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https://www.readbyqxmd.com/read/29161754/the-sorghum-bicolor-reference-genome-improved-assembly-gene-annotations-a-transcriptome-atlas-and-signatures-of-genome-organization
#1
Ryan F McCormick, Sandra K Truong, Avinash Sreedasyam, Jerry Jenkins, Shengqiang Shu, David Sims, Megan Kennedy, Mojgan Amirebrahimi, Brock D Weers, Brian McKinley, Ashley Mattison, Daryl T Morishige, Jane Grimwood, Jeremy Schmutz, John E Mullet
Sorghum bicolor is a drought tolerant C4 grass used for production of grain, forage, sugar, and lignocellulosic biomass and a genetic model for C4 grasses due to its relatively small genome (~800 Mbp), diploid genetics, diverse germplasm, and colinearity with other C4 grass genomes. In this study, deep sequencing, genetic linkage analysis, and transcriptome data were used to produce and annotate a high-quality reference genome sequence. Reference genome sequence order was improved, 29.6 Mbp of additional sequence was incorporated, the number of genes annotated increased 24% to 34,211, average gene length and N50 increased, and error frequency was reduced 10-fold to 1 per 100 kbp...
November 21, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/29161428/arabidopsis-inositol-polyphosphate-multikinase-delays-flowering-time-through-mediating-transcriptional-activation-of-flowering-locus-c
#2
Sihong Sang, Yao Chen, Qiaofeng Yang, Peng Wang
Timely flowering is critical for successful reproduction and seed yield in plants. A diverse range of regulators have been found to control flowering time in response to environmental and endogenous signals. Among these regulators, FLOWERING LOCUS C (FLC) acts as a central repressor of floral transition by blocking the expression of flowering integrator genes. Here, we report that Arabidopsis inositol polyphosphate multikinase (AtIPK2β) functions in flowering time control by mediating transcriptional regulation of FLC at the chromatin level...
November 17, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/29161427/natural-genetic-variation-and-hybridization-in-plants
#3
Ian R Henderson, David E Salt
No abstract text is available yet for this article.
November 17, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/29161206/a-hypersensitivity-like-response-to-meloidogyne-graminicola-in-rice-oryza-sativa-l
#4
Ngan Thi Phan, Dirk De Waele, Mathias Lorieux, Lizhong Xiong, Stephane Bellafiore
Meloidogyne graminicola (M. graminicola) is a major plant-parasitic nematode affecting rice cultivation in Asia. Resistance to this nematode was found in the African rice genotypes Oryza glaberrima and O. longistaminata, however, due to interspecific hybrid sterility, the introgression of resistance genes in the widely consumed O. sativa varieties remains challenging. Recently, resistance was found in O. sativa and here we report for the first time the histological and genetic characterization of the resistance to M...
November 21, 2017: Phytopathology
https://www.readbyqxmd.com/read/29160037/interactions-of-host-plant-resistance-and-seed-treatments-on-soybean-aphid-aphis-glycines-matsumura-and-soybean-cyst-nematode-heterodera-glycines-ichinohe
#5
Eric H Clifton, Gregory L Tylka, Aaron J Gassmann, Erin W Hodgson
BACKGROUND: Soybean cyst nematode, Heterodera glycines, and soybean aphid, Aphis glycines, are invasive, widespread and economically important pests of soybean, Glycines max, in North America. Management of these pests relies primarily on use of pesticides and soybean germplasm with genetic resistance. A three-year field study and complementary greenhouse experiment were conducted to determine the benefits of host-plant resistance (HPR) and pesticidal seed treatments for managing pest populations and preserving soybean yield...
