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G3: Genes—Genomes—Genetics

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https://www.readbyqxmd.com/read/28801508/intricate-and-cell-type-specific-populations-of-endogenous-circular-dna-eccdna-in-caenorhabditis-elegans-and-homo-sapiens
#1
Massa J Shoura, Idan Gabdank, Loren Hansen, Jason Merker, Jason Gotlib, Stephen D Levene, Andrew Z Fire
Investigations aimed at defining the 3-D configuration of eukaryotic chromosomes have consistently encountered an endogenous population of chromosome-derived circular genomic DNA, referred to as extrachromosomal circular DNA (eccDNA). While the production, distribution, and activities of eccDNAs remain understudied, eccDNA formation from specific regions of the linear genome has profound consequences on the regulatory and coding capabilities for these regions. Here, we define eccDNA distributions in C. elegans and in three human cell types, utilizing a set of DNA-topology dependent approaches for enrichment and characterization...
August 11, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28794063/the-glyphosate-based-herbicide-roundup%C3%A2-does-not-elevate-genome-wide-mutagenesis-of-escherichia-coli
#2
Clayton Tincher, Hongan Long, Megan G Behringer, Noah Walker, Michael Lynch
Mutations induced by pollutants may promote pathogen evolution for example by accelerating mutations conferring antibiotic resistance. Generally, evaluating the genome-wide mutagenic effects of long-term sublethal pollutant exposure at single-nucleotide resolution is extremely difficult. To overcome this technical barrier, we use the mutation accumulation/whole genome sequencing (MA/WGS) method as a mutagenicity test, to quantitatively evaluate genome-wide mutagenesis of Escherichia coli after long-term exposure to a wide gradient of the glyphosate-based herbicide (GBH) Roundup® Concentrate Plus...
August 9, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28794062/high-quality-de-novo-genome-assembly-of-the-dekkera-bruxellensis-yeast-isolate-using-nanopore-minion-sequencing
#3
Téo Fournier, Jean-Sébastien Gounot, Kelle Freel, Corinne Cruaud, Arnaud Lemainque, Jean-Marc Aury, Patrick Wincker, Joseph Schacherer, Anne Friedrich
Genetic variation in natural populations represents the raw material for phenotypic diversity. Species-wide characterization of genetic variants is crucial to have a deeper insight into the genotype-phenotype relationship. With the advent of new sequencing strategies and more recently the release of long-read sequencing platforms, it is now possible to explore the genetic diversity of any non-model organisms, representing a fundamental resource for biological research. In the frame of population genomic surveys, a first step is to obtain the complete sequence and high quality assembly of a reference genome...
August 9, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28790145/inter-chromosomal-transfer-of-immune-regulation-during-infection-of-barley-with-the-powdery-mildew-pathogen
#4
Priyanka Surana, Ruo Xu, Gregory Fuerst, Antony Ve Chapman, Dan Nettleton, Roger P Wise
Powdery mildew pathogens colonize over 9,500 plant species, causing critical yield loss. The Ascomycete fungus, Blumeria graminis f. sp. hordei (Bgh), causes powdery mildew disease in barley (Hordeum vulgare L.). Successful infection begins with penetration of host epidermal cells, culminating in haustorial feeding structures, facilitating delivery of fungal effectors to the plant and exchange of nutrients from host to pathogen. We used expression Quantitative Trait Locus (eQTL) analysis to dissect the temporal control of immunity-associated gene expression in a doubled haploid barley population challenged with Bgh Two highly significant regions possessing trans eQTL were identified near the telomeric ends of chromosomes 2HL and 1HS...
August 8, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28768689/accelerating-wright-fisher-forward-simulations-on-the-graphics-processing-unit
#5
David S Lawrie
Forward Wright-Fisher simulations are powerful in their ability to model complex demography and selection scenarios, but suffer from slow execution on the CPU, thus limiting their usefulness. The single-locus Wright-Fisher forward algorithm is, however, exceedingly parallelizable, with many steps which are so-called embarrassingly parallel, consisting of a vast number of individual computations that are all independent of each other and thus capable of being performed concurrently. The rise of modern Graphics Processing Units (GPUs) and programming languages designed to leverage the inherent parallel nature of these processors have allowed researchers to dramatically speed up many programs that have such high arithmetic intensity and intrinsic concurrency...
