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Oryza genus

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https://www.readbyqxmd.com/read/29741624/anaerobic-carbon-monoxide-metabolism-by-pleomorphomonas-carboxyditropha-sp-nov-a-new-mesophilic-hydrogenogenic-carboxydotroph
#1
Sofia Esquivel-Elizondo, Juan Maldonado, Rosa Krajmalnik-Brown
Carbon monoxide (CO)-metabolism and phenotypic and phylogenetic characterization of a novel anaerobic, mesophilic and hydrogenogenic carboxydotroph are reported. Strain SVCO-16 was isolated from anaerobic sludge and grows autotrophically and mixotrophically with CO. The genes cooS and cooF, coding for a CO dehydrogenase complex, and genes similar to hycE2, encoding a CO-induced hydrogenase, were present in its genome. The isolate produces H2 and CO2 from CO, and acetate and formate from organic substrates. Based on the 16S rRNA sequence, it is an Alphaproteobacterium most closely related to the genus Pleomorphomonas (98...
June 1, 2018: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/29710329/chronic-meningitis-investigated-via-metagenomic-next-generation-sequencing
#2
Michael R Wilson, Brian D O'Donovan, Jeffrey M Gelfand, Hannah A Sample, Felicia C Chow, John P Betjemann, Maulik P Shah, Megan B Richie, Mark P Gorman, Rula A Hajj-Ali, Leonard H Calabrese, Kelsey C Zorn, Eric D Chow, John E Greenlee, Jonathan H Blum, Gary Green, Lillian M Khan, Debarko Banerji, Charles Langelier, Chloe Bryson-Cahn, Whitney Harrington, Jairam R Lingappa, Niraj M Shanbhag, Ari J Green, Bruce J Brew, Ariane Soldatos, Luke Strnad, Sarah B Doernberg, Cheryl A Jay, Vanja Douglas, S Andrew Josephson, Joseph L DeRisi
Importance: Identifying infectious causes of subacute or chronic meningitis can be challenging. Enhanced, unbiased diagnostic approaches are needed. Objective: To present a case series of patients with diagnostically challenging subacute or chronic meningitis using metagenomic next-generation sequencing (mNGS) of cerebrospinal fluid (CSF) supported by a statistical framework generated from mNGS of control samples from the environment and from patients who were noninfectious...
April 16, 2018: JAMA Neurology
https://www.readbyqxmd.com/read/29704539/identification-of-pseudomonas-mosselii-bs011-gene-clusters-required-for-suppression-of-rice-blast-fungus-magnaporthe-oryzae
#3
Lijuan Wu, Wei Xiao, Guoqing Chen, Dawei Song, Maqsood Ahmed Khaskheli, Pei Li, Shiying Zhang, Guozhong Feng
Pseudomonas is a Gram-negative, rod-shaped bacteria. Many members of this genus displayed remarkable physiological and metabolic activity against different plant pathogens. However, Pseudomonas mosselii has not yet been characterized in biocontrol against plant disease. Here we isolated a strain of P. mosselii BS011 from the rhizosphere soil of rice plants, and the isolate showed strong inhibitory activity against the rice blast fungus Magnaporthe oryzae. Further we sequenced the complete genome of BS011, which consist of 5...
April 25, 2018: Journal of Biotechnology
https://www.readbyqxmd.com/read/29603592/the-pepper-bs4c-proteins-are-localized-to-the-er-membrane-and-confer-disease-resistance-to-bacterial-blight-in-transgenic-rice
#4
Jun Wang, Xuan Zeng, Dongsheng Tian, Xiaobei Yang, Lanlan Wang, Zhongchao Yin
Transcription activator-like effector (TALE)-dependent dominant disease resistance (R) genes in plants, also referred to as executor R genes, are induced upon infection by phytopathogenic bacteria of the genus Xanthomonas harbouring the corresponding TALE genes. Unlike the traditional R proteins, the executor R proteins do not determine the resistance specificity and may function broadly in different plant species. The executor R gene Bs4C-R in the resistant genotype PI 235047 of the pepper species Capsicum pubescens (CpBs4C-R) confers disease resistance to Xanthomonas campestris pv...