November 21, 2017: Pest Management Science
https://www.readbyqxmd.com/read/29159422/fine-mapping-of-qtls-for-individual-and-total-isoflavone-content-in-soybean-glycine-max-l-using-a-high-density-genetic-map
#6
Zhandong Cai, Yanbo Cheng, Zhuwen Ma, Xinguo Liu, Qibin Ma, Qiuju Xia, Gengyun Zhang, Yinghui Mu, Hai Nian
Fifteen stable QTLs were identified using a high-density soybean genetic map across multiple environments. One major QTL, qIF5-1, contributing to total isoflavone content explained phenotypic variance 49.38, 43.27, 46.59, 45.15 and 52.50%, respectively. Soybeans (Glycine max L.) are a major source of dietary isoflavones. To identify novel quantitative trait loci (QTL) underlying isoflavone content, and to improve the accuracy of marker-assisted breeding in soybean, a valuable mapping population comprised of 196 F7:8-10 recombinant inbred lines (RILs, Huachun 2 × Wayao) was utilized to evaluate individual and total isoflavone content in plants grown in four different environments in Guangdong...
November 20, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/29158642/insights-into-nuclear-dna-content-hydrogen-peroxide-and-antioxidative-enzyme-activities-during-transverse-thin-cell-layer-organogenesis-and-ex-vitro-acclimatization-of-malaxis-wallichii-a-threatened-medicinal-orchid
#7
Biswajit Bose, Suman Kumaria, Hiranjit Choudhury, Pramod Tandon
Malaxis wallichii (Lindl.) Deb, a small, perennial, monopodial, terrestrial orchid, is endemic to tropical Himalayas at an altitude of 1200-2000 m asl. The pseudobulbs are important ingredients of century old drug 'Ashtavarga' and a polyherbal energetic tonic 'Chyavanprash'. An efficient genetically stable in vitro propagation protocol using transverse thin cell layer culture system was established for M. wallichii. In the present report, meta-topolin alone proved to be three times more beneficial compared to other routinely used cytokinins in inducing highest number of shoot buds, plant height and growth of regenerated shoots...
October 2017: Physiology and Molecular Biology of Plants: An International Journal of Functional Plant Biology
https://www.readbyqxmd.com/read/29158625/comparative-genomic-hybridization-and-transcriptome-sequencing-reveal-that-two-genes-osi_14279-loc_os03g62620-and-osi_10794-loc_os03g14950-regulate-the-mutation-in-the-%C3%AE-rl-rice-mutant
#8
Xulong Wang, Fanhua Wang, Huiqiong Chen, Xiaoyu Liang, Yingmei Huang, Jicai Yi
We previously established the genetic locus of the rolled-leaf mutant, γ-rl, to chromosome 3. In this study, we performed a comparative genomic hybridization (CGH) analysis to identify the genes responsible for the γ-rl mutant phenotype. This was combined with RNA transcriptome sequencing (RNA-seq) to analyze differences in the mRNA expression in seeds 12 h after germination. Using the reference genome of the "indica type" rice from GenBank, we created a chip with 386,000 high density DNA probes designed to target chromosome 3...
October 2017: Physiology and Molecular Biology of Plants: An International Journal of Functional Plant Biology
https://www.readbyqxmd.com/read/29158439/differential-spatial-distribution-of-mir165-6-determines-variability-in-plant-root-anatomy
#9
G Di Ruocco, G Bertolotti, E Pacifici, L Polverari, M Tsiantis, S Sabatini, P Costantino, R Dello Ioio
A clear example of interspecific variation is the number of root cortical layers in plants. The genetic mechanisms underlying this variability are poorly understood, partly due to the lack of a convenient model. Here, we demonstrate that Cardamine hirsuta, unlike Arabidopsis thaliana, has two cortical layers that are patterned during late embryogenesis. We show that a miR165/6-dependent distribution of the HOMEODOMAIN LEUCINE ZIPPER III (HD-ZIPIII) transcription factor PHABULOSA (PHB) controls this pattern...
November 20, 2017: Development
https://www.readbyqxmd.com/read/29158240/novel-genes-and-regulators-that-influence-production-of-cell-surface-exopolysaccharides-in-sinorhizobium-meliloti
#10
Melanie J Barnett, Sharon R Long
Sinorhizobium meliloti is a soil-dwelling α-proteobacterium that engages in a nitrogen-fixing root nodule symbiosis with leguminous plants. Cell surface polysaccharides are important for both adapting to stresses in the soil and development of an effective symbiotic interaction. Among the polysaccharides characterized to date, the acidic exopolysaccharides EPS-I (succinoglycan) and EPS-II (galactoglucan) are particularly important for protection from abiotic stresses, biofilm formation, root colonization, and infection of plant roots...
