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Plant genomics

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https://www.readbyqxmd.com/read/28934492/concerted-action-of-two-3-cap-independent-translation-enhancers-increases-the-competitive-strength-of-translated-viral-genomes
#1
Zhiyou Du, Olga M Alekhina, Konstantin S Vassilenko, Anne E Simon
Several families of plant viruses evolved cap-independent translation enhancers (3'CITE) in the 3' untranslated regions of their genomic (g)RNAs to compete with ongoing cap-dependent translation of cellular mRNAs. Umbravirus Pea enation mosaic virus (PEMV)2 is the only example where three 3'CITEs enhance translation: the eIF4E-binding Panicum mosaic virus-like translational enhancer (PTE) and ribosome-binding 3' T-shaped structure (TSS) have been found in viruses of different genera, while the ribosome-binding kl-TSS that provides a long-distance interaction with the 5' end is unique...
September 19, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28934377/the-environmental-acinetobacter-baumannii-isolate-dsm30011-reveals-clues-into-the-preantibiotic-era-genome-diversity-virulence-potential-and-niche-range-of-a-predominant-nosocomial-pathogen
#2
Guillermo D Repizo, Alejandro M Viale, Vítor Borges, María M Cameranesi, Najwa Taib, Martín Espariz, Céline Brochier-Armanet, João Paulo Gomes, Suzana P Salcedo
Acinetobacter baumannii represents nowadays an important nosocomial opportunistic pathogen whose reservoirs outside the clinical setting are obscure. Here, we traced the origins of the collection strain A. baumannii DSM30011 to an isolate first reported in 1944, obtained from the enriched microbiota responsible of the aerobic decomposition of the resinous desert shrub guayule. Whole-genome sequencing and phylogenetic analysis based on core genes confirmed DSM30011 affiliation to A. baumannii. Comparative studies with 32 complete A...
September 1, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28934298/transcriptome-analysis-of-callery-pear-pyrus-calleryana-reveals-a-comprehensive-signalling-network-in-response-to-alternaria-alternata
#3
Jialiang Kan, Tingli Liu, Na Ma, Hui Li, Xiaogang Li, Jinyan Wang, Baolong Zhang, Youhong Chang, Jing Lin
The pear is an important temperate fruit worldwide that is produced by a group of species in the genus Pyrus. Callery pear (Pyrus calleryana Decne) is characterized by high resistance to multiple diseases, good adaptability, and high ornamental value, and is therefore widely planted in pear orchards for edible fruit production or as stock. Plant pathogens are a major threat to pear yield. Black spot disease, caused by the filamentous fungus Alternaria alternata, is one of the most serious diseases in pear. Elucidation of resistant genes to black spot disease is extremely important for understanding the underlying mechanisms as well as for the development of resistant cultivars...
2017: PloS One
https://www.readbyqxmd.com/read/28934201/forensic-genetics-and-genomics-much-more-than-just-a-human-affair
#4
REVIEW
Miguel Arenas, Filipe Pereira, Manuela Oliveira, Nadia Pinto, Alexandra M Lopes, Veronica Gomes, Angel Carracedo, Antonio Amorim
While traditional forensic genetics has been oriented towards using human DNA in criminal investigation and civil court cases, it currently presents a much wider application range, including not only legal situations sensu stricto but also and, increasingly often, to preemptively avoid judicial processes. Despite some difficulties, current forensic genetics is progressively incorporating the analysis of nonhuman genetic material to a greater extent. The analysis of this material-including other animal species, plants, or microorganisms-is now broadly used, providing ancillary evidence in criminalistics in cases such as animal attacks, trafficking of species, bioterrorism and biocrimes, and identification of fraudulent food composition, among many others...
September 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28934148/tomato-leaf-curl-new-delhi-virus-an-emerging-virus-complex-threatening-vegetable-and-fiber-crops
#5
REVIEW
Enrique Moriones, Shelly Praveen, Supriya Chakraborty
The tomato leaf curl New Delhi virus (ToLCNDV) (genus Begomovirus, family Geminiviridae) represents an important constraint to tomato production, as it causes the most predominant and economically important disease affecting tomato in the Indian sub-continent. However, in recent years, ToLCNDV has been fast extending its host range and spreading to new geographical regions, including the Middle East and the western Mediterranean Basin. Extensive research on the genome structure, protein functions, molecular biology, and plant-virus interactions of ToLCNDV has been conducted in the last decade...
