genetic elements in bacteria are repetitive extragenic palindromic doublets forming hairpins (REPINs) that can occur hundreds of times within a genome. The sum of all REPINs in a genome can be viewed as an evolving population because REPINs replicate and mutate. In contrast to most other biological populations, we know the exact composition of the REPIN population and the sequence of each member of the population. Here, we model the evolution of REPINs as quasispecies. We fit our quasispecies model to 10 different REPI...
Source: Genetics - August 4, 2017 Category: Genetics & Stem Cells Authors: Bertels, F., Gokhale, C. S., Traulsen, A. Tags: Population and Evolutionary Genetics Source Type: research
Cis- and Trans-regulatory Effects on Gene Expression in a Natural Population of Drosophila melanogaster [Population and Evolutionary Genetics]
Cis- and trans-regulatory mutations are important contributors to transcriptome evolution. Quantifying their relative contributions to intraspecific variation in gene expression is essential for understanding the population genetic processes that underlie evolutionary changes in gene expression. Here, we have examined this issue by quantifying genome-wide, allele-specific expression (ASE) variation using a crossing scheme that produces F1 hybrids between 18 different Drosophila melanogaster strains sampled from the Drosophila Genetic Reference Panel and a reference strain from another population. Head and body samples from...
Source: Genetics - August 4, 2017 Category: Genetics & Stem Cells Authors: Osada, N., Miyagi, R., Takahashi, A. Tags: Population and Evolutionary Genetics Source Type: research
Rapid Evolution of Ovarian-Biased Genes in the Yellow Fever Mosquito (Aedes aegypti) [Population and Evolutionary Genetics]
Males and females exhibit highly dimorphic phenotypes, particularly in their gonads, which is believed to be driven largely by differential gene expression. Typically, the protein sequences of genes upregulated in males, or male-biased genes, evolve rapidly as compared to female-biased and unbiased genes. To date, the specific study of gonad-biased genes remains uncommon in metazoans. Here, we identified and studied a total of 2927, 2013, and 4449 coding sequences (CDS) with ovary-biased, testis-biased, and unbiased expression, respectively, in the yellow fever mosquito Aedes aegypti. The results showed that ovary-biased a...
Source: Genetics - August 4, 2017 Category: Genetics & Stem Cells Authors: Whittle, C. A., Extavour, C. G. Tags: Population and Evolutionary Genetics Source Type: research
Distributions of Mutational Effects and the Estimation of Directional Selection in Divergent Lineages of Arabidopsis thaliana [Population and Evolutionary Genetics]
Mutations are crucial to evolution, providing the ultimate source of variation on which natural selection acts. Due to their key role, the distribution of mutational effects on quantitative traits is a key component to any inference regarding historical selection on phenotypic traits. In this paper, we expand on a previously developed test for selection that could be conducted assuming a Gaussian mutation effect distribution by developing approaches to also incorporate any of a family of heavy-tailed Laplace distributions of mutational effects. We apply the test to detect directional natural selection on five traits along ...
Source: Genetics - August 4, 2017 Category: Genetics & Stem Cells Authors: Park, B., Rutter, M. T., Fenster, C. B., Symonds, V. V., Ungerer, M. C., Townsend, J. P. Tags: Population and Evolutionary Genetics Source Type: research
A Unified Characterization of Population Structure and Relatedness [Population and Evolutionary Genetics]
Many population genetic activities, ranging from evolutionary studies to association mapping, to forensic identification, rely on appropriate estimates of population structure or relatedness. All applications require recognition that quantities with an underlying meaning of allelic dependence are not defined in an absolute sense, but instead are made "relative to" some set of alleles other than the target set. The 1984 Weir and Cockerham $${F}_{\mathrm{ST}}$$ estimate made explicit that the reference set of alleles was across populations, whereas standard kinship estimates do not make the reference explicit. Weir and Cocke...