November 20, 2017: Journal of Bacteriology
https://www.readbyqxmd.com/read/29156589/genome-wide-development-of-microrna-based-ssr-markers-in-medicago-truncatula-with-their-transferability-analysis-and-utilization-in-related-legume-species
#11
Xueyang Min, Zhengshe Zhang, Yisong Liu, Xingyi Wei, Zhipeng Liu, Yanrong Wang, Wenxian Liu
Microsatellite (simple sequence repeats, SSRs) marker is one of the most widely used markers in marker-assisted breeding. As one type of functional markers, MicroRNA-based SSR (miRNA-SSR) markers have been exploited mainly in animals, but the development and characterization of miRNA-SSR markers in plants are still limited. In the present study, miRNA-SSR markers for Medicago truncatula (M. truncatula) were developed and their cross-species transferability in six leguminous species was evaluated. A total of 169 primer pairs were successfully designed from 130 M...
November 18, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29156585/pan-cellulosomics-of-mesophilic-clostridia-variations-on-a-theme
#12
Bareket Dassa, Ilya Borovok, Vincent Lombard, Bernard Henrissat, Raphael Lamed, Edward A Bayer, Sarah Moraïs
The bacterial cellulosome is an extracellular, multi-enzyme machinery, which efficiently depolymerizes plant biomass by degrading plant cell wall polysaccharides. Several cellulolytic bacteria have evolved various elaborate modular architectures of active cellulosomes. We present here a genome-wide analysis of a dozen mesophilic clostridia species, including both well-studied and yet-undescribed cellulosome-producing bacteria. We first report here, the presence of cellulosomal elements, thus expanding our knowledge regarding the prevalence of the cellulosomal paradigm in nature...
November 18, 2017: Microorganisms
https://www.readbyqxmd.com/read/29156057/prgdb-3-0-a-comprehensive-platform-for-prediction-and-analysis-of-plant-disease-resistance-genes
#13
Cristina M O Cruz, Andreu Paytuvi-Gallart, Antimo Di Donato, Vicky Sundesha, Giuseppe Andolfo, Riccardo Aiese Cigliano, Walter Sanseverino, Maria R Ercolano
The Plant Resistance Genes database (PRGdb; http://prgdb.org) has been redesigned with a new user interface, new sections, new tools and new data for genetic improvement, allowing easy access not only to the plant science research community but also to breeders who want to improve plant disease resistance. The home page offers an overview of easy-to-read search boxes that streamline data queries and directly show plant species for which data from candidate or cloned genes have been collected. Bulk data files and curated resistance gene annotations are made available for each plant species hosted...
November 16, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29155894/estimating-virus-effective-population-size-and-selection-without-neutral-markers
#14
Elsa Rousseau, Benoît Moury, Ludovic Mailleret, Rachid Senoussi, Alain Palloix, Vincent Simon, Sophie Valière, Frédéric Grognard, Frédéric Fabre
By combining high-throughput sequencing (HTS) with experimental evolution, we can observe the within-host dynamics of pathogen variants of biomedical or ecological interest. We studied the evolutionary dynamics of five variants of Potato virus Y (PVY) in 15 doubled-haploid lines of pepper. All plants were inoculated with the same mixture of virus variants and, variant frequencies were determined by HTS in eight plants of each pepper line, at each of six sampling dates. We developed a method for estimating the intensities of selection and genetic drift in a multi-allelic Wright-Fisher model, applicable whether these forces are strong or weak, and in the absence of neutral markers...
November 20, 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/29155836/genetic-variation-in-dip5-an-amino-acid-permease-and-pdr5-a-multiple-drug-transporter-regulates-glyphosate-resistance-in-s-cerevisiae
#15
Xiaoqing Rong-Mullins, Apoorva Ravishankar, Kirsten A McNeal, Zachery R Lonergan, Audrey C Biega, J Philip Creamer, Jennifer E G Gallagher
S. cerevisiae from different environments are subject to a wide range of selective pressures, whether intentional or by happenstance. Chemicals classified by their application, such as herbicides, fungicides and antibiotics, can affect non-target organisms. First marketed as RoundUp™, glyphosate is the most widely used herbicide. In plants, glyphosate inhibits EPSPS, of the shikimate pathway, which is present in many organisms but lacking in mammals. The shikimate pathway produces chorismate which is the precursor to all the aromatic amino acids, para-aminobenzoic acid, and Coenzyme Q10...
