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G3: Genes—Genomes—Genetics

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https://read.qxmd.com/read/30770412/chromosome-wide-evolution-and-sex-determination-in-the-three-sexed-nematode-auanema-rhodensis
#1
Sophie Tandonnet, Georgios D Koutsovoulos, Sally Adams, Delphine Cloarec, Manish Parihar, Mark L Blaxter, Andre Pires-daSilva
Trioecy, a mating system in which males, females and hermaphrodites co-exist, is a useful system to investigate the origin and maintenance of alternative mating In the trioecious nematode Auanema rhodensis , males have one X chromosome (XO), whereas females and hermaphrodites have two (XX). The female versus hermaphrodite sex determination mechanisms have remained elusive. In this study, RNA-seq analyses show a 20% difference between the L2 hermaphrodite and female gene expression profiles. RNAi experiments targeting the DM ( doublesex / mab-3 ) domain transcription factor dmd-10/11 suggest that the hermaphrodite sexual fate requires the upregulation of this gene...
February 15, 2019: G3: Genes—Genomes—Genetics
https://read.qxmd.com/read/30765418/genome-analyses-of-a-new-mycoplasma-species-from-the-scorpion-centruroides-vittatus
#2
Tsunemi Yamashita, Douglas D Rhoads, Jeff Pummill
Arthropod Mycoplasma are little known endosymbionts in insects, primarily known as plant disease vectors. Mycoplasma in other arthropods such as arachnids are unknown. We report the first complete Mycoplasma genome sequenced, identified, and annotated from a scorpion, Centruroides vittatus , and designate it as Mycoplasma vittatus We find the genome is at least a 683,827 bp single circular chromosome with a GC content of 42.7% and with 987 protein-coding genes. The putative virulence determinants include 11 genes associated with the virulence operon associated with protein synthesis or DNA transcription and ten genes with antibiotic and toxic compound resistance...
February 14, 2019: G3: Genes—Genomes—Genetics
https://read.qxmd.com/read/30760541/lost-in-translation-on-the-problem-of-data-coding-in-penalized-whole-genome-regression-with-interactions
#3
Johannes W R Martini, Francisco Rosales, Ngoc-Thuy Ha, Johannes Heise, Valentin Wimmer, Thomas Kneib
Mixed models can be considered as a type of penalized regression and are everyday tools in statistical genetics. The standard mixed model for whole genome regression (WGR) is ridge regression best linear unbiased prediction (RRBLUP) which is based on an additive marker effect model. Many publications have extended the additive WGR approach by incorporating interactions between loci or between genes and environment. In this context of penalized regressions with interactions, it has been reported that translating the coding of single nucleotide polymorphisms -for instance from -1,0,1 to 0,1,2- has an impact on the prediction of genetic values and interaction effects...
February 13, 2019: G3: Genes—Genomes—Genetics
https://read.qxmd.com/read/30760540/understanding-the-loss-of-maternal-care-in-avian-brood-parasites-using-preoptic-area-transcriptome-comparisons-in-brood-parasitic-and-non-parasitic-blackbirds
#4
Kathleen S Lynch, Lauren A O'Connell, Matthew I M Louder, Christopher N Balakrishnan, Eva K Fischer
Parental care is critical for offspring survival in many species. However, parental behaviors have been lost in roughly 1% of avian species known as the obligate brood parasites. To shed light on molecular and neurobiological mechanisms mediating brood parasitic behavior, we compared brain gene expression patterns between two brood parasitic species and one closely related non-parasitic Icterid (blackbird) species. Our analyses focused on gene expression changes specifically in the preoptic area (POA), a brain region known to play a critical role in parental behavior across vertebrates...
February 13, 2019: G3: Genes—Genomes—Genetics
https://read.qxmd.com/read/30755409/qtl-underlying-circadian-clock-parameters-under-seasonally-variable-field-settings-in-arabidopsis-thaliana
#5
Matthew J Rubin, Marcus T Brock, Seth J Davis, Cynthia Weinig
The circadian clock facilitates coordination of the internal rhythms of an organism to daily environmental conditions, such as the light-dark cycle of one day. Circadian period length (the duration of one endogenous cycle) and phase (the timing of peak activity) exhibit quantitative variation in natural populations. Here, we measured circadian period and phase in June, July and September in three Arabidopsis thaliana recombinant inbred line populations. Circadian period and phase were estimated from bioluminescence of a genetic construct between a native circadian clock gene ( COLD CIRCADIAN RHYTHM RNA BINDING 2 ) and the reporter gene ( LUCIFERASE ) after lines were entrained under field settings...