March 30, 2018: Molecular Plant Pathology
https://www.readbyqxmd.com/read/29523074/in-silico-comparative-analysis-of-ggdef-and-eal-domain-signaling-proteins-from-the-azospirillum-genomes
#5
Alberto Ramírez Mata, César Millán Pacheco, José F Cruz Pérez, Martha Minjárez Sáenz, Beatriz E Baca
BACKGROUND: The cyclic-di-GMP (c-di-GMP) second messenger exemplifies a signaling system that regulates many bacterial behaviors of key importance; among them, c-di-GMP controls the transition between motile and sessile life-styles in bacteria. Cellular c-di-GMP levels in bacteria are regulated by the opposite enzymatic activities of diguanylate cyclases and phosphodiesterases, which are proteins that have GGDEF and EAL domains, respectively. Azospirillum is a genus of plant-growth-promoting bacteria, and members of this genus have beneficial effects in many agronomically and ecologically essential plants...
March 9, 2018: BMC Microbiology
https://www.readbyqxmd.com/read/29518024/fungal-disease-prevention-in-seedlings-of-rice-oryza-sativa-and-other-grasses-by-growth-promoting-seed-associated-endophytic-bacteria-from-invasive-phragmites-australis
#6
Satish K Verma, Kathryn L Kingsley, Marshall S Bergen, Kurt P Kowalski, James F White
Non-cultivated plants carry microbial endophytes that may be used to enhance development and disease resistance of crop species where growth-promoting and protective microbes may have been lost. During seedling establishment, seedlings may be infected by several fungal pathogens that are seed or soil borne. Several species of Fusarium , Pythium and other water moulds cause seed rots during germination. Fusarium blights of seedlings are also very common and significantly affect seedling development. In the present study we screened nine endophytic bacteria isolated from the seeds of invasive Phragmites australis by inoculating onto rice, Bermuda grass ( Cynodon dactylon ), or annual bluegrass ( Poa annua ) seeds to evaluate plant growth promotion and protection from disease caused by Fusarium oxysporum ...
March 8, 2018: Microorganisms
https://www.readbyqxmd.com/read/29487238/gene-flow-between-divergent-cereal-and-grass-specific-lineages-of-the-rice-blast-fungus-magnaporthe-oryzae
#7
Pierre Gladieux, Bradford Condon, Sebastien Ravel, Darren Soanes, Joao Leodato Nunes Maciel, Antonio Nhani, Li Chen, Ryohei Terauchi, Marc-Henri Lebrun, Didier Tharreau, Thomas Mitchell, Kerry F Pedley, Barbara Valent, Nicholas J Talbot, Mark Farman, Elisabeth Fournier
Delineating species and epidemic lineages in fungal plant pathogens is critical to our understanding of disease emergence and the structure of fungal biodiversity and also informs international regulatory decisions. Pyricularia oryzae (syn. Magnaporthe oryzae ) is a multihost pathogen that infects multiple grasses and cereals, is responsible for the most damaging rice disease (rice blast), and is of growing concern due to the recent introduction of wheat blast to Bangladesh from South America. However, the genetic structure and evolutionary history of M...
February 27, 2018: MBio
https://www.readbyqxmd.com/read/29461180/pedobacter-mongoliensis-sp-nov-isolated-from-grassland-soil
#8
Kai Yuan, Min Cao, Jingxin Li, Gejiao Wang
A Gram-stain-negative, rod-shaped, motile by gliding and strictly aerobic bacterial strain, named 1-32T , was isolated from soil of the Ordos grassland in Inner Mongolia, PR China. Strain 1-32T showed highest 16S rRNA gene sequence similarities to Pedobacter luteus N7d-4T (95.4 %), Pedobacter oryzae DSM 19973T (95.3 %), 'Pedobacter xinjiangensis' 12157T (95.2 %) and Pedobacter tournemirensis TF5-37.2-LB10T (95.1 %). Phylogenetic analyses clustered strain 1-32T with 'P. xinjiangensis' 12157T and P. tournemirensis TF5-37...
