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Plant Taxonomy

Albert Barberán, Hildamarie Caceres Velazquez, Stuart Jones, Noah Fierer
Cultivation in the laboratory is essential for understanding the phenotypic characteristics and environmental preferences of bacteria. However, basic phenotypic information is not readily accessible. Here, we compiled phenotypic and environmental tolerance information for >5,000 bacterial strains described in the International Journal of Systematic and Evolutionary Microbiology (IJSEM) with all information made publicly available in an updatable database. Although the data span 23 different bacterial phyla, most entries described aerobic, mesophilic, neutrophilic strains from Proteobacteria (mainly Alpha- and Gammaproteobacteria), Actinobacteria, Firmicutes, and Bacteroidetes isolated from soils, marine habitats, and plants...
July 2017: MSphere
Olov Svartström, Johannes Alneberg, Nicolas Terrapon, Vincent Lombard, Ino de Bruijn, Jonas Malmsten, Ann-Marie Dalin, Emilie El Muller, Pranjul Shah, Paul Wilmes, Bernard Henrissat, Henrik Aspeborg, Anders F Andersson
The moose (Alces alces) is a ruminant that harvests energy from fiber-rich lignocellulose material through carbohydrate-active enzymes (CAZymes) produced by its rumen microbes. We applied shotgun metagenomics to rumen contents from six moose to obtain insights into this microbiome. Following binning, 99 metagenome-assembled genomes (MAGs) belonging to 11 prokaryotic phyla were reconstructed and characterized based on phylogeny and CAZyme profile. The taxonomy of these MAGs reflected the overall composition of the metagenome, with dominance of the phyla Bacteroidetes and Firmicutes...
July 21, 2017: ISME Journal
Shuyan Lin, Li Zhang, Gadi V P Reddy, Cang Hui, Johan Gielis, Yulong Ding, Peijian Shi
The size and shape of plant leaves change with growth, and an accurate description of leaf shape is crucial for describing plant morphogenesis and development. Bilateral symmetry, which has been widely observed but poorly examined, occurs in both dicot and monocot leaves, including all nominated bamboo species (approximately 1,300 species), of which at least 500 are found in China. Although there are apparent differences in leaf size among bamboo species due to genetic and environmental profiles, bamboo leaves have bilateral symmetry with parallel venation and appear similar across species...
October 2016: Ecology and Evolution
David Gilmer, Claudio Ratti, Ictv Report Consortium
The Benyviridae is a family of multipartite plant viruses with rod-shaped virions. Genomes are segmented and comprised of single-stranded, positive-sense RNAs, each with a 5' m7G cap. Unlike rod-shaped viruses classified in the Virgaviridae family, the genome segments have a 3' polyA tract and there is post-translational cleavage of the viral replicase. The better-known members are transmitted by root-infecting vectors in the Plasmodiphorales family, once described as fungi but now classified as Cercozoa. The family has a single genus...
July 2017: Journal of General Virology
Wenpan Dong, Chao Xu, Wenqing Li, Xiaoman Xie, Yizeng Lu, Yanlei Liu, Xiaobai Jin, Zhili Suo
Walnuts (Juglans of the Juglandaceae) are well-known economically important resource plants for the edible nuts, high-quality wood, and medicinal use, with a distribution from tropical to temperate zones and from Asia to Europe and Americas. There are about 21 species in Juglans. Classification of Juglans at section level is problematic, because the phylogenetic position of Juglans cinerea is disputable. Lacking morphological and DNA markers severely inhibited the development of related researches. In this study, the complete chloroplast genomes and two nuclear DNA regions (the internal transcribed spacer and ubiquitin ligase gene) of 10 representative taxa of Juglans were used for comparative genomic analyses in order to deepen the understanding on the application value of genetic information for inferring the phylogenetic relationship of the genus...
2017: Frontiers in Plant Science
Q Chen, L W Hou, W J Duan, P W Crous, L Cai
The Didymellaceae is one of the most species-rich families in the fungal kingdom, and includes species that inhabit a wide range of ecosystems. The taxonomy of Didymellaceae has recently been revised on the basis of multi-locus DNA sequence data. In the present study, we investigated 108 Didymellaceae isolates newly obtained from 40 host plant species in 27 plant families, and various substrates from caves, including air, water and carbonatite, originating from Argentina, Australia, Canada, China, Hungary, Israel, Italy, Japan, South Africa, the Netherlands, the USA and former Yugoslavia...
June 2017: Studies in Mycology
Davide Dagnino, Luigi Minuto, Gabriele Casazza
Delimiting taxa boundaries is a crucial point for any evolutionary research and conservation regulation. In order to avoid mistaken description of species, the approach of integrative taxonomy recommends to consider multidisciplinary lines of evidence, including ecology. Unfortunately, ecological data are often difficult to quantify in an objective way. Here we test and discuss the potential use of Ecological Niche Models for validating taxa boundaries, using three pairs of closely related plant taxa endemic to South-western Alps as a case study...
July 10, 2017: Plant Biology
Cheng-Hong Yang, Kuo-Chuan Wu, Hans-Uwe Dahms, Li-Yeh Chuang, Hsueh-Wei Chang
DNA barcodes are widely used in taxonomy, systematics, species identification, food safety, and forensic science. Most of the conventional DNA barcode sequences contain the whole information of a given barcoding gene. Most of the sequence information does not vary and is uninformative for a given group of taxa within a monophylum. We suggest here a method that reduces the amount of noninformative nucleotides in a given barcoding sequence of a major taxon, like the prokaryotes, or eukaryotic animals, plants, or fungi...