February 12, 2019: G3: Genes—Genomes—Genetics
https://read.qxmd.com/read/30755408/short-homology-mediated-crispr-cas9-based-method-for-genome-editing-in-fission-yeast
#6
Aki Hayashi, Katsunori Tanaka
The CRISPR/Cas9 system enables the editing of genomes of numerous organisms through the induction of the double-strand breaks (DSB) at specific chromosomal targets. We improved the CRISPR/Cas9 system to ease the direct introduction of a point mutation or a tagging sequence into the chromosome by combining it with the noncanonical homology-directed DNA repair (HDR) based genome editing in fission yeast. We constructed convenient cloning vectors, which possessed a guide RNA (gRNA) expression module, or the humanized Streptococcus pyogenes Cas9 gene that is expressed under the control of an inducible promoter to avoid the needless expression, or both a gRNA and Cas9 gene...
February 12, 2019: G3: Genes—Genomes—Genetics
https://read.qxmd.com/read/30745378/mitochondrial-dna-fitness-depends-on-nuclear-genetic-background-in-drosophila
#7
Jim A Mossman, Jennifer Y Ge, Freddy Navarro, David M Rand
Mitochondrial DNA (mtDNA) has been one of the most extensively studied molecules in ecological, evolutionary and clinical genetics. In its early application in evolutionary genetics, mtDNA was assumed to be a selectively neutral marker conferring negligible fitness consequences for its host. However, this dogma has been overturned in recent years due to now extensive evidence for non-neutral evolutionary dynamics. Since mtDNA proteins physically interact with nuclear proteins to provide the mitochondrial machinery for aerobic ATP production, among other cell functions, co-variation of the respective genes is predicted to affect organismal fitness...
February 11, 2019: G3: Genes—Genomes—Genetics
https://read.qxmd.com/read/30737239/bidirectional-selection-for-body-weight-on-standing-genetic-variation-in-a-chicken-model
#8
Mette Lillie, Christa F Honaker, Paul B Siegel, Örjan Carlborg
Experimental populations of model organisms provide valuable opportunities to unravel the genomic impact of selection in a controlled system. The Virginia body weight chicken lines represent a unique resource to investigate signatures of selection in a system where long-term, single-trait, bidirectional selection has been carried out for more than 60 generations. At 55 generations of divergent selection, earlier analyses of pooled genome resequencing data from these lines revealed that 14.2% of the genome showed extreme differentiation between the selected lines, contained within 395 genomic regions...
February 8, 2019: G3: Genes—Genomes—Genetics
https://read.qxmd.com/read/30737238/analysis-of-genetic-diversity-and-population-structure-in-three-forest-musk-deer-captive-populations-with-different-origins
#9
Jiamin Fan, Xueli Zheng, Hongyong Wang, Hong Qi, Benmo Jiang, Meiping Qiao, Jianwen Zhou, Shuhai Bu
Musk deer (Moschidae), whose secretion is an expensive and irreplaceable component of traditional medicine, have become endangered in the wild due to habitat fragmentation and over-exploitation. In recent years, China has had success in the artificial breeding of forest musk deer, thus relieving the pressure on wild populations. However, many farmed populations are experiencing degradation, and little genetic information is available for conservation management. In this study, we selected 274 individuals from three typical captive populations (originated from the Ta-pa Mountains (Tp), the midrange of the Qinling Mountains (Ql) and the Western Sichuan Plateau (WS), respectively) to evaluate the genetic variations...
February 8, 2019: G3: Genes—Genomes—Genetics
https://read.qxmd.com/read/30733383/identification-and-functional-testing-of-novel-interacting-protein-partners-for-the-stress-sensors-wsc1p-and-mid2p-of-saccharomyces-cerevisiae
#10
Ednalise Santiago-Cartagena, Sahily González-Crespo, Vladimir Vélez, Nelson Martínez, Jamie Snider, Matthew Jessulat, Hiroyuki Aoki, Zoran Minic, Pearl Akamine, Inoushka Mejías, Luis M Pérez, Brian C Rymond, Mohan Babu, Igor Stagljar, José R Rodríguez-Medina
Wsc1p and Mid2p are transmembrane signaling proteins of cell wall stress in the budding yeast Saccharomyces cerevisiae. When an environmental stress compromises cell wall integrity, they activate a cell response through the Cell Wall Integrity (CWI) pathway. Studies have shown that the cytoplasmic domain of Wsc1p initiates the CWI signaling cascade by interacting with Rom2p, a Rho1-GDP-GTP exchange factor. Binding of Rom2p to the cytoplasmic tail of Wsc1p requires dephosphorylation of specific serine residues but the mechanism by which the sensor is dephosphorylated and how it subsequently interacts with Rom2p remains unclear...
