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G3: Genes—Genomes—Genetics

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https://www.readbyqxmd.com/read/29792315/genomic-variation-among-and-within-six-juglans-species
#1
Kristian A Stevens, Keith Woeste, Sandeep Chakraborty, Marc W Crepeau, Charles A Leslie, Pedro J Martínez-García, Daniela Puiu, Jeanne Romero-Severson, Mark Coggeshall, Abhaya M Dandekar, Daniel Kluepfel, David B Neale, Steven L Salzberg, Charles H Langley
Genomic analysis in Juglans (walnuts) is expected to transform the breeding and agricultural production of both nuts and lumber. To that end, we report here the determination of reference sequences for six additional relatives of Juglans regia : Juglans sigillata (also from section Dioscaryon ), Juglans nigra , Juglans microcarpa, Juglans hindsii (from section Rhysocaryon ) , Juglans cathayensis (from section Cardiocaryon ), and the closely related Pterocarya stenoptera. While these are 'draft' genomes, ranging in size between 640Mbp and 990Mbp, their contiguities and accuracies can support powerful annotations of genomic variation that are often the foundation of new avenues of research and breeding...
May 23, 2018: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/29789313/blast-xyplot-viewer-a-tool-for-performing-blast-in-whole-genome-sequenced-bacteria-archaea-and-visualize-whole-results-simultaneously
#2
Yagul Pedraza-Pérez, Rodrigo Alberto Cuevas-Vede, Ángel Bernardo Canto-Gómez, Liliana López-Pliego, Rosa María Gutiérrez-Ríos, Ismael Hernández-Lucas, Gustavo Rubín-Linares, Ygnacio Martínez-Laguna, Jesús Francisco López-Olguín, Luis Ernesto Fuentes-Ramírez
One of the most commonly used tools to compare protein or DNA sequences against databases is BLAST. We introduce a web tool that allows the performance of BLAST-searches of protein/DNA sequences in whole-genome sequenced bacteria/archaea, and displays a large amount of BLAST-results simultaneously. The circular bacterial replicons are projected as horizontal lines with fixed length of 360, representing the degrees of a circle. A coordinate system is created with length of the replicon along the x -axis and the number of replicon used on the y -axis...
May 22, 2018: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/29789312/development-of-diagnostic-snp-markers-to-monitor-hybridization-between-sika-deer-cervus-nippon-and-wapiti-cervus-elaphus
#3
Hengxing Ba, Zhipeng Li, Yifeng Yang, Chunyi Li
Sika deer ( Cervus Nippon ) and wapiti ( Cervus elaphus ) are closely related species and their hybridization can result in significant allele-shift of their gene pool. Additive genetic effects and putative heterotic effects of their hybridization on growth performance could confer considerable economic advantage in deer farming. Here, we used double-digest restriction site-associated DNA sequencing technology (ddRAD-seq) and detected ∼320,000 genome-wide SNPs from 30 captive individuals: 7 sika deer, 6 wapiti and 17 F1 hybrids (reciprocal cross)...
May 22, 2018: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/29776970/the-e3-ubiquitin-ligase-mib-1-is-necessary-to-form-the-nuclear-halo-in-caenorhabditis-elegans-sperm
#4
Leslie A Herrera, Daniel A Starr
Unlike the classical nuclear envelope with two membranes found in other eukaryotic cells, most nematode sperm nuclei are not encapsulated by membranes. Instead, they are surrounded by a nuclear halo of unknown composition. How the halo is formed and regulated is unknown. We used forward genetics to identify molecular lesions behind three classical fer (fertilization defective) mutations that disrupt the ultrastructure of the Caenorhabditis elegans sperm nuclear halo. We found fer-2 and fer-4 alleles to be nonsense mutations in mib-1...
