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Oryza genus

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https://www.readbyqxmd.com/read/29143556/datalbase-a-database-for-genomic-and-transcriptomic-data-related-to-tal-effectors
#1
Alvaro L Pérez-Quintero, Léo Lamy, Carlos A Zarate, Sébastien Cunnac, Erin L Doyle, Adam J Bogdanove, Boris Szurek, Alexis Derepeer
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 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 sequence. New candidate susceptibility genes can then be discovered by finding the intersection between genes induced in the presence of TALEs and genes containing predicted effector binding elements (EBEs)...
November 16, 2017: 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
#2
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...
November 10, 2017: 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
#3
Tapan Kumar Mondal, Hukam Chand Rawal, Kishor Gaikwad, Tilak Raj Sharma, Nagendra Kumar Singh
Oryza coarctata plants, collected from Sundarban delta of West Bengal, India, have 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 that more than 85.71 % of the genome coverage and the data have been deposited 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
#4
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
#5
Katharina Frindte, Sarah A Maarastawi, André Lipski, Joachim Hamacher, Claudia Knief
Three gammaproteobacterial methanotrophic strains (73a(T), 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 73a(T) contains high quantities of C16 : 1ω5c...
October 6, 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
#6
Onuma Kaewkla, Christopher Milton Mathew Franco
An endophytic actinobacterium, strain WES2(T), 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 4799(T) and Streptomyces lavenduligriseus NRRL-ISP 5487(T) at 99...
October 6, 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
#7
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
https://www.readbyqxmd.com/read/28905700/roseomonas-aerofrigidensis-sp-nov-isolated-from-an-air-conditioner
#8
Jong Woo Hyeon, Che Ok Jeon
A Gram-stain-negative, strictly aerobic bacterium, designated HC1(T), was isolated from an air conditioner in South Korea. Cells were orange, non-motile cocci with oxidase- and catalase-positive activities and did not contain bacteriochlorophyll a. Growth of strain HC1(T) was observed at 10-45 °C (optimum, 30 °C), pH 4.5-9.5 (optimum, pH 7.0) and 0-3 % (w/v) NaCl (optimum, 0 %). Strain HC1(T) contained summed feature 8 (comprising C18 : 1ω7c/C18 : 1ω6c), C16 : 0 and cyclo-C19 : 0ω8c as the major fatty acids and ubiquinone-10 as the sole isoprenoid quinone...
October 2017: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/28853686/serratia-oryzae-sp-nov-isolated-from-rice-stems
#9
Cai-Wen Zhang, Jun Zhang, Juan-Juan Zhao, Xia Zhao, Dong-Fang Zhao, Hua-Qun Yin, Xiao-Xia Zhang
A novel endophytic bacterium, strain J11-6T, was isolated from rice stems. Its taxonomic position was investigated using a polyphasic approach. The novel strain was Gram-staining-negative, facultatively anaerobic, motile and rod-shaped. Although the results of phylogenetic analysis based on 16S rRNA gene sequences indicated that J11-6T represented a member of the genus Rahnella, multilocus sequence analysis (MLSA) on the basis of concatenated partial atpD, gyrB, rpoB and infB gene sequences showed a clear distinction of J11-6T from the type strains of species of the genus Rahnella but indicated that it lay within the clade of the genus Serratia...
August 2017: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/28820105/roseomonas-hibiscisoli-sp-nov-isolated-from-the-rhizosphere-of-mugunghwa-hibiscus-syriacus
#10
Zheng-Fei Yan, Pei Lin, Chang-Tian Li, MooChang Kook, Qi-Jun Wang, Tae-Hoo Yi
A Gram-stain-negative, aerobic, non-motile and coccoid to short-rod-shaped bacterial strain (THG-N2.22T) was isolated from the rhizosphere of Mugunghwa (Hibiscus syriacus). Growth occurred at 20-40 °C (optimum 28 °C), at pH 5-9 (optimum 7) and with 0-4 % (w/v) NaCl (optimum 1 %). Based on 16S rRNA gene sequence analysis, the nearest phylogenetic neighbours of strain THG-N2.22T were identified as Roseomonas rhizosphaerae YW11T (98.5 % similarity), Roseomonas rubra S5T (98.5 %), Roseomonas cervicalis ATCC 49957T (98...