February 7, 2019: G3: Genes—Genomes—Genetics
https://read.qxmd.com/read/30733382/rnai-screen-in-tribolium-reveals-involvement-of-f-bar-proteins-in-myoblast-fusion-and-visceral-muscle-morphogenesis-in-insects
#11
Dorothea Schultheis, Jonas Schwirz, Manfred Frasch
In a large-scale RNAi screen in Tribolium castaneum for genes with knock-down phenotypes in the larval somatic musculature, one recurring phenotype was the appearance of larval muscle fibers that were significantly thinner than those in control animals. Several of the genes producing this knock-down phenotype corresponded to orthologs of Drosophila genes that are known to participate in myoblast fusion, particularly via their effects on actin polymerization. A new gene previously not implicated in myoblast fusion but displaying a similar thin-muscle knock-down phenotype was the Tribolium ortholog of Nostrin , which encodes an F-BAR and SH3 domain protein...
February 7, 2019: G3: Genes—Genomes—Genetics
https://read.qxmd.com/read/30733381/a-large-scale-systemic-rnai-screen-in-the-red-flour-beetle-tribolium-castaneum-identifies-novel-genes-involved-in-insect-muscle-development
#12
Dorothea Schultheis, Matthias Weißkopf, Christoph Schaub, Salim Ansari, Van Anh Dao, Daniela Grossmann, Upalparna Majumdar, Muhammad Salim Hakeemi, Nicole Troelenberg, Tobias Richter, Christian Schmitt-Engel, Jonas Schwirz, Nadia Ströhlein, Matthias Teuscher, Gregor Bucher, Manfred Frasch
Although muscle development has been widely studied in Drosophila melanogaster there are still many gaps in our knowledge, and it is not known to which extent this knowledge can be transferred to other insects. To help in closing these gaps we participated in a large-scale RNAi screen that used the red flour beetle, Tribolium castaneum , as a screening platform. The effects of systemic RNAi were screened upon double-stranded RNA injections into appropriate muscle-EGFP tester strains. Injections into pupae were followed by the analysis of the late embryonic/early larval muscle patterns, and injections into larvae by the analysis of the adult thoracic muscle patterns...
February 7, 2019: G3: Genes—Genomes—Genetics
https://read.qxmd.com/read/30733380/ion-channel-contributions-to-wing-development-in-drosophila-melanogaster
#13
Laura F George, Sarala J Pradhan, Danae Mitchell, Megan Josey, Justin Casey, Matthew T Belus, Giri R Dahal, Emily A Bates
During morphogenesis, cells communicate with each other to shape tissues and organs. Several lines of recent evidence indicate that ion channels play a key role in cellular signaling and tissue morphogenesis. However, little is known about the scope of specific ion-channel types that impinge upon developmental pathways. The Drosophila melanogaster wing is an excellent model in which to address this problem as wing vein patterning is acutely sensitive to changes in developmental pathways. We conducted a screen of 180 ion channels expressed in the wing using loss-of-function mutant and RNAi lines...
February 7, 2019: G3: Genes—Genomes—Genetics
https://read.qxmd.com/read/30723103/evidence-for-an-integrated-gene-repression-mechanism-based-on-mrna-isoform-toggling-in-human-cells
#14
Ina Hollerer, Juliet C Barker, Victoria Jorgensen, Amy Tresenrider, Claire Dugast-Darzacq, Leon Y Chan, Xavier Darzacq, Robert Tjian, Elçin Ünal, Gloria A Brar
We recently described an unconventional mode of gene regulation in budding yeast by which transcriptional and translational interference collaborate to down-regulate protein expression. Developmentally timed transcriptional interference inhibited production of a well translated mRNA isoform and resulted in the production of an mRNA isoform containing inhibitory upstream open reading frames (uORFs) that prevented translation of the main ORF. Transcriptional interference and uORF-based translational repression are established mechanisms outside of yeast, but whether this type of integrated regulation was conserved was unknown...
February 5, 2019: G3: Genes—Genomes—Genetics
https://read.qxmd.com/read/30723102/testes-proteases-expression-and-hybrid-male-sterility-between-subspecies-of-drosophila-pseudoobscura
#15
Doaa Alhazmi, Seth Kaleb Fudyk, Alberto Civetta
Hybrid male sterility (HMS) is a form of postmating postzygotic isolation among closely related species that can act as an effective barrier to gene flow. The Dobzhansky-Muller model provides a framework to explain how gene interactions can cause HMS between species. Genomics highlights the preponderance of non-coding DNA targets that could be involved in gene interactions resulting in gene expression changes and the establishment of isolating barriers. However, we have limited knowledge of changes in gene expression associated with HMS, gene interacting partners linked to HMS, and whether substitutions in DNA regulatory regions ( cis ) causes misexpression (i...