Source: Genetics - August 4, 2017 Category: Genetics & Stem Cells Authors: Weir, B. S., Goudet, J. Tags: Population and Evolutionary Genetics Source Type: research
Caenorhabditis elegans CES-1 Snail Represses pig-1 MELK Expression To Control Asymmetric Cell Division [Developmental and Behavioral Genetics]
Snail-like transcription factors affect stem cell function through mechanisms that are incompletely understood. In the Caenorhabditis elegans neurosecretory motor neuron (NSM) neuroblast lineage, CES-1 Snail coordinates cell cycle progression and cell polarity to ensure the asymmetric division of the NSM neuroblast and the generation of two daughter cells of different sizes and fates. We have previously shown that CES-1 Snail controls cell cycle progression by repressing the expression of cdc-25.2 CDC25. However, the mechanism through which CES-1 Snail affects cell polarity has been elusive. Here, we systematically searche...
Source: Genetics - August 4, 2017 Category: Genetics & Stem Cells Authors: Wei, H., Yan, B., Gagneur, J., Conradt, B. Tags: Developmental and Behavioral Genetics Source Type: research
The Exon Junction Complex and Srp54 Contribute to Hedgehog Signaling via ci RNA Splicing in Drosophila melanogaster [Developmental and Behavioral Genetics]
Hedgehog (Hh) regulates the Cubitus interruptus (Ci) transcription factor in Drosophila melanogaster by activating full-length Ci-155 and blocking processing to the Ci-75 repressor. However, the interplay between the regulation of Ci-155 levels and activity, as well as processing-independent mechanisms that affect Ci-155 levels, have not been explored extensively. Here, we identified Mago Nashi (Mago) and Y14 core Exon Junction Complex (EJC) proteins, as well as the Srp54 splicing factor, as modifiers of Hh pathway activity under sensitized conditions. Mago inhibition reduced Hh pathway activity by altering the splicing pa...
Source: Genetics - August 4, 2017 Category: Genetics & Stem Cells Authors: Garcia-Garcia, E., Little, J. C., Kalderon, D. Tags: Developmental and Behavioral Genetics Source Type: research
The Combined Action of Duplicated Boron Transporters Is Required for Maize Growth in Boron-Deficient Conditions [Developmental and Behavioral Genetics]
The micronutrient boron is essential in maintaining the structure of plant cell walls and is critical for high yields in crop species. Boron can move into plants by diffusion or by active and facilitated transport mechanisms. We recently showed that mutations in the maize boron efflux transporter ROTTEN EAR (RTE) cause severe developmental defects and sterility. RTE is part of a small gene family containing five additional members (RTE2–RTE6) that show tissue-specific expression. The close paralogous gene RTE2 encodes a protein with 95% amino acid identity with RTE and is similarly expressed in shoot and root cells s...
Source: Genetics - August 4, 2017 Category: Genetics & Stem Cells Authors: Chatterjee, M., Liu, Q., Menello, C., Galli, M., Gallavotti, A. Tags: Developmental and Behavioral Genetics Source Type: research
LIN-41 and OMA Ribonucleoprotein Complexes Mediate a Translational Repression-to-Activation Switch Controlling Oocyte Meiotic Maturation and the Oocyte-to-Embryo Transition in Caenorhabditis elegans [Developmental and Behavioral Genetics]
This study defines a translational repression-to-activation switch as a key element of cytoplasmic maturation. (Source: Genetics)
Source: Genetics - August 4, 2017 Category: Genetics & Stem Cells Authors: Tsukamoto, T., Gearhart, M. D., Spike, C. A., Huelgas-Morales, G., Mews, M., Boag, P. R., Beilharz, T. H., Greenstein, D. Tags: Developmental and Behavioral Genetics Source Type: research
Canalization by Selection of de Novo Induced Mutations [Developmental and Behavioral Genetics]
One of the most fascinating scientific problems, and a subject of intense debate, is that of the mechanisms of biological evolution. In this context, Waddington elaborated the concepts of "canalization and assimilation" to explain how an apparently somatic variant induced by stress could become heritable through the germline in Drosophila. He resolved this seemingly Lamarckian phenomenon by positing the existence of cryptic mutations that can be expressed and selected under stress. To investigate the relevance of such mechanisms, we performed experiments following the Waddington procedure, then isolated and fixed three phe...
Source: Genetics - August 4, 2017 Category: Genetics & Stem Cells Authors: Fanti, L., Piacentini, L., Cappucci, U., Casale, A. M., Pimpinelli, S. Tags: Developmental and Behavioral Genetics Source Type: research