August 2, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28754725/genome-wide-analysis-of-the-first-sequenced-mycoplasma-capricolum-subsp-capripneumoniae-strain-m1601
#6
Shengli Chen, Huafang Hao, Ping Zhao, Ying He, Pengcheng Gao, Han Guo, Wenheng Ji, Zhanhui Wang, Zhongxin Lu, Yuefeng Chu, Yongsheng Liu
Mycoplasma capricolum subsp. capripneumoniae (Mccp) is a common pathogen of goats that causes contagious caprine pleuropneumonia. We closed the gap and corrected rRNA operons in the draft genome of Mccp M1601, a strain isolated from an infected goat in a farm in Gansu, China. The genome size of M1601 is 1,016,707 bp with a GC content of 23.67%. We identified 915 genes (occupying 90.27% of the genome), of which 713 are protein-coding genes (excluding 163 pseudogenes). No genomic islands and complete insertion sequences were found in the genome...
July 28, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28754724/trans-ancestry-fine-mapping-and-molecular-assays-identify-regulatory-variants-at-the-angptl8-hdl-c-gwas-locus
#7
Maren E Cannon, Qing Duan, Ying Wu, Monica Zeynalzadeh, Zheng Xu, Antti J Kangas, Pasi Soininen, Mika Ala-Korpela, Mete Civelek, Aldons J Lusis, Johanna Kuusisto, Francis S Collins, Michael Boehnke, Hua Tang, Markku Laakso, Yun Li, Karen Mohlke
Recent genome-wide association studies (GWAS) have identified variants associated with high-density lipoprotein cholesterol (HDL-C) located in or near the ANGPTL8 gene. Given the extensive sharing of GWAS loci across populations, we hypothesized that at least one shared variant at this locus affects HDL-C. The HDL-C-associated variants are coincident with expression quantitative trait loci for ANGPTL8 and DOCK6 in subcutaneous adipose tissue; however, only ANGPTL8 expression levels are associated with HDL-C levels...
July 28, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28754723/a-functional-link-between-bir1-and-the-saccharomyces-cerevisiae-ctf19-kinetochore-complex-revealed-through-quantitative-fitness-analysis
#8
Vasso Makrantoni, Adam Ciesiolka, Conor Lawless, Josefin Fernius, Adele Marston, David Lydall, Michael J R Stark
The chromosomal passenger complex (CPC) is a key regulator of eukaryotic cell division, consisting of the protein kinase Aurora B/Ipl1 in association with its activator (INCENP/Sli15) and two additional proteins (Survivin/Bir1 and Borealin/Nbl1). Here we report a genome-wide genetic interaction screen in Saccharomyces cerevisiae using the bir1-17 mutant, identifying through quantitative fitness analysis deletion mutations that act as enhancers and suppressors. Gene knockouts affecting the Ctf19 kinetochore complex were identified as the strongest enhancers of bir1-17, while mutations affecting the large ribosomal subunit or the mRNA nonsense-mediated decay (NMD) pathway caused strong phenotypic suppression...
July 28, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28751505/the-integrated-genomic-architecture-and-evolution-of-dental-divergence-in-east-african-cichlid-fishes-haplochromis-chilotes-x-h-nyererei
#9
C Darrin Hulsey, Gonzalo Machado-Schiaffino, Lara Keicher, Diego Ellis-Soto, Frederico Henning, Axel Meyer
The independent evolution of the two toothed jaws of cichlid fishes is thought to have promoted their unparalleled ecological divergence and species richness. However, dental divergence in cichlids could exhibit substantial genetic covariance and this could dictate how traits like tooth numbers evolve in different African Lakes and on their two jaws. To test this hypothesis, we used a hybrid mapping cross of two trophically divergent Lake Victoria species (Haplochromis chilotes x Haplochromis nyererei) to examine genomic regions associated with cichlid tooth diversity...
July 27, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28751504/the-caenorhabditis-elegans-female-state-decoupling-the-transcriptomic-effects-of-aging-and-sperm-status
#10
David Angeles-Albores, Daniel H W Leighton, Tiffany Tsou, Tiffany H Khaw, Igor Antoshechkin, Paul W Sternberg
Understanding genome and gene function in a whole organism requires us to fully comprehend the life cycle and the physiology of the organism in question. Caenorhabditis elegans XX animals are hermaphrodites that exhaust their sperm after 3 days of egg-laying. Even though C. elegans can live for many days after cessation of egg-laying, the molecular physiology of this state has not been as intensely studied as other parts of the life cycle, despite documented changes in behavior and metabolism. To study the effects of sperm depletion and aging of C...