February 5, 2019: G3: Genes—Genomes—Genetics
https://read.qxmd.com/read/30718274/turning-observed-founder-alleles-into-expected-relationships-in-an-intercross-population
#16
Jilun Meng, Manfred Mayer, Erika Wytrwat, Martina Langhammer, Norbert Reinsch
Pedigree-derived relationships for individuals from an intercross of several lines cannot easily account for the segregation variance that is mainly caused by loci with alternative alleles fixed in different lines. However, when all founders are genotyped for a large number of markers, such relationships can be derived for descendants as expected genomic relationships conditional on the observed founder allele frequencies. A tabular method was derived in detail for autosomes and the X chromosome. As a case study, we analyzed litter size and body weights at three different ages in an advanced mouse intercross (29 generations, total pedigree size 19,266) between a line selected for high litter size (FL1) and a highly inbred control line (DUKsi)...
February 4, 2019: G3: Genes—Genomes—Genetics
https://read.qxmd.com/read/30705120/genomic-resources-for-goniozus-legneri-aleochara-bilineata-and-paykullia-maculata-representing-three-independent-origins-of-the-parasitoid-lifestyle-in-insects
#17
Ken Kraaijeveld, Peter Neleman, Janine Mariën, Emile de Meijer, Jacintha Ellers
Parasitoid insects are important model systems for a multitude of biological research topics and widely used as biological control agents against insect pests. While the parasitoid lifestyle has evolved numerous times in different insect groups, research has focused almost exclusively on Hymenoptera from the Parasitica clade. The genomes of several members of this group have been sequenced, but no genomic resources are available from any of the other, independent evolutionary origins of the parasitoid lifestyle...
January 31, 2019: G3: Genes—Genomes—Genetics
https://read.qxmd.com/read/30705119/evaluation-of-inseq-to-identify-genes-essential-for-pseudomonas-aeruginosa-pgpr2-corn-root-colonization
#18
Ramamoorthy Sivakumar, Jothi Ranjani, Udayakumar S Vishnu, Sathyanarayanan Jayashree, Gabriel L Lozano, Jessica Miles, Nichole A Broderick, Changhui Guan, Paramasamy Gunasekaran, Jo Handelsman, Jeyaprakash Rajendhran
The reciprocal interaction between rhizosphere bacteria and their plant hosts results in a complex battery of genetic and physiological responses. In this study, we used insertion sequencing (INSeq) to reveal the genetic determinants responsible for the fitness of Pseudomonas aeruginosa PGPR2 during root colonization. We generated a random transposon mutant library of Pseudomonas aeruginosa PGPR2 comprising 39,500 unique insertions and identified genes required for growth in culture and on corn roots. A total of 108 genes were identified as contributing to the fitness of strain PGPR2 on roots...
January 31, 2019: G3: Genes—Genomes—Genetics
https://read.qxmd.com/read/30696702/tp901-1-phage-recombinase-facilitates-genome-engineering-in-drosophila-melanogaster
#19
Roumen Voutev, Richard S Mann
Molecular biology techniques have a large impact on biomedical research and the availability of diverse tools to perform genome manipulations advances the ease of executing complicated genetic research. Here, we introduce in the fruit fly another such tool by harnessing the phage recombinase TP901-1 to perform site-directed recombination that leads to recombinase-mediated cassette exchange (RMCE). The TP901-1 system complements already existing recombination systems and enhances genome engineering in the fruit fly and other organisms...
January 29, 2019: G3: Genes—Genomes—Genetics
https://read.qxmd.com/read/30696701/arginine-to-glutamine-variant-in-olfactomedin-like-3-olfml3-is-a-candidate-for-severe-goniodysgenesis-and-glaucoma-in-the-border-collie-dog-breed
#20
Carys A Pugh, Lindsay L Farrell, Ailsa J Carlisle, Stephen J Bush, Adam Ewing, Violeta Trejo-Reveles, Oswald Matika, Arne de Kloet, Caitlin Walsh, Stephen C Bishop, James G D Prendergast, Joe Rainger, Jeffrey J Schoenebeck, Kim M Summers
Goniodysgenesis is a developmental abnormality of the anterior chamber of the eye. It is generally considered to be congenital in dogs ( Canis lupus familiaris ), and has been associated with glaucoma and blindness. Goniodysgenesis and early-onset glaucoma initially emerged in Border Collies in Australia in the late 1990s and has subsequently been found in this breed in Europe and the USA. The objective of the present study was to determine the genetic basis of goniodysgenesis in Border Collies. Clinical diagnosis was based on results of examinations by veterinary ophthalmologists of affected and unaffected dogs from eleven different countries...
January 29, 2019: G3: Genes—Genomes—Genetics
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