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Plant genomics

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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
#1
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
#2
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
#3
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/29155849/unusual-occurrence-of-a-dag-motif-in-the-ipomovirus-cassava-brown-streak-virus-and-implications-for-its-vector-transmission
#4
Elijah Ateka, Titus Alicai, Joseph Ndunguru, Fred Tairo, Peter Sseruwagi, Samuel Kiarie, Timothy Makori, Monica A Kehoe, Laura M Boykin
Cassava is the main staple food for over 800 million people globally. Its production in eastern Africa is being constrained by two devastating Ipomoviruses that cause cassava brown streak disease (CBSD); Cassava brown streak virus (CBSV) and Ugandan cassava brown streak virus (UCBSV), with up to 100% yield loss for smallholder farmers in the region. To date, vector studies have not resulted in reproducible and highly efficient transmission of CBSV and UCBSV. Most virus transmission studies have used Bemisia tabaci (whitefly), but a maximum of 41% U/CBSV transmission efficiency has been documented for this vector...
2017: PloS One
https://www.readbyqxmd.com/read/29155326/genome-wide-identification-of-the-sweet-gene-family-in-wheat
#5
Yue Gao, Zi Yuan Wang, Vikranth Kumar, Xiao Feng Xu, De Peng Yuan, Xiao Feng Zhu, Tian Ya Li, Bao Lei Jia, Yuan Hu Xuan
The SWEET (sugars will eventually be exported transporter) family is a newly characterized group of sugar transporters. In plants, the key roles of SWEETs in phloem transport, nectar secretion, pollen nutrition, stress tolerance, and plant-pathogen interactions have been identified. SWEET family genes have been characterized in many plant species, but a comprehensive analysis of SWEET members has not yet been performed in wheat. Here, 59 wheat SWEETs (hereafter TaSWEETs) were identified through homology searches...
November 16, 2017: Gene
https://www.readbyqxmd.com/read/29153832/drastic-genome-reduction-in-an-herbivore-s-pectinolytic-symbiont
#6
Hassan Salem, Eugen Bauer, Roy Kirsch, Aileen Berasategui, Michael Cripps, Benjamin Weiss, Ryuichi Koga, Kayoko Fukumori, Heiko Vogel, Takema Fukatsu, Martin Kaltenpoth
Pectin, an integral component of the plant cell wall, is a recalcitrant substrate against enzymatic challenges by most animals. In characterizing the source of a leaf beetle's (Cassida rubiginosa) pectin-degrading phenotype, we demonstrate its dependency on an extracellular bacterium housed in specialized organs connected to the foregut. Despite possessing the smallest genome (0.27 Mb) of any organism not subsisting within a host cell, the symbiont nonetheless retained a functional pectinolytic metabolism targeting the polysaccharide's two most abundant classes: homogalacturonan and rhamnogalacturonan I...
November 10, 2017: Cell
https://www.readbyqxmd.com/read/29153405/describing-genomic-and-epigenomic-traits-underpinning-emerging-fungal-pathogens
#7
Rhys A Farrer, Matthew C Fisher
An unprecedented number of pathogenic fungi are emerging and causing disease in animals and plants, putting the resilience of wild and managed ecosystems in jeopardy. While the past decades have seen an increase in the number of pathogenic fungi, they have also seen the birth of new big data technologies and analytical approaches to tackle these emerging pathogens. We review how the linked fields of genomics and epigenomics are transforming our ability to address the challenge of emerging fungal pathogens. We explore the methodologies and bioinformatic toolkits that currently exist to rapidly analyze the genomes of unknown fungi, then discuss how these data can be used to address key questions that shed light on their epidemiology...
2017: Advances in Genetics
https://www.readbyqxmd.com/read/29153402/phylogenetics-and-phylogenomics-of-rust-fungi
#8
M Catherine Aime, Alistair R McTaggart, Stephen J Mondo, Sébastien Duplessis
Rust fungi (Pucciniales) are the most speciose and the most complex group of plant pathogens. Historically, rust taxonomy was largely influenced by host and phenotypic characters, which are potentially plastic. Molecular systematic studies suggest that the extant diversity of this group was largely shaped by host jumps and subsequent shifts. However, it has been challenging to reconstruct the evolutionary history for the order, especially at deeper (family-level) nodes. Phylogenomics offer a potentially powerful tool to reconstruct the Pucciniales tree of life, although researchers working at this vanguard still face unprecedented challenges working with nonculturable organisms that possess some of the largest and most repetitive genomes now known in kingdom fungi...