July 27, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28751503/ankyrin-1-gene-exhibits-allelic-heterogeneity-in-conferring-protection-against-malaria
#11
Hong Ming Huang, Denis C Bauer, Patrick M Lelliott, Matthew Wa Dixon, Leann Tilley, Brendan J McMorran, Simon J Foote, Gaetan Burgio
Allelic heterogeneity is a common phenomenon where a gene exhibit different phenotype depending on the nature of its genetic mutations. In the context of genes affecting malaria susceptibility, it allowed us to explore and understand the intricate host-parasite interactions during malaria infections. In this study, we described a gene encoding erythrocytic ankyrin-1 (Ank-1) which exhibits allelic-dependent heterogeneous phenotypes during malaria infections. We conducted an ENU mutagenesis screen on mice and identified two Ank-1 mutations, one resulted in an amino acid substitution (MRI95845), and the other a truncated Ank-1 protein (MRI96570)...
July 27, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28751502/the-douglas-fir-genome-sequence-reveals-specialization-of-the-photosynthetic-apparatus-in-pinaceae
#12
David B Neale, Patrick E McGuire, Nicholas C Wheeler, Kristian A Stevens, Marc W Crepeau, Charis Cardeno, Aleksey V Zimin, Daniela Puiu, Geo M Pertea, U Uzay Sezen, Claudio Casola, Tomasz E Koralewski, Robin Paul, Daniel Gonzalez-Ibeas, Sumaira Zaman, Richard Cronn, Mark Yandell, Carson Holt, Charles H Langley, James A Yorke, Steven L Salzberg, Jill L Wegrzyn
A reference genome sequence for Pseudotsuga menziesii var. menziesii (Mirb.) Franco (Coastal Douglas-fir) is reported, thus providing a reference sequence for a third genus of the family Pinaceae. The contiguity and quality of the genome assembly far exceeds that of other conifer reference genome sequences (contig N50 = 44,136 bp and scaffold N50 = 340,704 bp). Incremental improvements in sequencing and assembly technologies are in part responsible for the higher quality reference genome, but it may also be due to a slightly lower exact repeat content in Douglas-fir versus pine and spruce...
July 27, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28751501/ras-mapk-modifier-loci-revealed-by-eqtl-in-caenorhabditis-elegans
#13
Mark G Sterken, Linda van Bemmelen van der Plaat, Joost A Riksen, Miriam Rodriguez, Tobias Schmid, Alex Hajnal, Jan E Kammenga, Basten L Snoek
The oncogenic Ras/MAPK pathway is evolutionarily conserved across metazoans. Yet, almost all our knowledge on this pathway comes from studies using single genetic backgrounds, whereas mutational effects can be highly background dependent. Therefore, we lack insight in the interplay between genetic backgrounds and the Ras/MAPK-signaling pathway. Here, we used a Caenorhabditis elegans RIL population containing a gain-of-function mutation in the Ras/MAPK pathway gene let-60 and measured how gene expression regulation is affected by this mutation...
July 27, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28751500/genome-wide-snp-discovery-and-analysis-of-genetic-diversity-in-farmed-sika-deer-cervus-nippon-in-northeast-china-using-double-digest-restriction-site-associated-dna-sequencing
#14
Hengxing Ba, Boyin Jia, Guiwu Wang, Yifeng Yang, Gilead Kedem, Chunyi Li
Sika deer are an economically valuable species for their use in traditional Chinese medicine, particularly velvet antlers. Sika deer in northeast China are mostly farmed in enclosure. Therefore, genetic management of farmed sika deer would benefit from detailed knowledge of their genetic diversity. In this study, we generated over 1.45 billion high-quality paired-end reads (288 Gbp) across 42 unrelated individuals using double-digest restriction-site associated DNA sequencing (ddRAD-seq). A total of 96,188 (29...
July 27, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28743807/genome-wide-screen-for-genes-involved-in-caenorhabditis-elegans-developmentally-timed-sleep
#15
Huiyan Huang, Chen-Tseh Zhu, Lukas L Skuja, Dustin J Hayden, Anne C Hart
In Caenorhabditis elegans, Notch signaling regulates developmentally timed sleep during the transition from L4 larval stage to adulthood (L4/A). To identify core sleep pathways and to find genes acting downstream of Notch signaling, we undertook the first genome-wide, classical genetic screen focused on C. elegans developmentally timed sleep. To increase screen efficiency, we first looked for mutations that suppressed inappropriate anachronistic sleep in adult hsp::osm-11 animals over-expressing the Notch co-ligand OSM-11 after heat shock...
