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G3: Genes—Genomes—Genetics

Lauren E Ryan, Eric S Haag
Within the nematode genus Caenorhabditis, C. briggsae and C. nigoni are among the most closely related species known. They differ in sexual mode, with C. nigoni retaining the ancestral XO male-XX female outcrossing system, while C. briggsae recently evolved self-fertility and an XX-biased sex ratio. Wild-type C. briggsae and C. nigoni can produce fertile hybrid XX female progeny, but XO progeny are either 100% inviable (when C. briggsae is the mother) or viable but sterile (when C. nigoni is the mother). A recent study provided evidence suggesting that loss of the Cbr-him-8 meiotic regulator in C...
February 16, 2017: G3: Genes—Genomes—Genetics
Nancy S Bae, Andrew P Seberg, Leslie P Carroll, Mark J Swanson
The yeast Saccharomyces cerevisiae responds to amino acid deprivation by activating a pathway conserved in eukaryotes to overcome the starvation stress. We have screened the entire yeast heterozygous deletion collection to identify strains haploinsufficient for growth in the presence of sulfometuron methyl, which causes starvation for isoleucine and valine. We have discovered that cells devoid of MET15 are sensitive to sulfometuron methyl, and loss of heterozygosity at the MET15 locus can complicate screening the heterozygous deletion collection...
February 16, 2017: G3: Genes—Genomes—Genetics
Dongsheng Zhang, Mengchao Yu, Peng Hu, Sihua Peng, Yimeng Liu, Weiwen Li, Congcong Wang, Shunping He, Wanying Zhai, Qianghua Xu, Liangbiao Chen
Many species of Schizothoracine, a sub-family of Cyprinidae, are highly endemic to the Qinghai-Tibetan Plateau (QTP). To characterize the adaptive changes associated with the Schizothoracine expansion in high-altitudes, we sequenced tissue transcriptomes of two highland and two sub-highland Schizothoracines, and analyzed gene evolution patterns by comparing to lowland cyprinids. Phylogenetic tree reconstruction and divergence time estimation indicated that the common ancestor of Schizothoracine fishes lived around 32...
February 16, 2017: G3: Genes—Genomes—Genetics
Jasdeep S Mutti, Ramanjot K Bhullar, Kulvinder S Gill
Polyploidy is a major evolutionary process in eukaryotes, yet the expression balance of homoeologs in natural polyploids is largely unknown. To study this expression balance, expression pattern of 2180 structurally well-characterized genes of wheat was studied of which 813 had the expected three copies and 375 had less than three. Copy number of the remaining 992 ranged from 4-14 including homoeologs, orthologs and paralogs. Of the genes with three structural copies corresponding to homoeologs, 55% expressed from all three, 38% from two, and the remaining 7% expressed from only one of the three copies...
February 13, 2017: G3: Genes—Genomes—Genetics
Anke Samel, Adam Rudner, Ann E Ehrenhofer-Murray
Heterochromatin formation in the yeast Saccharomyces cerevisiae is characterized by the assembly of the Silent Information Regulator (SIR) complex, which consists of the histone deacetylase Sir2 and the structural components Sir3 and Sir4 and binds to unmodified nucleosomes to provide gene silencing. Sir3 contains an AAA(+) ATPase-like domain, and mutations in an exposed loop on the surface of this domain abrogate Sir3 silencing function in vivo as well in vitro binding to the Sir2/ Sir4 subcomplex. Here, we found that the removal of a single methyl group in the C-terminal coiled-coil domain (mutation T1314S) of Sir4 was sufficient to restore silencing at the silent mating-type loci HMR and HML to a Sir3 version with a mutation in this loop...
February 10, 2017: G3: Genes—Genomes—Genetics
Fernando A Rabanal, Viktoria Nizhynska, Terezie Mandáková, Polina Yu Novikova, Martin A Lysak, Richard Mott, Magnus Nordborg
The considerable genome size variation in Arabidopsis thaliana has been shown largely to be due to copy number variation (CNV) in 45S ribosomal RNA (rRNA) genes. Surprisingly, attempts to map this variation by means of genome-wide association studies (GWAS) failed to identify either of the two likely sources, namely the nucleolar organizer regions (NORs). Instead, GWAS implicated a trans-acting locus, as if rRNA CNV was a phenotype rather than a genotype. To explain these results, we investigated the inheritance and stability of rRNA gene copy number using the variety of genetic resources available in A...
February 10, 2017: G3: Genes—Genomes—Genetics
Avinash Karn, Jason D Gillman, Sherry A Flint-Garcia
Teosinte (Zea mays ssp. parviglumis) is the wild ancestor of modern maize (Zea mays ssp. mays). Teosinte contains greater genetic diversity compared to maize inbreds and landraces, but its use is limited by insufficient genetic resources to evaluate its value. A population of teosinte near isogenic lines (teosinte NILs) was previously developed to broaden the resources for genetic diversity of maize, and to discover novel alleles for agronomic and domestication traits. The 961 teosinte NILs were developed by backcrossing ten geographically diverse parviglumis accessions into the B73 (reference genome inbred) background...