2017: Advances in Genetics
https://www.readbyqxmd.com/read/29153400/deciphering-pathogenicity-of-fusarium-oxysporum-from-a-phylogenomics-perspective
#9
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/29153257/pseudomonas-silesiensis-sp-nov-strain-a3-t-isolated-from-a-biological-pesticide-sewage-treatment-plant-and-analysis-of-the-complete-genome-sequence
#10
Michał A Kaminski, Ewa M Furmanczyk, Adam Sobczak, Andrzej Dziembowski, Leszek Lipinski
Microorganisms classified in to the Pseudomonas genus are a ubiquitous bacteria inhabiting variety of environmental niches and have been isolated from soil, sediment, water and different parts of higher organisms (plants and animals). Members of this genus are known for their metabolic versatility and are able to utilize different chemical compounds as a source of carbon, nitrogen or phosphorus, which makes them an interesting microorganism for bioremediation or bio-transformation. Moreover, Pseudomonas sp...
November 3, 2017: Systematic and Applied Microbiology
https://www.readbyqxmd.com/read/29153071/-mycoviruses-and-importance-in-mycology
#11
Sema Aşkın Keçeli
Opportunistic fungal infections like invasive candidiasis and aspergillozis have high mortality rate particularly in immunosupressive patients. The rate of therapy success with antifungal agents is usually low. Although immunotherapy methods have been developed to increase the host response against antifungals, there has been a need for new antifungal therapeutic agents in the treatment of invasive aspergillozis and other opportunistic fungal infections. Mycoviruses are the viruses that specifically infect fungi...
October 2017: Mikrobiyoloji Bülteni
https://www.readbyqxmd.com/read/29153016/whole-root-transcriptomic-analysis-suggests-a-role-for-auxin-pathways-in-resistance-to-ralstonia-solanacearum-in-tomato
#12
Elizabeth French, Bong-Suk Kim, Katherine Rivera-Zuluaga, Anjali Iyer-Pascuzzi
The soilborne pathogen Ralstonia solanacearum is the causal agent of bacterial wilt, and causes significant crop loss in the Solanaceae family. The pathogen first infects roots, which are a critical source of resistance in tomato (Solanum lycopersicum L.). Roots of both resistant and susceptible plants are colonized by the pathogen, yet rootstocks can provide significant levels of resistance. Currently, mechanisms of this 'root-mediated resistance' remain largely unknown. To identify the molecular basis of this resistance, we analyzed the genome-wide transcriptional response of roots of resistant (Hawaii 7996) and susceptible (West Virginia700) tomatoes at multiple time points after inoculation with R...
November 20, 2017: Molecular Plant-microbe Interactions: MPMI
https://www.readbyqxmd.com/read/29152703/multiplex-pcr-to-detect-bacteriophages-from-natural-whey-cultures-of-buffalo-milk-and-characterisation-of-two-phages-active-against-lactococcus-lactis-%C3%AE-apr-1-and-%C3%AE-apr-2
#13
Giuseppe Aprea, William Michael Mullan, Nicoletta Murru, Gerald Fitzgerald, Marialuisa Buonanno, Maria Luisa Cortesi, Vincenza Annunziata Prencipe, Giacomo Migliorati
This work investigated bacteriophage induced starter failures in artisanal buffalo Mozzarella production plants in Southern Italy. Two hundred and ten samples of whey starter cultures were screened for bacteriophage infection. Multiplex polymerase chain reaction (PCR) revealed phage infection in 28.56% of samples, all showing acidification problems during cheese making. Based on DNA sequences, bacteriophages for Lactococcus lactis (L. lactis), Lactobacillus delbruekii (L. delbruekii) and Streptococcus thermophilus (S...
September 30, 2017: Veterinaria Italiana
https://www.readbyqxmd.com/read/29152037/complete-genome-sequence-of-pseudomonas-corrugata-strain-rm1-1-4-a-stress-protecting-agent-from-the-rhizosphere-of-an-oilseed-rape-bait-plant
#14
Christin Zachow, Henry Müller, Christina M Laireiter, Ralf Tilcher, Gabriele Berg
10.1601/nm.2592 strain RM1-1-4 is a rhizosphere colonizer of oilseed rape. A previous study has shown that this motile, Gram-negative, non-sporulating bacterium is an effective stress protecting and biocontrol agent, which protects their hosts against abiotic and biotic stresses. Here, we announce and describe the complete genome sequence of P. corrugata RM1-1-4 consisting of a single 6.1 Mb circular chromosome that encodes 5189 protein coding genes and 85 RNA-only encoding genes. Genome analysis revealed genes predicting functions such as detoxifying mechanisms, stress inhibitors, exoproteases, lipoproteins or volatile components as well as rhizobactin siderophores and spermidine...
2017: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/29150594/mating-design-and-genetic-structure-of-a-multi-parent-advanced-generation-inter-cross-magic-population-of-sorghum-sorghum-bicolor-l-moench
#15
Patrick O Ongom, Gebisa Ejeta
MAGIC populations are powerful next generation mapping resources. We describe here the mating design and structure of the first MAGIC population in sorghum and test its utility for mapping. The population was developed by intercrossing 19 diverse founder lines, through a series of paired crosses with a genetic male sterile source, followed by 10 generations of random mating. At the final stage of random mating, one thousand random fertile plants in the population were identified and subjected to six generations of selfing to produce 1000 immortal MAGIC inbred lines...