May 18, 2018: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/29776969/identifying-genetic-players-in-cell-sheet-morphogenesis-using-a-drosophila-deficiency-screen-for-genes-on-chromosome-2r-involved-in-dorsal-closure
#5
Richard D Mortensen, Regan P Moore, Stephanie M Fogerson, Hellen Y Chiou, Chimdindu V Obinero, Neel K Prabhu, Angela H Wei, Janice M Crawford, Daniel P Kiehart
Cell sheet morphogenesis characterizes key developmental transitions and homeostasis, in vertebrates and throughout phylogeny, including gastrulation, neural tube formation and wound healing. Dorsal closure, a process during Drosophila embryogenesis, has emerged as a model for cell sheet morphogenesis. ∼140 genes are currently known to affect dorsal closure and new genes are identified each year. Many of these genes were identified in screens that resulted in arrested development. Dorsal closure is remarkably robust and many questions regarding the molecular mechanisms involved in this complex biological process remain...
May 18, 2018: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/29773558/genetic-analyses-of-elys-mutations-in-drosophila-show-maternal-effect-lethality-and-interactions-with-nucleoporin-genes
#6
Kazuyuki Hirai, Zhuo Wang, Kohei Miura, Takaaki Hayashi, Takeshi Awasaki, Moe Wada, Yoko Keira, Hiroyuki O Ishikawa, Kyoichi Sawamura
ELYS determines the subcellular localizations of Nucleoporins (Nups) during interphase and mitosis. We made loss-of-function mutations of Elys in Drosophila melanogaster and found that ELYS is dispensable for zygotic viability and male fertility but the maternal supply is necessary for embryonic development. Subsequent to fertilization, mitotic progression of the embryos produced by the mutant females is severely disrupted at the first cleavage division, accompanied by irregular behavior of mitotic centrosomes...
May 18, 2018: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/29769292/a-genome-wide-assay-specifies-only-grea-as-a-transcription-fidelity-factor-in-escherichia-coli
#7
Charles C Traverse, Howard Ochman
Although mutations are the basis for adaptation and heritable genetic change, transient errors occur during transcription at rates that are orders of magnitude higher than the mutation rate. High rates of transcription errors can be detrimental by causing the production of erroneous proteins that need to be degraded. Two transcription fidelity factors, GreA and GreB, have previously been reported to stimulate the removal of errors that occur during transcription, and a third fidelity factor, DksA, is thought to decrease the error rate through an unknown mechanism...
May 16, 2018: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/29769291/key-transport-and-ammonia-recycling-genes-involved-in-aphid-symbiosis-respond-to-host-plant-specialization
#8
Dohyup Kim, Bushra F Minhas, Hongmei Li-Byarlay, Allison K Hansen
Microbes are known to influence insect-plant interactions; however, it is unclear if host-plant diet influences the regulation of nutritional insect symbioses. The pea aphid, Acyrthosiphon pisum , requires its nutritional endosymbiont, Buchnera , for the production of essential amino acids. We hypothesize that key aphid genes that regulate the nutritional symbioses respond to host-plant diet when aphids feed on a specialized (alfalfa) compared to a universal host-plant diet (fava), which vary in amino acid profiles...
May 16, 2018: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/29769290/assessment-of-an-organ-specific-de-novo-transcriptome-of-the-nematode-trap-crop-solanum-sisymbriifolium
#9
Alexander Q Wixom, N Carol Casavant, Joseph C Kuhl, Fangming Xiao, Louise-Marie Dandurand, Allan B Caplan
Solanum sisymbriifolium , also known as "Litchi Tomato" or "Sticky Nightshade," is an undomesticated and poorly researched plant related to potato and tomato. Unlike the latter species, S. sisymbriifolium induces eggs of the cyst nematode, Globodera pallida , to hatch and migrate into its roots, but then arrests further nematode maturation. In order to provide researchers with a partial blueprint of its genetic make-up so that the mechanism of this response might be identified, we used single molecule real time (SMRT) sequencing to compile a high quality de novo transcriptome of 41,189 unigenes drawn from individually sequenced bud, root, stem, and leaf RNA populations...
