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Plant Taxonomy

Pedro W Crous, Johannes Z Groenewald
Species of Coleophoma have been reported as plant pathogenic, saprobic or endophytic on a wide host range. The genus is characterised by having pycnidial conidiomata, phialidic conidiogenous cells intermingled among paraphyses, and cylindrical conidia. Coleophoma has had a confusing taxonomic history with numerous synonyms, and its phylogeny has remained unresolved. The aim of the present study was to use a polyphasic approach incorporating morphology, ecology, and molecular data of the partial large subunit of nrDNA (LSU), the internal transcribed spacer region with intervening 5...
November 2016: Fungal Biology
Chen Chen, Gerard J M Verkley, Guangyu Sun, Johannes Z Groenewald, Pedro W Crous
Species in Neofabraea, Pezicula, and related genera have been reported as saprobes, plant pathogens or endophytes from a wide range of hosts. The asexual morphs of Neofabraea and Pezicula had been placed in Cryptosporiopsis, now a synonym of Pezicula, while Neofabraea was also linked to Phlyctema. Based on morphology and molecular data of the partial large subunit nrDNA (LSU), the internal transcribed spacer region with intervening 5.8S nrDNA (ITS), partial β-tubulin region (tub2), and the partial RNA polymerase II second largest subunit region (rpb2), the taxonomy and phylogenetic relationships of these fungi were investigated...
November 2016: Fungal Biology
Laura Gálvez, Jéssica Gil-Serna, Marta García, Concepción Iglesias, Daniel Palmero
The most serious aerial disease of garlic is leaf blight caused by Stemphylium spp. Geographical variation in the causal agent of this disease is indicated. Stemphylium vesicarium has been reported in Spain, whereas S. solani is the most prevalent species recorded in China. In this study, Stemphylium isolates were obtained from symptomatic garlic plants sampled from the main Spanish production areas. Sequence data for the ITS1-5.8S-ITS2 region enabled assignation of the isolates to the Pleospora herbarum complex and clearly distinguished the isolates from S...
October 2016: Plant Pathology Journal
Katalin Solymosi, Attila Köfalvi
Cannabis is one of the earliest cultivated plants. Cannabis of industrial utility and culinary value is generally termed as hemp. Conversely, cannabis that is bred for medical, spiritual and recreational purposes is called marijuana. The female marijuana plant produces a significant quantity of bio- and psychoactive phytocannabinoids, which regained the spotlight with the discovery of the endocannabinoid system of the animals in the early 90's. Nevertheless, marijuana is surrounded by controversies, debates and misconceptions related to its taxonomic classification, forensic identification, medical potential, legalization and its long-term health consequences...
October 4, 2016: Mini Reviews in Medicinal Chemistry
Sanna Olsson, Pedro Seoane Zonjic, Rocío Bautista, M Gonzalo Claros, Santiago C González-Martínez, Ivan Scotti, Caroline Scotti-Saintagne, Olivier J Hardy, Myriam Heuertz
Population genetic studies in tropical plants are often challenging because of limited information on taxonomy, phylogenetic relationships and distribution ranges, scarce genomic information and logistic challenges in sampling. We describe a strategy to develop robust and widely applicable genetic markers based on a modest development of genomic resources in the ancient tropical tree species Symphonia globulifera L. f. (Clusiaceae), a keystone species in African and Neotropical rainforests. We provide the first low-coverage (11X) fragmented draft genome sequenced on an individual from Cameroon, covering 1...
October 8, 2016: Molecular Ecology Resources
Łukasz P Haliński, Piotr Stepnowski
The tomato (Solanum lycopersicum L.) is one of the most important vegetables worldwide. Due to the limited genetic variability, wild related species are considered as potential gene pool for breeding cultivated plants with enriched genetic basis. Taxonomic relations between tomato species at the level of single groups and taxa still remain, however, not fully resolved. Hence, in addition to already reported classification based on the morphology of the plants and molecular markers, we proposed chemotaxonomic approach to unveil some aspects of tomato taxonomy...
October 4, 2016: Phytochemistry
Xianzong Wang, Xiaolin Liu
BACKGROUND: Horizontal transfer (HT) of genetic materials is increasingly being found in both animals and plants and mainly concerns transposable elements (TEs). Many crustaceans have big genome sizes and are thus likely to harbor high TE contents. Their habitat might offer them ample opportunities to exchange genetic materials with organisms that are ecologically close but taxonomically distant to them. RESULTS: In this study, we analyzed the transcriptome of Pacific white shrimp (Litopenaeus vannamei), an important economic crustacean, to explore traces of HT events...