November 17, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/29150511/sulfolobus-acidocaldarius-uptakes-pentoses-via-a-cut2-type-abc-transporter-and-metabolizes-them-through-the-aldolase-independent-weimberg-pathway
#16
Michaela Wagner, Lu Shen, Andreas Albersmeier, Nienke van der Kolk, Sujin Kim, Jaeho Cha, Christopher Bräsen, Jörn Kalinowski, Bettina Siebers, Sonja-Verena Albers
Sulfolobus spp. possess a great metabolic versatility and grow heterotrophically on various carbon sources such as different sugars and peptides. Known sugar transporters in Archaea predominantly belong to ABC transport systems. Although several ABC transporters for sugar uptake have been characterized in the crenarchaeon Sulfolobus solfataricus, only one homologue of these transporters, the maltose/maltooligomer transporter, could be identified in the closely related Sulfolobus acidocaldarius Comparison of the transcriptome of S...
November 17, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29149287/genomic-and-epigenomic-immunity-in-common-bean-the-unusual-features-of-nb-lrr-gene-family
#17
Manon M S Richard, Ariane Gratias, Vincent Thareau, Kyung Do Kim, Sandrine Balzergue, Johann Joets, Scott A Jackson, Valérie Geffroy
In plants, a key class of genes comprising most of disease resistance (R) genes encodes Nucleotide-binding leucine-rich repeat (NL) proteins. Access to common bean (Phaseolus vulgaris) genome sequence provides unparalleled insight into the organization and evolution of this large gene family (∼400 NL) in this important crop. As observed in other plant species, most common bean NL are organized in cluster of genes. However, a particularity of common bean is that these clusters are often located in subtelomeric regions close to terminal knobs containing the satellite DNA khipu...
November 15, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/29149280/whole-genome-re-sequencing-of-two-italian-tomato-landraces-reveals-sequence-variations-in-genes-associated-with-stress-tolerance-fruit-quality-and-long-shelf-life-traits
#18
Valentina Tranchida-Lombardo, Riccardo Aiese Cigliano, Irantzu Anzar, Simone Landi, Samuela Palombieri, Chiara Colantuono, Hamed Bostan, Pasquale Termolino, Riccardo Aversano, Giorgia Batelli, Maria Cammareri, Domenico Carputo, Maria Luisa Chiusano, Clara Conicella, Federica Consiglio, Nunzio D'Agostino, Monica De Palma, Antonio Di Matteo, Silvana Grandillo, Walter Sanseverino, Marina Tucci, Stefania Grillo
Tomato is a high value crop and the primary model for fleshy fruit development and ripening. Breeding priorities include increased fruit quality, shelf life and tolerance to stresses. To contribute towards this goal, we re-sequenced the genomes of Corbarino (COR) and Lucariello (LUC) landraces, which both possess the traits of plant adaptation to water deficit, prolonged fruit shelf-life and good fruit quality. Through the newly developed pipeline Reconstructor, we generated the genome sequences of COR and LUC using datasets of 65...
November 14, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/29149093/evolutionarily-distant-streptophyta-respond-differently-to-genotoxic-stress
#19
Radka Vágnerová, Alena Lukešová, Martin Lukeš, Petra Rožnovská, Marcela Holá, Jana Fulnečková, Jiří Fajkus, Karel J Angelis
Research in algae usually focuses on the description and characterization of morpho-and phenotype as a result of adaptation to a particular habitat and its conditions. To better understand the evolution of lineages we characterized responses of filamentous streptophyte green algae of the genera Klebsormidium and Zygnema, and of a land plant-the moss Physcomitrellapatens-to genotoxic stress that might be relevant to their environment. We studied the induction and repair of DNA double strand breaks (DSBs) elicited by the radiomimetic drug bleomycin, DNA single strand breaks (SSB) as consequence of base modification by the alkylation agent methyl methanesulfonate (MMS) and of ultra violet (UV)-induced photo-dimers, because the mode of action of these three genotoxic agents is well understood...
November 17, 2017: Genes
https://www.readbyqxmd.com/read/29147792/characterization-of-a-novel-single-stranded-rna-mycovirus-related-to-invertebrate-viruses-from-the-plant-pathogen-verticillium-dahliae
#20
M Carmen Cañizares, Francisco J López-Escudero, Encarnación Pérez-Artés, María D García-Pedrajas
Fungal viruses, also known as mycoviruses, are widespread in all major groups of fungi. Mycoviruses from plant pathogens can reduce the virulence of their host fungus and have therefore potential as biological control agents. This has spurred the identification of novel mycoviruses in plant pathogens, research which is greatly contributing to our understanding of these organisms. In this work, we report the characterization of a novel monopartite mycovirus from Verticillium dahliae, the main causal agent of Verticillium wilt...
November 16, 2017: Archives of Virology
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