April 2018: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/29388546/roseomonas-deserti-sp-nov-isolated-from-crude-oil-contaminated-desert-sand
#9
Y Subhash, Sang-Seob Lee
Two dark pink pigmented bacterial strains (M3T and M11) were isolated from crude oil contaminated desert sand from Kuwait. Both strains were Gram-stain-negative and small-rod to oval-shaped bacteria. Strains M3T and M11 grew at 13-42 °C (optimum, 30-35 °C) and pH 6.5-9.0 (optimum, 7.0-7.5). No additional NaCl was required for the growth of both strains. The genomic DNA G+C content of strains M3T and M11 were 69.5 and 69.0 mol%, respectively. Both strains were closely related and the mean DNA-DNA hybridization value was 92±1 %...
February 2018: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/29358651/genomes-of-13-domesticated-and-wild-rice-relatives-highlight-genetic-conservation-turnover-and-innovation-across-the-genus-oryza
#10
Joshua C Stein, Yeisoo Yu, Dario Copetti, Derrick J Zwickl, Li Zhang, Chengjun Zhang, Kapeel Chougule, Dongying Gao, Aiko Iwata, Jose Luis Goicoechea, Sharon Wei, Jun Wang, Yi Liao, Muhua Wang, Julie Jacquemin, Claude Becker, Dave Kudrna, Jianwei Zhang, Carlos E M Londono, Xiang Song, Seunghee Lee, Paul Sanchez, Andrea Zuccolo, Jetty S S Ammiraju, Jayson Talag, Ann Danowitz, Luis F Rivera, Andrea R Gschwend, Christos Noutsos, Cheng-Chieh Wu, Shu-Min Kao, Jhih-Wun Zeng, Fu-Jin Wei, Qiang Zhao, Qi Feng, Moaine El Baidouri, Marie-Christine Carpentier, Eric Lasserre, Richard Cooke, Daniel da Rosa Farias, Luciano Carlos da Maia, Railson S Dos Santos, Kevin G Nyberg, Kenneth L McNally, Ramil Mauleon, Nickolai Alexandrov, Jeremy Schmutz, Dave Flowers, Chuanzhu Fan, Detlef Weigel, Kshirod K Jena, Thomas Wicker, Mingsheng Chen, Bin Han, Robert Henry, Yue-Ie C Hsing, Nori Kurata, Antonio Costa de Oliveira, Olivier Panaud, Scott A Jackson, Carlos A Machado, Michael J Sanderson, Manyuan Long, Doreen Ware, Rod A Wing
The genus Oryza is a model system for the study of molecular evolution over time scales ranging from a few thousand to 15 million years. Using 13 reference genomes spanning the Oryza species tree, we show that despite few large-scale chromosomal rearrangements rapid species diversification is mirrored by lineage-specific emergence and turnover of many novel elements, including transposons, and potential new coding and noncoding genes. Our study resolves controversial areas of the Oryza phylogeny, showing a complex history of introgression among different chromosomes in the young 'AA' subclade containing the two domesticated species...
February 2018: Nature Genetics
https://www.readbyqxmd.com/read/29330361/discovery-of-microrna-target-modules-of-african-rice-oryza-glaberrima-under-salinity-stress
#11
Tapan Kumar Mondal, Alok Kumar Panda, Hukam C Rawal, Tilak Raj Sharma
Oryza glaberrima is the second edible rice in the genus Oryza. It is grown in the African countries. miRNAs are regulatory molecules that are involved in every domains of gene expression including salinity stress response. Although several miRNAs have been reported from various species of Oryza, yet none of them are from this species. Salt treated (200 mM NaCl for 48 h) and control smallRNA libraries of RAM-100, a salt tolerant genotype, each with 2 replications generated 150 conserve and 348 novel miRNAs...