February 10, 2017: G3: Genes—Genomes—Genetics
Johanna Rhodes, Mathew A Beale, Mathieu Vanhove, Joseph N Jarvis, Shichina Kannambath, John A Simpson, Anthea Ryan, Graeme Meintjes, Thomas S Harrison, Matthew C Fisher, Tihana Bicanic
Recurrence of meningitis due to Cryptococcus neoformans after treatment causes substantial mortality in HIV/AIDS patients across sub-Saharan Africa. In order to determine whether recurrence occurred due to relapse of the original infecting isolate or reinfection with a different isolate weeks or months after initial treatment, we used whole-genome sequencing to assess the genetic basis of infection in 17 HIV-infected individuals with recurrent cryptococcal meningitis. Comparisons revealed a clonal relationship for 15 pairs of isolates recovered before and after recurrence showing relapse of the original infection...
February 10, 2017: G3: Genes—Genomes—Genetics
Zhao Liu, Gerald J Seiler, Thomas J Gulya, Jiuhuan Feng, Khalid Y Rashid, Xiwen Cai, Chao-Chien Jan
Wild Helianthus species are a valuable genetic resource for the improvement of cultivated sunflower. We report the discovery and characterization of a unique high frequency production of triploids when cultivated sunflower was pollinated by specific accessions of diploid Helianthus nuttallii T. &. G. and H. maximiliani Schr. Genomic in situ hybridization (GISH) analyses indicated that the triploid F1s had two genomes from the wild pollen sources and one from the cultivated line. Mitotic chromosome analyses indicated that the frequency of triploid progenies from the crosses of cultivated lines × H...
February 7, 2017: G3: Genes—Genomes—Genetics
Grzegorz Zapotoczny, Jeff Sekelsky
DNA double-strand breaks (DSBs) are one of the most deleterious types of lesions to the genome. Synthesis-dependent strand annealing (SDSA) is thought to be a major pathway of DSB repair, but direct tests of this model have only been conducted in budding yeast and Drosophila To better understand this pathway, we developed an SDSA assay for use in human cells. Our results support the hypothesis that SDSA is an important DSB repair mechanism in human cells. We used siRNA knockdown to assess the roles of a number of helicases suggested to promote SDSA...
February 7, 2017: G3: Genes—Genomes—Genetics
Logan M Decker, Hua Xiao, Erin C Boone, Michael M Vierling, Benjamin S Shanker, Shanika L Kingston, Shannon F Boone, Jackson B Haynes, Patrick K T Shiu
In the filamentous fungus Neurospora crassa, cross walls between individual cells are normally incomplete, making the entire fungal network vulnerable to attack by viruses and selfish DNAs. Accordingly, several genome surveillance mechanisms are maintained to help the fungus to combat these repetitive elements. One of these defense mechanisms is known as meiotic silencing by unpaired DNA (MSUD), which is an RNA silencing system that identifies and silences unpaired genes during meiosis. Utilizing common RNAi proteins such as Dicer and Argonaute, MSUD targets mRNAs homologous to the unpaired sequence to achieve silencing...
February 7, 2017: G3: Genes—Genomes—Genetics
Natalia Martin, Jogender Singh, Alejandro Aballay
Caenorhabditis elegans responds to pathogenic microorganisms by activating its innate immune system, which consists of physical barriers, behavioral responses, and microbial killing mechanisms. We examined whether natural variation plays a role in the response of C. elegans to Pseudomonas aeruginosa using two C. elegans strains that carry the same allele of npr-1, a gene that encodes a G-protein-coupled receptor related to mammalian neuropeptide Y receptors, but that differ in their genetic backgrounds. Strains carrying an allele for the NPR-1 215F isoform have been shown to exhibit lack of pathogen avoidance behavior and deficient immune response towards P...
February 7, 2017: G3: Genes—Genomes—Genetics
Bryan J Cassone, Raissa G G Kay, Matthew P Daugherty, Bradley J White
Testes-biased genes evolve rapidly and are important in the establishment, solidification, and maintenance of reproductive isolation between incipient species. The Anopheles gambiae complex, a group of at least eight isomorphic mosquito species endemic to Sub-Saharan Africa, is an excellent system to explore the evolution of testes-biased genes. Within this group, the testes are an important tissue in the diversification process since hybridization between species results in sterile hybrid males, but fully fertile females...