September 21, 2017: Viruses
https://www.readbyqxmd.com/read/28933690/ictv-virus-taxonomy-profile-cystoviridae
#6
Minna M Poranen, Sari Mäntynen, Ictv Report Consortium
The family Cystoviridae includes enveloped viruses with a tri-segmented dsRNA genome and a double-layered protein capsid. The innermost protein shell is a polymerase complex responsible for genome packaging, replication and transcription. Cystoviruses infect Gram-negative bacteria, primarily plant-pathogenic Pseudomonas syringae strains. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the taxonomy of the Cystoviridae, which is available at http://www.ictv.global/report/cystoviridae...
September 20, 2017: Journal of General Virology
https://www.readbyqxmd.com/read/28933688/v2-from-a-curtovirus-is-a-suppressor-of-post-transcriptional-gene-silencing
#7
Ana P Luna, Edgar A Rodríguez-Negrete, Gabriel Morilla, Liping Wang, Rosa Lozano-Durán, Araceli G Castillo, Eduardo R Bejarano
The suppression of gene silencing is a key mechanism for the success of viral infection in plants. DNA viruses from the Geminiviridae family encode several proteins that suppress transcriptional and post-transcriptional gene silencing (TGS/PTGS). In Begomovirus, the most abundant genus of this family, three out of six genome-encoded proteins, namely C2, C4 and V2, have been shown to suppress PTGS, with V2 being the strongest PTGS suppressor in transient assays. Beet curly top virus (BCTV), the model species for the Curtovirus genus, is able to infect the widest range of plants among geminiviruses...
September 21, 2017: Journal of General Virology
https://www.readbyqxmd.com/read/28933079/-advance-in-transcriptomic-studies-of-ginseng-species
#8
Li-Qiu Zou, Xue-Jun Kuang, Ying Li, Chao Sun
There are many valuable medicinal plants in Ginseng genus belonging to Araliaceae. Among them, Panax ginseng, P. quinquefolium and P. notoginseng are the most famous species. With the development of next-generation sequencing (NGS) technologies, sequencing and analysis of transcriptomes have become powerful tools for discovery of novel genes, screening molecular markers and elucidation of specific biosynthetic pathway of secondary metabolites. Their transcriptomes provided abundant genes for further study on functional genomics...
November 2016: Zhongguo Zhong Yao za Zhi, Zhongguo Zhongyao Zazhi, China Journal of Chinese Materia Medica
https://www.readbyqxmd.com/read/28933076/-strategies-of-elucidation-of-biosynthetic-pathways-of-natural-products
#9
Li-Qiu Zou, Xue-Jun Kuang, Chao Sun, Shi-Lin Chen
Elucidation of the biosynthetic pathways of natural products is not only the major goal of herb genomics, but also the solid foundation of synthetic biology of natural products. Here, this paper reviewed recent advance in this field and put forward strategies to elucidate the biosynthetic pathway of natural products. Firstly, a proposed biosynthetic pathway should be set up based on well-known knowledge about chemical reactions and information on the identified compounds, as well as studies with isotope tracer...
November 2016: Zhongguo Zhong Yao za Zhi, Zhongguo Zhongyao Zazhi, China Journal of Chinese Materia Medica
https://www.readbyqxmd.com/read/28933072/-metabolomics-research-of-medicinal-plants
#10
Li-Xin Duan, Yun-Tao Dai, Chao Sun, Shi-Lin Chen
Metabolomics is the comprehensively study of chemical processes involving small molecule metabolites. It is an important part of systems biology, and is widely applied in complex traditional Chinese medicine(TCM)system. Metabolites biosynthesized by medicinal plants are the effective basis for TCM. Metabolomics studies of medicinal plants will usher in a new period of vigorous development with the implementation of Herb Genome Program and the development of TCM synthetic biology. This manuscript introduces the recent research progresses of metabolomics technology and the main research contents of metabolomics studies for medicinal plants, including identification and quality evaluation for medicinal plants, cultivars breeding, stress resistance, metabolic pathways, metabolic network, metabolic engineering and synthetic biology researches...