January 12, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29302791/molecular-characterization-of-a-putative-gammapartitivirus-in-the-phytopathogenic-fungus-nigrospora-oryzae
#12
Jin Xiu Yu, Jun Zi Zhu, Ying Wang, Chao Jun Zhang, Jie Zhong, Hong Jian Zhu, Bi Da Gao, Qian Zhou
We report the molecular attributes of a novel bisegmented double-stranded RNA (dsRNA) virus, designated "Nigrospora oryzae partitivirus 1" (NoPV1), from a phytopathogenic fungus Nigrospora oryzae. The genome of NoPV1 contains two dsRNA segments (dsRNA1 and 2), 1875 bp and 1601 bp in length, respectively. dsRNA1 and -2 both have a single open reading frame encoding the RNA-dependent RNA polymerase and coat protein, respectively. NoPV1 has a high degree of sequence identity to members of genus Gammapartitivirus in the family Partitiviridae...
April 2018: Archives of Virology
https://www.readbyqxmd.com/read/29164433/distal-lateral-subungual-onychomycosis-owing-to-tritirachium-oryzae-a-bystander-or-invader
#13
Hari Pankaj Vanam, P Narsimha Rao, Kalyani Mohanram, Prakash Peralam Yegneswaran, Shiva Prakash Mandya Rudramurthy
The genus Tritirachium is a mitosporic fungus which inhabits in soil and decaying plant material and also a notable insect pathogen. Human infections with Tritirachium species though rare were previously reported to cause corneal ulcers, otomycosis, onychomycosis, and dermatomycosis of the scalp and hence may be considered as a potential pathogen. Here we report a case of distal lateral subungual onychomycosis involving right great toenail in a 22-year-old female, wherein direct potassium hydroxide preparations, fungal cultures, and molecular sequencing of the isolate established Tritirachium oryzae as the etiological agent...
April 2018: Mycopathologia
https://www.readbyqxmd.com/read/29143556/datalbase-a-database-for-genomic-and-transcriptomic-data-related-to-tal-effectors
#14
Alvaro L Pérez-Quintero, Léo Lamy, Carlos A Zarate, Sébastien Cunnac, Erin Doyle, Adam Bogdanove, Boris Szurek, Alexis Dereeper
Transcription activator-like effectors (TALEs) are proteins found in the genus Xanthomonas of phytopathogenic bacteria. These proteins enter the nucleus of cells in the host plant and can induce the expression of susceptibility genes (S genes), triggering disease. TALEs bind the promoter region of S genes following a specific code, which allows the prediction of binding sites based on TALEs amino acid sequences. New candidate S genes can then be discovered by finding the intersection between genes induced in the presence of TALEs and genes containing predicted effector binding elements...
April 2018: Molecular Plant-microbe Interactions: MPMI
https://www.readbyqxmd.com/read/29125457/emended-description-of-the-genus-phytobacter-its-type-species-phytobacter-diazotrophicus-zhang-2008-and-description-of-phytobacter-ursingii-sp-nov
#15
Marcelo Pillonetto, Lavinia N Arend, Helisson Faoro, Helena R S D'Espindula, Jochen Blom, Theo H M Smits, Marcelo T Mira, Fabio Rezzonico
The species Phytobacter diazotrophicus and the associated genus Phytobacter were originally described by Zhanget al. [Arch Microbiol189 (2008), 431-439] on the basis of few endophytic nitrogen-fixing bacteria isolated from wild rice (Oryza rufipogon) in China. In this study, we demonstrate that a number of clinical isolates that were either described in the literature, preserved in culture collections, or obtained during a 2013 multi-state sepsis outbreak in Brazil also belong to the same genus. 16S rRNA gene sequencing, multilocus sequence analysis based on gyrB, rpoB, atpD and infB genes, as well as digital DNA-DNA hybridization support the existence of a second species within the genus Phytobacter...
January 2018: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/29123646/first-de-novo-draft-genome-sequence-of-oryza-coarctata-the-only-halophytic-species-in-the-genus-oryza
#16
Tapan Kumar Mondal, Hukam Chand Rawal, Kishor Gaikwad, Tilak Raj Sharma, Nagendra Kumar Singh
Oryza coarctata plant, collected from Sundarban delta of West Bengal, India,  has been used in the present study to generate draft genome sequences, employing the hybrid genome assembly with Illumina reads and third generation Oxford Nanopore sequencing technology. We report for the first time the draft genome with the coverage of 85.71 %  and  deposited the raw data in NCBI SRA, with BioProject ID PRJNA396417.