May 16, 2018: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/29764961/genome-wide-search-for-quantitative-trait-loci-controlling-important-plant-and-flower-traits-in-petunia-using-an-interspecific-recombinant-inbred-population-of-petunia-axillaris-and-petunia-exserta
#10
Zhe Cao, Yufang Guo, Qian Yang, Yanhong He, Mohammed Fetouh, Ryan M Warner, Zhanao Deng
A major bottleneck in plant breeding has been the much limited genetic base and much reduced genetic diversity in domesticated, cultivated germplasm. Identification and utilization of favorable gene loci or alleles from wild or progenitor species can serve as an effective approach to increasing genetic diversity and breaking this bottleneck in plant breeding. This study was conducted to identify quantitative trait loci (QTL) in wild or progenitor petunia species that can be used to improve important horticultural traits in garden petunia...
May 15, 2018: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/29764960/a-genomic-region-containing-rec8-and-rnf212b-is-associated-with-individual-recombination-rate-variation-in-a-wild-population-of-red-deer-cervus-elaphus
#11
Susan E Johnston, Jisca Huisman, Josephine M Pemberton
Recombination is a fundamental feature of sexual reproduction, ensuring proper disjunction, preventing mutation accumulation and generating new allelic combinations upon which selection can act. However it is also mutagenic, and breaks up favourable allelic combinations previously built up by selection. Identifying the genetic drivers of recombination rate variation is a key step in understanding the causes and consequences of this variation, how loci associated with recombination are evolving and how they affect the potential of a population to respond to selection...
May 15, 2018: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/29764959/a-targeted-rnai-screen-reveals-drosophila-female-sterile-genes-that-control-the-size-of-germline-stem-cell-niche-during-development
#12
Yueh Cho, Chun-Ming Lai, Kun-Yang Lin, Hwei-Jan Hsu
Adult stem cells maintain tissue homeostasis. This unique capability largely depends on the stem cell niche, a specialized microenvironment, which preserves stem cell identity through physical contacts and secreted factors. In many cancers, latent tumor cell niches are thought to house stem cells and aid tumor initiation. However, in developing tissue and cancer it is unclear how the niche is established. The well-characterized germline stem cells (GSCs) and niches in the Drosophila melanogaster ovary provide an excellent model to address this fundamental issue...
May 15, 2018: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/29760203/a-dense-linkage-map-of-lake-victoria-cichlids-improved-the-pundamilia-genome-assembly-and-revealed-a-major-qtl-for-sex-determination
#13
Philine G D Feulner, Julia Schwarzer, Marcel P Haesler, Joana I Meier, Ole Seehausen
Genetic linkage maps are essential for comparative genomics, high quality genome sequence assembly and fine scale quantitative trait locus (QTL) mapping. In the present study we identified and genotyped markers via restriction-site associated DNA (RAD) sequencing and constructed a genetic linkage map based on 1,597 SNP markers of an interspecific F2 cross of two closely related Lake Victoria cichlids ( Pundamilia pundamilia and P. sp. 'red head'). The SNP markers were distributed on 22 linkage groups and the total map size was 1,594 cM with an average marker distance of 1...
May 14, 2018: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/29760202/survey-of-human-chromosome-21-gene-expression-effects-on-early-development-in-danio-rerio
#14
Sarah Edie, Norann A Zaghloul, Carmen C Leitch, Donna K Klinedinst, Janette Lebron, Joey F Thole, Andrew S McCallion, Nicholas Katsanis, Roger H Reeves
Trisomy for human chromosome 21 (Hsa21) results in Down syndrome (DS), one of the most genetically complex conditions compatible with human survival. Assessment of the physiological consequences of dosage-driven overexpression of individual Hsa21 genes during early embryogenesis and the resulting contributions to DS pathology in mammals are not tractable in a systematic way. A recent study looked loss-of-function of C. elegans orthologues of Hsa21 genes and identified ten candidates with behavioral phenotypes, but the equivalent over-expression experiment has not been done...
May 14, 2018: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/29760201/a-high-resolution-genetic-map-for-the-laboratory-rat
#15
John Littrell, Shirng-Wern Tsaih, Amelie Baud, Pasi Rastas, Leah Solberg-Woods, Michael J Flister
An accurate and high-resolution genetic map is critical for mapping complex traits, yet the resolution of the current rat genetic map is far lower than human and mouse, and has not been updated since the original Jensen-Seaman map in 2004. For the first time, we have refined the rat genetic map to sub-centimorgan (cM) resolution (<0.02 cM) by using 95,769 genetic markers and 870 informative meiosis from a cohort of 528 heterogeneous stock (HS) rats. Global recombination rates in the revised sex-averaged map (0...