November 2016: Zhongguo Zhong Yao za Zhi, Zhongguo Zhongyao Zazhi, China Journal of Chinese Materia Medica
https://www.readbyqxmd.com/read/28932215/identification-characterization-and-full-length-sequence-analysis-of-a-novel-polerovirus-associated-with-wheat-leaf-yellowing-disease
#11
Peipei Zhang, Yan Liu, Wenwen Liu, Mengji Cao, Sebastien Massart, Xifeng Wang
To identify the pathogens responsible for leaf yellowing symptoms on wheat samples collected from Jinan, China, we tested for the presence of three known barley/wheat yellow dwarf viruses (BYDV-GAV, -PAV, WYDV-GPV) (most likely pathogens) using RT-PCR. A sample that tested negative for the three viruses was selected for small RNA sequencing. Twenty-five million sequences were generated, among which 5% were of viral origin. A novel polerovirus was discovered and temporarily named wheat leaf yellowing-associated virus (WLYaV)...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28931465/chronic-radiation-exposure-as-an-ecological-factor-hypermethylation-and-genetic-differentiation-in-irradiated-scots-pine-populations
#12
P Yu Volkova, S A Geras'kin, N Horemans, E S Makarenko, E Saenen, G T Duarte, R Nauts, V S Bondarenko, G Jacobs, S Voorspoels, M Kudin
Genetic and epigenetic changes were investigated in chronically irradiated Scots pine (Pinus sylvestris L.) populations from territories that were heavily contaminated by radionuclides as result of the Chernobyl Nuclear Power Plant accident. In comparison to the reference site, the genetic diversity revealed by electrophoretic mobility of AFLPs was found to be significantly higher at the radioactively contaminated areas. In addition, the genome of pine trees was significantly hypermethylated at 4 of the 7 affected sites...
September 18, 2017: Environmental Pollution
https://www.readbyqxmd.com/read/28931375/identification-of-fasciclin-like-arabinogalactan-proteins-in-textile-hemp-cannabis-sativa-l-in-silico-analyses-and-gene-expression-patterns-in-different-tissues
#13
Gea Guerriero, Lauralie Mangeot-Peter, Sylvain Legay, Marc Behr, Stanley Lutts, Khawar Sohail Siddiqui, Jean-Francois Hausman
BACKGROUND: The fasciclin-like arabinogalactan proteins (FLAs) belong to the arabinogalactan protein (AGP) superfamily and are known to play different physiological roles in plants. This class of proteins was shown to participate in plant growth, development, defense against abiotic stresses and, notably, cell wall biosynthesis. Although some studies are available on the characterization of FLA genes from different species, both woody and herbaceous, no detailed information is available on the FLA family of textile hemp (Cannabis sativa L...
September 20, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28931093/synthesis-of-udp-apiose-in-bacteria-the-marine-phototroph-geminicoccus-roseus-and-the-plant-pathogen-xanthomonas-pisi
#14
James Amor Smith, Maor Bar-Peled
The branched-chain sugar apiose was widely assumed to be synthesized only by plant species. In plants, apiose-containing polysaccharides are found in vascularized plant cell walls as the pectic polymers rhamnogalacturonan II and apiogalacturonan. Apiosylated secondary metabolites are also common in many plant species including ancestral avascular bryophytes and green algae. Apiosyl-residues have not been documented in bacteria. In a screen for new bacterial glycan structures, we detected small amounts of apiose in methanolic extracts of the aerobic phototroph Geminicoccus roseus and the pathogenic soil-dwelling bacteria Xanthomonas pisi...
2017: PloS One
https://www.readbyqxmd.com/read/28931057/challenges-and-advances-for-transcriptome-assembly-in-non-model-species
#15
Arnaud Ungaro, Nicolas Pech, Jean-François Martin, R J Scott McCairns, Jean-Philippe Mévy, Rémi Chappaz, André Gilles
Analyses of high-throughput transcriptome sequences of non-model organisms are based on two main approaches: de novo assembly and genome-guided assembly using mapping to assign reads prior to assembly. Given the limits of mapping reads to a reference when it is highly divergent, as is frequently the case for non-model species, we evaluate whether using blastn would outperform mapping methods for read assignment in such situations (>15% divergence). We demonstrate its high performance by using simulated reads of lengths corresponding to those generated by the most common sequencing platforms, and over a realistic range of genetic divergence (0% to 30% divergence)...