July 25, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28743806/the-stress-inducible-peroxidase-tsa2-underlies-a-conditionally-beneficial-chromosomal-duplication-in-saccharomyces-cerevisiae
#16
Robert A Linder, John P Greco, Fabian Seidl, Takeshi Matsui, Ian M Ehrenreich
Although chromosomal duplications are often deleterious, in some cases they enhance cells' abilities to tolerate specific genetic or environmental challenges. Identifying the genes that confer these conditionally beneficial effects to particular chromosomal duplications can improve our understanding of the genetic and molecular mechanisms that enable certain aneuploidies to persist in cell populations and contribute to disease and evolution. Here, we perform a screen for spontaneous mutations that improve the tolerance of haploid Saccharomyces cerevisiae to hydrogen peroxide...
July 25, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28739600/whole-genome-sequencing-and-concordance-between-antimicrobial-susceptibility-genotypes-and-phenotypes-of-bacterial-isolates-associated-with-bovine-respiratory-disease
#17
Joseph R Owen, Noelle Noyes, Amy E Young, Daniel J Prince, Patricia C Blanchard, Terry W Lehenbauer, Sharif S Aly, Jessica H Davis, Sean M O'Rourke, Zaid Abdo, Keith Belk, Michael R Miller, Paul Morley, Alison Van Eenennaam
Extended laboratory culture and antimicrobial susceptibility testing timelines hinder rapid species identification and susceptibility profiling of bacterial pathogens associated with bovine respiratory disease, the most prevalent cause of cattle mortality in the United States. Whole genome sequencing offers a culture-independent alternative to current bacterial identification methods but requires a library of bacterial reference genomes for comparison. To contribute new bacterial genome assemblies and evaluate genetic diversity and variation in antimicrobial resistance genotypes, whole-genome sequencing was performed on bovine respiratory disease associated bacterial isolates (Histophilus somni, Mycoplasma bovis, Mannheimia haemolytica, and Pasteurella multocida) from dairy and beef cattle...
July 24, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28739599/evolutionary-dynamics-of-male-reproductive-genes-in-the-drosophila-virilis-subgroup
#18
Yasir H Ahmed-Braimah, Robert L Unckless, Andrew G Clark
Postcopulatory sexual selection (PCSS) is a potent evolutionary force that can drive rapid changes of reproductive genes within species, and thus has the potential to generate reproductive incompatibilities between species. Male seminal fluid proteins (SFPs) are major players in postmating interactions, and are important targets of PCSS in males. The virilis subgroup of Drosophila exhibits strong interspecific gametic incompatibilities, and can serve as a model to study the genetic basis of PCSS and gametic isolation...
July 24, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28739598/sequence-based-mapping-and-genome-editing-reveal-mutations-in-stickleback-hps5-cause-oculocutaneous-albinism-and-the-casper-phenotype
#19
Craig T Miller, James C Hart
Here we present and characterize the spontaneous X-linked recessive mutation casper, which causes oculocutaneous albinism in threespine sticklebacks (Gasterosteus aculeatus). In humans, Hermansky-Pudlak syndrome results in pigmentation defects due to disrupted formation of the melanin-containing lysosomal-related organelle (LRO), the melanosome. casper mutants display not only reduced pigmentation of melanosomes in melanophores, but also reductions in the iridescent silver color from iridophores, while the yellow pigmentation from xanthophores appears unaffected...
July 24, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28739597/a-large-deletion-in-the-nsdhl-gene-in-labrador-retrievers-with-a-congenital-cornification-disorder
#20
Anina Bauer, Michela De Lucia, Vidhya Jagannathan, Giorgia Mezzalira, Margaret L Casal, Monika M Welle, Tosso Leeb
In heterozygous females affected by an X-linked skin disorder, lesions often appear in a characteristic pattern, the so-called Blaschko's lines. We investigated a female Labrador Retriever and her crossbred daughter, which both showed similar clinical lesions that followed Blaschko's lines. The two male littermates of the affected daughter had died at birth suggesting a monogenic X-chromosomal semi-dominant mode of inheritance. Whole genome sequencing of the affected daughter and subsequent automated variant filtering with respect to 188 non-affected control dogs of different breeds revealed 332 heterozygous variants on the X-chromosome private to the affected dog...
July 24, 2017: G3: Genes—Genomes—Genetics
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