February 7, 2017: G3: Genes—Genomes—Genetics
Alison L Thompson, Aaron K Mahoney, Richard W Smiley, Timothy C Paulitz, Scot Hulbert, Kim Garland-Campbell
Soil-borne pathogens of the Pacific Northwest, U.S.A. decrease yields in both spring and winter wheat. Pathogens of economic importance include Fusarium culmorum, Pratylenchus neglectus, P. thornei, and Rhizoctonia solani AG8. Few options are available to growers to manage these pathogens and reduce yield loss, therefore the focus for breeding programs is on developing resistant wheat cultivars. A recombinant inbred line population, LouAu (MP-7, NSL 511036), was developed to identify quantitative trait loci associated with resistance to P...
February 3, 2017: G3: Genes—Genomes—Genetics
Evan Koch, John Novembre
When mutations have small effects on fitness, population size plays an important role in determining the amount and nature of deleterious genetic variation. The extent to which recent population size changes have impacted deleterious variation in humans has been a question of considerable interest and debate. An emerging consensus is that the Out-of-Africa bottleneck and subsequent growth events have been too short to cause meaningful differences in genetic load between populations; though changes in the number and average frequencies of deleterious variants have taken place...
February 3, 2017: G3: Genes—Genomes—Genetics
Scott L Allen, Emily K Delaney, Artyom Kopp, Stephen F Chenoweth
Long read sequencing technology promises to greatly enhance de novo assembly of genomes for non-model species. Although the high error rates of long reads have been a stumbling block, sequencing at high coverage permits the self-correction of many errors. Here we sequence and de novo assemble the genome of Drosophila serrata, a species from the montium subgroup that has been well studied for latitudinal clines, sexual selection, and gene expression but which lacks a reference genome. Using 11 PacBio SMRT cells, we generated 12 Gbp of raw sequence data comprising approximately 65x whole genome coverage...
January 30, 2017: G3: Genes—Genomes—Genetics
Erika B Kruse, Scott W Carle, Nuan Wen, Daniel Z Skinner, Timothy D Murray, Kimberly A Garland-Campbell, Arron H Carter
Plants grown through the winter are subject to selective pressures that vary with each year's unique conditions, necessitating tolerance of numerous abiotic and biotic stress factors. The objective of this study was to identify molecular markers in winter wheat (Triticum aestivum L.) associated with tolerance of two of these stresses, freezing temperatures and snow mold, a fungal disease complex active under snow cover. A population of 155 F2:5 recombinant inbred lines from a cross between soft white wheat cultivars 'Finch' and 'Eltan' were evaluated for snow mold tolerance in the field, and for freezing tolerance under controlled conditions...
January 30, 2017: G3: Genes—Genomes—Genetics
Aaron J Stevens, Millie G Taylor, F Grant Pearce, Martin A Kennedy
Loss of one allele during polymerase chain reaction (PCR) amplification of DNA, known as allelic drop-out, can be caused by a variety of mechanisms. Allelic drop-out during PCR may have profound implications for molecular diagnostic and research procedures that depend on PCR and assume biallelic amplification has occurred. Complete allelic drop-out due to the combined effects of cytosine methylation and G-quadruplex formation was previously described for a differentially methylated region of the human imprinted gene, MEST We now demonstrate that this parent-of-origin specific allelic drop-out can potentially occur at several other genomic regions that display genomic imprinting and have propensity for G-quadruplex formation, including AIM1, BLCAP, DNMT1, PLAGL1, KCNQ1 and GRB10 These findings demonstrate that systematic allelic drop-out during PCR is a general phenomenon for regions of the genome where differential allelic methylation and G-quadruplex motifs coincide, and suggest that great care must be taken to ensure biallelic amplification is occurring in such situations...
January 30, 2017: G3: Genes—Genomes—Genetics
Michael J Law, Michael A Finger
In the budding yeast Saccharomyces cerevisiae, nutrient depletion induces massive transcriptional reprogramming that relies upon communication between transcription factors, post-translational histone modifications, and the RNA polymerase II holoenzyme complex. Histone H3Lys4 methylation, regulated by the Set1p-containing COMPASS methyltransferase complex and Jhd2p demethylase, is one of the most well-studied histone modifications. We previously demonstrated that the RNA polymerase II mediator components cyclin C-Cdk8p inhibit locus specific H3Lys4 3me independently of Jhd2p...
January 30, 2017: G3: Genes—Genomes—Genetics
Rebecca C Deed, Bruno Fedrizzi, Richard C Gardner
Low fermentation temperatures are of importance to food and beverage industries working with Saccharomyces cerevisiae Therefore, the identification of genes demonstrating a positive impact on fermentation kinetics is of significant interest. A set of 121 mapped F1 progeny, derived from a cross between haploid strains BY4716, a derivative of the laboratory yeast S288C, and wine yeast RM11-1a, were fermented in New Zealand Sauvignon Blanc grape juice at 12.5 °C. Analyses of five key fermentation kinetic parameters amongst the F1 progeny identified a quantitative trait locus on chromosome I with a significant degree of linkage to maximal fermentation rate (Vmax) at low temperature...
January 30, 2017: G3: Genes—Genomes—Genetics
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