2017: PloS One
https://www.readbyqxmd.com/read/28931056/heterogeneity-in-the-expression-and-subcellular-localization-of-polyol-monosaccharide-transporter-genes-in-lotus-japonicus
#16
Lu Tian, Leru Liu, Yehu Yin, Mingchao Huang, Yanbo Chen, Xinlan Xu, Pingzhi Wu, Meiru Li, Guojiang Wu, Huawu Jiang, Yaping Chen
Polyols can serve as a means for the translocation of carbon skeletons and energy between source and sink organs as well as being osmoprotective solutes and antioxidants which may be involved in the resistance of some plants to biotic and abiotic stresses. Polyol/Monosaccharide transporter (PLT) proteins previously identified in plants are involved in the loading of polyols into the phloem and are reported to be located in the plasma membrane. The functions of PLT proteins in leguminous plants are not yet clear...
2017: PloS One
https://www.readbyqxmd.com/read/28930608/anti-tick-vaccines-in-the-omics-era
#17
Manuel Rodriguez Valle, Felix D Guerrero
Tick vaccines have been available for more than 20 years. They are useful and effective control agents when used properly. However, no new products have emerged since the Bm86-based Gavac vaccine was commercialized. Acaricide resistance is a problem with no abatement in sight and anti-tick vaccines are likely to be relied upon even more in the coming years. As human medicine and plant agriculture has embraced the various Omics technologies, the search for anti-tick vaccines would be well served to follow; so that new vaccine antigens and adjuvants might be developed to assist tick control programs...
January 1, 2018: Frontiers in Bioscience (Elite Edition)
https://www.readbyqxmd.com/read/28929670/-herbgenomics
#18
Shi-Lin Chen, Jing-Yuan Song
Traditional Chinese medicine (TCM) has contributad greatly to improving human health. However, the biological characteristics and molecular mechanisms of TCM in the treatment of human diseases remain largely unknown. Genomics plays an important role in modern medicine and biology. Here, we introduce genomics and other related omics to the study of herbs to propose a new discipline, Herbgenomics, that aims to uncover the genetic information and regulatory networks of herbs and to clarify their molecular mechanisms in the prevention and treatment of human diseases...
November 2016: Zhongguo Zhong Yao za Zhi, Zhongguo Zhongyao Zazhi, China Journal of Chinese Materia Medica
https://www.readbyqxmd.com/read/28929273/complete-genome-sequence-of-a-novel-lytic-bacteriophage-isolated-from-ralstonia-solanacearum
#19
Jingfang Su, Hongwei Sun, Junjie Liu, Zhaokui Guo, Guoquan Fan, Gang Gu, Guanghua Wang
A lytic podophage RSPI1 was isolated from tobacco field soil collected in Fujian Province, South China using host bacterium Ralstonia solanacearum Tb15-14. Whole genome sequencing of this phage was performed using the high-throughput Ion Torrent PGM Sequencer. The complete genome of RSPI1 was 43,211 bp in length with a mean DNA G + C content of 61.5%. A total of 48 open reading frames were identified with lengths ranging from 132 bp to 5,061 bp, of which, 11, 12 and 25 were identified as functional, structural and unknown genes, respectively...
September 19, 2017: Archives of Virology
https://www.readbyqxmd.com/read/28928963/recent-advances-in-understanding-the-roles-of-whole-genome-duplications-in-evolution
#20
REVIEW
Carol MacKintosh, David E K Ferrier
Ancient whole-genome duplications (WGDs)- paleopolyploidy events-are key to solving Darwin's 'abominable mystery' of how flowering plants evolved and radiated into a rich variety of species. The vertebrates also emerged from their invertebrate ancestors via two WGDs, and genomes of diverse gymnosperm trees, unicellular eukaryotes, invertebrates, fishes, amphibians and even a rodent carry evidence of lineage-specific WGDs. Modern polyploidy is common in eukaryotes, and it can be induced, enabling mechanisms and short-term cost-benefit assessments of polyploidy to be studied experimentally...
2017: F1000Research
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