October 7, 2016: BMC Evolutionary Biology
J C Polonio, A D Polli, J L Azevedo, J A Pamphile
Endophytic microorganisms, mainly bacteria and fungi, have intrinsic relationships with the host plants, involving complex chemical and genetic communication networks. The relationship among these organisms involves the development of regulatory mechanisms of gene expression that control their development and response to different interactions. Although RNA molecules are already being used in studies of microorganism diversity and taxonomy, for example, using comparisons of rRNA regions, they may also be useful tools in the exploration of gene regulation and modeling of other molecules, such as the analysis of microRNA and small interfering RNAs...
September 19, 2016: Genetics and Molecular Research: GMR
S L Y Ma, Y M Lu
The Chinese hawthorn (Crataegus pinnatifida Bge. var. major N.E.Br.) is uniquely originated in northern China. The ecological and horticultural importance of Chinese hawthorn is considerable and some varieties are valued for their fruit or medicine extracts. Its taxonomy and phylogeny remain poorly understood. Apart from general plant morphological traits, pollen is an important trait for the classification of plants and their evolutionary origin. However, few studies have investigated the pollen of Chinese hawthorn...
September 19, 2016: Genetics and Molecular Research: GMR
Rui-Lan Huang
No abstract text is available yet for this article.
September 27, 2016: Protein & Cell
Jamie W L Ong, Hua Li, Krishnapillai Sivasithamparam, Kingsley W Dixon, Michael G K Jones, Stephen J Wylie
Viruses associated with wild orchids and their mycorrhizal fungi are poorly studied. Using a shotgun sequencing approach, we identified eight novel endornavirus-like genome sequences from isolates of Ceratobasidium fungi isolated from pelotons within root cortical cells of wild indigenous orchid species Microtis media, Pterostylis sanguinea and an undetermined species of Pterostylis in Western Australia. They represent the first endornaviruses to be described from orchid mycorrhizal fungi and from the Australian continent...
September 24, 2016: Virology
Andrea R Ottesen, Sasha Gorham, Elizabeth Reed, Michael J Newell, Padmini Ramachandran, Travis Canida, Marc Allard, Peter Evans, Eric Brown, James Robert White
An important data gap in our understanding of the phyllosphere surrounds the origin of the many microbes described as phyllosphere communities. Most sampling in phyllosphere research has focused on the collection of microbiota without the use of a control, so the opportunity to determine which taxa are actually driven by the biology and physiology of plants as opposed to introduced by environmental forces has yet to be fully realized. To address this data gap, we used plastic plants as inanimate controls adjacent to live tomato plants (phyllosphere) in the field with the hope of distinguishing between bacterial microbiota that may be endemic to plants as opposed to introduced by environmental forces...
2016: PloS One
Juan M Palazzini, Christopher A Dunlap, Michael J Bowman, Sofía N Chulze
Bacillus subtilis RC 218 was originally isolated from wheat anthers as a potential antagonist of Fusarium graminearum, the causal agent of Fusarium head blight (FHB). It was demonstrated to have antagonist activity against the plant pathogen under in vitro and greenhouse assays. The current study extends characterizing B. subtilis RC 218 with a field study and genome sequencing. The field study demonstrated that B. subtilis RC 218 could reduce disease severity and the associated mycotoxin (deoxynivalenol) accumulation, under field conditions...
November 2016: Microbiological Research
S Mehra, P D Morrison, F Coates, A C Lawrie
Terrestrial orchids depend on orchid mycorrhizal fungi (OMF) as symbionts for their survival, growth and nutrition. The ability of OMF from endangered orchid species to compete for available resources with OMF from common species may affect the distribution, abundance and therefore conservation status of their orchid hosts. Eight symbiotically effective OMF from endangered and more common Caladenia species were tested for their ability to utilise complex insoluble and simple soluble carbon sources produced during litter degradation by growth with different carbon sources in liquid medium to measure the degree of OMF variation with host conservation status or taxonomy...
September 17, 2016: Mycorrhiza
M Sandoval-Denis, J Gené, D A Sutton, J F Cano-Lira, G S de Hoog, C A Decock, N P Wiederhold, J Guarro
The genera Microascus and Scopulariopsis comprise species commonly isolated from soil, decaying plant material and indoor environments. A few species are also recognised as opportunistic pathogens of insects and animals, including humans. In the past, the taxonomy of these fungi has been based on morphology only. With the aim to clarify the taxonomy and phylogeny of these fungi, we studied a large set of clinical and environmental isolates, including the available ex-type strains of numerous species, by means of morphological, physiological and molecular analyses...