August 2017: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/28818885/draft-genome-sequences-of-two-gammaproteobacterial-methanotrophs-isolated-from-rice-ecosystems
#11
Katharina Frindte, Marina G Kalyuzhnaya, Françoise Bringel, Peter F Dunfield, Mike S M Jetten, Valentina N Khmelenina, Martin G Klotz, J Colin Murrell, Huub J M Op den Camp, Yasuyoshi Sakai, Jeremy D Semrau, Nicole Shapiro, Alan A DiSpirito, Lisa Y Stein, Mette M Svenning, Yuri A Trotsenko, Stéphane Vuilleumier, Tanja Woyke, Claudia Knief
The genomes of the aerobic methanotrophs "Methyloterricola oryzae" strain 73a(T) and Methylomagnum ishizawai strain 175 were sequenced. Both strains were isolated from rice plants. Methyloterricola oryzae strain 73a(T) represents the first isolate of rice paddy cluster I, and strain 175 is the second representative of the recently described genus Methylomagnum.
August 17, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28755328/alternaria-toxins-in-south-african-sunflower-seeds-cooperative-study
#12
Sebastian Hickert, Lena Hermes, Lucas Maciel Mauriz Marques, Christine Focke, Benedikt Cramer, Norberto Peporine Lopes, Bradley Flett, Hans-Ulrich Humpf
Sunflower seed samples (N = 80) from different sunflower cultivars originating from different localities in South Africa were analyzed for 15 toxins produced by fungi of the genus Alternaria by means of a simple one-step extraction dilute-and-shoot HPLC-MS/MS approach. References for valine-tenuazonic acid (Val-TeA), altenusin (ALTS), and altenuisol (ALTSOH) were isolated from fungal culture extracts and spectroscopically characterized. Additionally, valine-tenuazonic acid was tested regarding its cytotoxicity in comparison with tenuazonic acid (TeA) and showed less activity on HT-29 cells...
November 2017: Mycotoxin Research
https://www.readbyqxmd.com/read/28736890/insect-frass-in-stored-cereal-products-as-a-potential-source-of-lactobacillus-sanfranciscensis-for-sourdough-ecosystem
#13
F Boiocchi, D Porcellato, L Limonta, C Picozzi, I Vigentini, D P Locatelli, R Foschino
AIM: Insect frass samples were collected from Drosophila melanogaster, Plodia interpunctella, Rhyzopertha dominica, Sitophilus granarius, Sitophilus oryzae, Sitophilus zeamais, Tribolium confusum and Tribolium castaneum to elucidate if they can be the origin of Type I sourdough micro-organisms (Lactobacillus sanfranciscensis and Candida milleri). METHODS AND RESULTS: Selective enrichments were carried out to isolate lactic acid bacteria (LBA) and yeast. A metagenetic analysis, targeted on bacterial 16S rRNA gene and fungal ITS region, was performed by using Illumina MiSeq protocol...
July 23, 2017: Journal of Applied Microbiology
https://www.readbyqxmd.com/read/28732553/diversity-application-and-synthetic-biology-of-industrially-important-aspergillus-fungi
#14
REVIEW
Hee-Soo Park, Sang-Cheol Jun, Kap-Hoon Han, Seung-Beom Hong, Jae-Hyuk Yu
The filamentous fungal genus Aspergillus consists of over 340 officially recognized species. A handful of these Aspergillus fungi are predominantly used for food fermentation and large-scale production of enzymes, organic acids, and bioactive compounds. These industrially important Aspergilli primarily belong to the two major Aspergillus sections, Nigri and Flavi. Aspergillus oryzae (section Flavi) is the most commonly used mold for the fermentation of soybeans, rice, grains, and potatoes. Aspergillus niger (section Nigri) is used in the industrial production of various enzymes and organic acids, including 99% (1...
2017: Advances in Applied Microbiology
https://www.readbyqxmd.com/read/28714843/roseomonas-suffusca-sp-nov-isolated-from-lagoon-sediments
#15
Y Subhash, Sang-Seob Lee
Three light-brown-coloured, Gram-stain-negative, small rod- to oval-shaped, motile bacteria were isolated from lagoon sediments collected from North Carolina, USA. The strains (S1T, AS3 and AS6) grew aerobically at 13-42 °C (optimum, 30-35 °C) and pH 6.5-9.1 (optimum, pH 7.0-7.5). All three strains were positive for catalase and oxidase activity, and no added NaCl was required for growth. C18 : 1ω6c/C18 : 1ω7c, C16 : 1ω6c/C16 : 1ω7c, C18 : 1ω7c 11-methyl and C16 : 0 were the predominant fatty acids (>5 %)...