2017: F1000Research
https://www.readbyqxmd.com/read/29016662/fine-mapping-of-pi57-t-conferring-broad-spectrum-resistance-against-magnaporthe-oryzae-in-introgression-line-il-e1454-derived-from-oryza-longistaminata
#17
Liying Dong, Shufang Liu, Peng Xu, Wei Deng, Xundong Li, Didier Tharreau, Jing Li, Jiawu Zhou, Qun Wang, Dayun Tao, Qinzhong Yang
Wild species of the genus Oryza are excellent gene pools for improvement of agronomic traits of Asian cultivated rice. The blast resistance gene Pi57(t) in the introgression line IL-E1454 derived from Oryza longistaminata was previously mapped on rice chromosome 12. Inoculation with 322 Magnaporthe oryzae isolates collected from 6 countries indicated that Pi57(t) conferred broad spectrum resistance against M. oryzae. Two mapping populations consisting of 29070 and 10375 F2 plants derived from the crosses of resistant donor IL-E1454 with susceptible parents RD23 and Lijiangxintuanheigu respectively, were used for fine mapping of Pi57(t) locus...
2017: PloS One
https://www.readbyqxmd.com/read/28984554/characterization-of-the-first-rice-paddy-cluster-i-isolate-methyloterricola-oryzae-gen-nov-sp-nov-and-amended-description-of-methylomagnum-ishizawai
#18
Katharina Frindte, Sarah A Maarastawi, André Lipski, Joachim Hamacher, Claudia Knief
Three gammaproteobacterial methanotrophic strains (73aT , 175 and 114) were isolated from stems of rice plants. All strains are Gram-negative, motile and grow on methane or methanol as sole carbon sources. They oxidize methane using the particulate methane monooxygenase. Strains 114 and 175 possess additionally a soluble methane monooxygenase. All strains contain significant amounts of the cellular fatty acids C16 : 0, C16 : 1ω6c and C16 : 1ω7c, typical for type Ib methanotrophs. Characteristic for strains 114 and 175 are high amounts of C14 : 0 and C16 : 1ω6c , while strain 73aT contains high quantities of C16 : 1ω5c...
November 2017: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/28984216/streptomyces-roietensis-sp-nov-an-endophytic-actinobacterium-isolated-from-the-surface-sterilized-stem-of-jasmine-rice-oryza-sativa-kdml-105
#19
Onuma Kaewkla, Christopher Milton Mathew Franco
An endophytic actinobacterium, strain WES2T , was isolated from the stem of a jasmine rice plant collected from a paddy field in Thung Gura Rong Hai, Roi Et province, Thailand. As a result of a polyphasic study, this strain was identified as representing a novel member of the genus Streptomyces. This strain was a Gram-stain-positive, aerobic actinobacterium with well-developed substrate mycelia and forming chains of looped spores. The closest phylogenetic relations, which shared the highest 16S rRNA gene sequence similarity, were Streptomyces nogalater JCM 4799T and Streptomyces lavenduligriseus NRRL-ISP 5487T at 99...
November 2017: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/28982185/promoter-variants-of-xa23-alleles-affect-bacterial-blight-resistance-and-evolutionary-pattern
#20
Hua Cui, Chunlian Wang, Tengfei Qin, Feifei Xu, Yongchao Tang, Ying Gao, Kaijun Zhao
Bacterial blight, caused by Xanthomonas oryzae pv. oryzae (Xoo), is the most important bacterial disease in rice (Oryza sativa L.). Our previous studies have revealed that the bacterial blight resistance gene Xa23 from wild rice O. rufipogon Griff. confers the broadest-spectrum resistance against all the naturally occurring Xoo races. As a novel executor R gene, Xa23 is transcriptionally activated by the bacterial avirulence (Avr) protein AvrXa23 via binding to a 28-bp DNA element (EBEAvrXa23) in the promoter region...
2017: PloS One
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