2017: PloS One
https://www.readbyqxmd.com/read/29155358/criticism-of-efsa-s-scientific-on-combinatorial-effects-of-stacked-gm-plants
#16
Thomas Bøhn
Recent genetically modified plants tend to include both insect resistance and herbicide tolerance traits. Some of these 'stacked' GM plants have multiple Cry toxins expressed as well as tolerance to several herbicides. This means that non-target organisms in the environment (biodiversity) will be co-exposed to multiple stressors simultaneously. A similar co-exposure may happen to consumers through chemical residues in the food chain. EFSA, the responsible unit for minimizing risk of harm in European food chains, has expressed its scientific interest in combinatorial effects...
November 16, 2017: Food and Chemical Toxicology
https://www.readbyqxmd.com/read/29154499/fuzzyid2-a-software-package-for-large-dataset-species-identification-via-barcoding-and-metabarcoding-using-hidden-markov-models-and-fuzzy-set-methods
#17
Z Y Shi, C Q Yang, M D Hao, X Y Wang, R D Ward, A B Zhang
Species identification through DNA barcoding or metabarcoding has become a key approach for biodiversity evaluation and ecological studies. However, the rapid accumulation of barcoding data has created some difficulties: for instance, global enquiries to a large reference library can take a very long time. We here devise a two-step searching strategy to speed identification procedures of such queries. This firstly uses a Hidden Markov Model (HMM) algorithm to narrow the searching scope to genus level, and then determines the corresponding species using minimum genetic distance...
November 20, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/29153875/the-role-of-operating-parameters-and-oxidative-damage-mechanisms-of-advanced-chemical-oxidation-processes-in-the-combat-against-antibiotic-resistant-bacteria-and-resistance-genes-present-in-urban-wastewater
#18
REVIEW
I Michael-Kordatou, P Karaolia, D Fatta-Kassinos
An upsurge in the study of antibiotic resistance in the environment has been observed in the last decade. Nowadays, it is becoming increasingly clear that urban wastewater is a key source of antibiotic resistance determinants, i.e. antibiotic-resistant bacteria and antibiotic resistance genes (ARB&ARGs). Urban wastewater reuse has arisen as an important component of water resources management in the European Union and worldwide to address prolonged water scarcity issues. Especially, biological wastewater treatment processes (i...
October 27, 2017: Water Research
https://www.readbyqxmd.com/read/29153400/deciphering-pathogenicity-of-fusarium-oxysporum-from-a-phylogenomics-perspective
#19
Yong Zhang, Li-Jun Ma
Fusarium oxysporum is a large species complex of both plant and human pathogens that attack a diverse array of species in a host-specific manner. Comparative genomic studies have revealed that the host-specific pathogenicity of the F. oxysporum species complex (FOSC) was determined by distinct sets of supernumerary (SP) chromosomes. In contrast to common vertical transfer, where genetic materials are transmitted via cell division, SP chromosomes can be transmitted horizontally between phylogenetic lineages, explaining the polyphyletic nature of the host-specific pathogenicity of the FOSC...
2017: Advances in Genetics
https://www.readbyqxmd.com/read/29153182/a-100-year-review-cheese-production-and-quality
#20
M E Johnson
In the beginning, cheese making in the United States was all art, but embracing science and technology was necessary to make progress in producing a higher quality cheese. Traditional cheese making could not keep up with the demand for cheese, and the development of the factory system was necessary. Cheese quality suffered because of poor-quality milk, but 3 major innovations changed that: refrigeration, commercial starters, and the use of pasteurized milk for cheese making. Although by all accounts cold storage improved cheese quality, it was the improvement of milk quality, pasteurization of milk, and the use of reliable cultures for fermentation that had the biggest effect...
December 2017: Journal of Dairy Science
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