May 14, 2018: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/29760200/the-protein-arginine-methyltransferase-prmt-5-regulates-ser-2-tyramine-receptor-mediated-behaviors-in-caenorhabditis-elegans
#16
Alexander Bowitch, Kerry L Michaels, Michael C Yu, Denise M Ferkey
G protein-coupled receptors are 7-pass transmembrane receptors that couple to heterotrimeric G proteins to mediate cellular responses to a diverse array of stimuli. Understanding the mechanisms that regulate G protein-coupled receptors is crucial to manipulating their signaling for therapeutic benefit. One key regulatory mechanism that contributes to the functional diversity of many signaling proteins is post-translational modification. Whereas phosphorylation remains the best studied of such modifications, arginine methylation by protein arginine methyltransferases is emerging as a key regulator of protein function...
May 14, 2018: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/29752350/the-domino-swi2-snf2-gene-product-represses-cell-death-in-drosophila-melanogaster
#17
Kaitlyn Ellis, Joanna Wardwell-Ozgo, Kenneth H Moberg, Barry Yedvobnick
The Drosophila domino locus encodes DNA-dependent ATPases of the SWI2/SNF2 class. This class of chromatin remodeler is associated with an array of cellular activities encompassing transcription, replication, repair and recombination. Moreover, domino was observed initially to maintain a repressive chromatin state via genetic interaction studies with homeotic genes. Although domino mutations were also characterized with a cell death phenotype, its association with a death pathway has not been investigated. Here we have used targeted RNA interference to depress domino function in the wing...
May 11, 2018: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/29748199/gwas-by-gblup-single-and-multimarker-emmax-and-bayes-factors-with-an-example-in-detection-of-a-major-gene-for-horse-gait
#18
Andres Legarra, Anne Ricard, Luis Varona
Bayesian models for genomic prediction and association mapping are being increasingly used in genetics analysis of quantitative traits. Given a point estimate of variance components, the popular methods SNP-BLUP and GBLUP result in joint estimates of the effect of all markers on the analyzed trait; single and multiple marker frequentist tests (EMMAX) can be constructed from these estimates. Indeed, BLUP methods can be seen simultaneously as Bayesian or frequentist methods. So far there is no formal method to produce Bayesian statistics from GBLUP...
May 10, 2018: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/29748198/dynamic-changes-in-yeast-phosphatase-families-allow-for-specialization-in-phosphate-and-thiamine-starvation
#19
John V Nahas, Christine L Iosue, Noor F Shaik, Kathleen Selhorst, Bin Z He, Dennis D Wykoff
Convergent evolution is often due to selective pressures generating a similar phenotype. We observe relatively recent duplications in a spectrum of Saccharomycetaceae yeast species resulting in multiple phosphatases that are regulated by different nutrient conditions - thiamine and phosphate starvation. This specialization is both transcriptional and at the level of phosphatase substrate specificity. In Candida glabrata , loss of the ancestral phosphatase family was compensated by the co-option of a different histidine phosphatase family with three paralogs...
May 10, 2018: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/29743189/genomic-prediction-accounting-for-genotype-by-environment-interaction-offers-an-effective-framework-for-breeding-simultaneously-for-adaptation-to-an-abiotic-stress-and-performance-under-normal-cropping-conditions-in-rice
#20
Manel Ben Hassen, Jérôme Bartholomé, Giampiero Valè, Tuong-Vi Cao, Nourollah Ahmadi
Developing rice varieties adapted to alternate wetting and drying water management is crucial for the sustainability of irrigated rice cropping systems. Here we report the first study exploring the feasibility of breeding rice for adaptation to alternate wetting and drying using genomic prediction methods that account for genotype by environment interactions. Two breeding populations (a reference panel of 284 accessions and a progeny population of 97 advanced lines) were evaluated under alternate wetting and drying and continuous flooding management systems...
May 9, 2018: G3: Genes—Genomes—Genetics
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