July 2017: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/28643580/cyclophilins-less-studied-proteins-with-critical-roles-in-pathogenesis
#16
Khushwant Singh, Mark Winter, Miloslav Zouhar, Pavel Rysanek
Cyclophilins (EC 5.2.1.8) (CYPs) belong to a subgroup of proteins known as immunophilins, which also include FK-506 binding proteins (FKBPs) and parvulins. Members of the immunophilins have two main characteristic properties: I) peptidyl-prolyl cis-trans isomerase activity (PPIases) and II) the ability to bind immunosuppressant molecules of fungal origin. Cyclophilins are some of the most conserved proteins present in eukaryotes and prokaryotes, and they have been implicated in diverse cellular processes and responses to multiple biotic and abiotic stresses...
June 23, 2017: Phytopathology
https://www.readbyqxmd.com/read/28621110/characterization-of-microbial-communities-in-chinese-rice-wine-collected-at-yichang-city-and-suzhou-city-in-china
#17
Yucai Lü, Yanli Gong, Yajie Li, Zejiang Pan, Yi Yao, Ning Li, Jinling Guo, Dachun Gong, Yihong Tian, Caiyun Peng
Two typical microbial communities from Chinese rice wine fermentation collected in Yichang city and Suzhou city in China were investigated. Both communities could ferment glutinous rice to rice wine in 2 days. The sugar and ethanol contents were 198.67 and 14.47 mg/g, respectively, for rice wine from Yichang city, and 292.50 and 12.31 mg/g, respectively, for rice wine from Suzhou city. Acetic acid and lactic acid were the most abundant organic acids. Abundant fungi and bacteria were detected in both communities by high-throughput sequencing...
August 28, 2017: Journal of Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28619808/first-insights-into-the-genome-sequence-of-clostridium-oryzae-dsm-28571-isolated-from-the-soil-of-a-japanese-rice-field
#18
Anja Poehlein, Anna Lena Gippert, Maaike J Bierenbroodspot, Rolf Daniel
Clostridium oryzae was originally isolated from the soil of a Japanese rice field. C. oryzae represents a novel species within the genus Clostridium and is associated with anaerobic rice straw degradation. Here, we present the draft genome sequence of C. oryzae DSM 28571 (5.076 Mbp), containing 4,590 predicted protein-coding genes.
June 15, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28475028/chthonobacter-albigriseus-gen-nov-sp-nov-isolated-from-grass-field-soil
#19
Dohak Kim, Keunsoo Kang, Tae-Young Ahn
A novel aerobic, Gram-stain-negative and non-motile bacterial strain, designated ED7T, was isolated from grass-field soil in Cheonan, Korea. Strain ED7T utilized methanol and methylamine, but not formate, as carbon and energy sources. The strain was able to grow at 20-42 °C (optimum 30-35 °C), at pH 7.0-8.5 (optimum pH 7.5-8.0), and in the absence of NaCl. According to the similarities of the 16S rRNA gene sequences, strain ED7T was most closely related to the genera Labrenzia (≤93.3 % 16S rRNA gene sequence similarity), Pleomorphomonas (≤93...
April 2017: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/28323300/a-walk-on-the-wild-side-oryza-species-as-source-for-rice-abiotic-stress-tolerance
#20
Paloma Koprovski Menguer, Raul Antonio Sperotto, Felipe Klein Ricachenevsky
Oryza sativa, the common cultivated rice, is one of the most important crops for human consumption, but production is increasingly threatened by abiotic stresses. Although many efforts have resulted in breeding rice cultivars that are relatively tolerant to their local environments, climate changes and population increase are expected to soon call for new, fast generation of stress tolerant rice germplasm, and current within-species rice diversity might not be enough to overcome such needs. The Oryza genus contains other 23 wild species, with only Oryza glaberrima being also domesticated...
2017: Genetics and Molecular Biology
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