June 2016: Persoonia
Arantxa Peña, Antonio Busquets, Margarita Gomila, Magdalena Mulet, Rosa M Gomila, T B K Reddy, Marcel Huntemann, Amrita Pati, Natalia Ivanova, Victor Markowitz, Elena García-Valdés, Markus Göker, Tanja Woyke, Hans-Peter Klenk, Nikos Kyrpides, Jorge Lalucat
Pseudomonas has the highest number of species out of any genus of Gram-negative bacteria and is phylogenetically divided into several groups. The Pseudomonas putida phylogenetic branch includes at least 13 species of environmental and industrial interest, plant-associated bacteria, insect pathogens, and even some members that have been found in clinical specimens. In the context of the Genomic Encyclopedia of Bacteria and Archaea project, we present the permanent, high-quality draft genomes of the type strains of 3 taxonomically and ecologically closely related species in the Pseudomonas putida phylogenetic branch: Pseudomonas fulva DSM 17717(T), Pseudomonas parafulva DSM 17004(T) and Pseudomonas cremoricolorata DSM 17059(T)...
2016: Standards in Genomic Sciences
Deeksha Singh, Uttam Singh Baghel, Anshoo Gautam, Dheeraj Singh Baghel, Divya Yadav, Jai Malik, Rakesh Yadav
ETHNOPHARMACOLOGICAL RELEVANCE: The genus Anogeissus (axlewood tree, ghatti tree, button tree and chewing stick tree) belongs to Combretaceae, includes eight species that are distributed in Asia and Africa. Plants are used as an ethnomedicine in Asia and Africa to treat various ailments like diabetes, fever, diarrhoea, dysentery, tuberculosis, wound healing, skin diseases (eczema, psoriasis), snake and scorpion venom. Based on the traditional knowledge, different phytochemical and pharmacological activities have been at the focus of research...
August 23, 2016: Journal of Ethnopharmacology
Haojie Su, Yao Wu, Ping Xie, Jun Chen, Te Cao, Wulai Xia
Carbon (C), nitrogen (N) and phosphorus (P) are the three most important essential elements limiting growth of primary producers. Submerged macrophytes generally absorb nutrients from sediments by root uptake. However, the C:N:P stoichiometric signatures of plant tissue are affected by many additional factors such as taxonomy, nutrient availability, and light availability. We first revealed the relative importance of taxonomy, sediment, and water column on plant C:N:P stoichiometry using variance partitioning based on partial redundancy analyses...
August 24, 2016: Environmental Science and Pollution Research International
Boris A Vinatzer, Alexandra J Weisberg, Caroline L Monteil, Haitham A Elmarakeby, Samuel K Sheppard, Lenwood S Heath
Taxonomy of plant pathogenic bacteria is challenging because pathogens of different crops often belong to the same named species but current taxonomy does not provide names for bacteria below the subspecies level. The introduction of the host range-based pathovar system in the 1980s provided a temporary solution to this problem but has many limitations. The affordability of genome sequencing now provides the opportunity for developing a new genome-based taxonomic framework. We already proposed to name individual bacterial isolates based on pairwise genome similarity...
October 14, 2016: Phytopathology
Brenda D Wingfield, Jon M Ambler, Martin P A Coetzee, Z Wilhelm de Beer, Tuan A Duong, Fourie Joubert, Almuth Hammerbacher, Alistair R McTaggart, Kershney Naidoo, Hai D T Nguyen, Ekaterina Ponomareva, Quentin S Santana, Keith A Seifert, Emma T Steenkamp, Conrad Trollip, Magriet A van der Nest, Cobus M Visagie, P Markus Wilken, Michael J Wingfield, Neriman Yilmaz
The genomes of Armillaria fuscipes, Ceratocystiopsis minuta, Ceratocystis adiposa, Endoconidiophora laricicola, E. polonica, and Penicillium freii DAOMC 242723 are presented in this genome announcement. These six genomes are from plant pathogens and otherwise economically important fungal species. The genome sizes range from 21 Mb in the case of Ceratocystiopsis minuta to 58 Mb for the basidiomycete Armillaria fuscipes. These genomes include the first reports of genomes for the genus Endoconidiophora. The availability of these genome data will provide opportunities to resolve longstanding questions regarding the taxonomy of species in these genera...
June 2016: IMA Fungus
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