July 2017: Ecology and Evolution
Julissa Rojas-Sandoval, Raymond L Tremblay, Pedro Acevedo-Rodríguez, Hilda Díaz-Soltero
The level of invasion (number or proportion of invasive species) in a given area depends on features of the invaded community, propagule pressure, and climate. In this study, we assess the invasive flora of nine islands in the West Indies to identify invasion patterns and evaluate whether invasive species diversity is related to geographical, ecological, and socioeconomic factors. We compiled a database of invasive plant species including information on their taxonomy, origin, pathways of introduction, habitats, and life history...
July 2017: Ecology and Evolution
Gunajit Goswami, Priyadarshini Deka, Pompi Das, Sudipta Sankar Bora, Ramkrishna Samanta, Robin Chandra Boro, Madhumita Barooah
In this study, we report on the bacterial diversity and their functional properties prevalent in tea garden soils of Assam that have low pH (3.8-5.5). Culture-dependent studies and phospholipid fatty acid analysis revealed a high abundance of Gram-positive bacteria. Further, 70 acid-tolerant bacterial isolates characterized using a polyphasic taxonomy approach could be grouped to the genus Bacillus, Lysinibacillus, Staphylococcus, Brevundimonas, Alcaligenes, Enterobacter, Klebsiella, Escherichia, and Aeromonas...
July 2017: 3 Biotech
Valentine Nakato, George Mahuku, Teresa Coutinho
Taxonomy: Bacteria; Phylum Proteobacteria; Class Gammaproteobacteria; Order Xanthomonadales; Family Xanthomonadaceae; Genus Xanthomonas; currently classified as X. campestris pv. musacearum (Xcm). However, fatty acid methyl esters analysis, genetic and genomic evidence suggest that this pathogen is X. vasicola and resides in a separate pathovar. Isolation and detection: Xcm can be isolated on Yeast Peptone Glucose Agar (YPGA), Cellobiose Cephalexin Agar and Yeast Tryptone Sucrose Agar (YTSA) complemented with 5-flouro-uracil, cephalexin and cycloheximide to confer semi-selectivity...
July 5, 2017: Molecular Plant Pathology
Vicki A Funk, Patrick Herendeen, Sandra Knapp
No abstract text is available yet for this article.
June 28, 2017: Nature
S A Burgess, S H Flint, D Lindsay, M P Cox, P J Biggs
BACKGROUND: The genus Geobacillus comprises bacteria that are Gram positive, thermophilic spore-formers, which are found in a variety of environments from hot-springs, cool soils, to food manufacturing plants, including dairy manufacturing plants. Despite considerable interest in the use of Geobacillus spp. for biotechnological applications, the taxonomy of this genus is unclear, in part because of differences in DNA-DNA hybridization (DDH) similarity values between studies. In addition, it is also difficult to use phenotypic characteristics to define a bacterial species...
June 26, 2017: BMC Microbiology
Tam Dang, Roderich D Süssmuth
The need for new drugs for the treatment of various diseases is enormous. From the previous century until the present, numerous peptide and peptide-derived natural products have been isolated from bacteria and fungi. Hence, microorganisms play a pivotal role as sources for novel drugs with an emphasis on anti-infective agents. Various disciplines from biology, chemistry, and medicine are involved in early stages of the search for peptide natural products including taxonomy, microbiology, bioanalytics, bioinformatics, and medicinal chemistry...
June 26, 2017: Accounts of Chemical Research
Tomasz Suchan, Anahí Espíndola, Sereina Rutschmann, Brent C Emerson, Kevin Gori, Christophe Dessimoz, Nils Arrigo, Michał Ronikier, Nadir Alvarez
Determining phylogenetic relationships among recently diverged species has long been a challenge in evolutionary biology. Cytoplasmic DNA markers, which have been widely used, notably in the context of molecular barcoding, have not always proved successful in resolving such phylogenies. However, with the advent of next-generation-sequencing technologies and associated techniques of reduced genome representation, phylogenies of closely related species have been resolved at a much higher detail in the last couple of years...
June 21, 2017: Molecular Phylogenetics and Evolution
María Laura García, Elena Dal Bó, John V da Graça, Selma Gago-Zachert, John Hammond, Pedro Moreno, Tomohide Natsuaki, Vicente Pallás, Jose A Navarro, Carina A Reyes, Gabriel Robles Luna, Takahide Sasaya, Ioannis E Tzanetakis, Anna María Vaira, Martin Verbeek, Ictv Report Consortium
The Ophioviridae is a family of filamentous plant viruses, with single-stranded negative, and possibly ambisense, RNA genomes of 11.3-12.5 kb divided into 3-4 segments, each encapsidated separately. Virions are naked filamentous nucleocapsids, forming kinked circles of at least two different contour lengths. The sole genus, Ophiovirus, includes seven species. Four ophioviruses are soil-transmitted and their natural hosts include trees, shrubs, vegetables and bulbous or corm-forming ornamentals, both monocots and dicots...
June 2017: Journal of General Virology
Yu Sun, Yuan Liu, Guan Wang, Haiyan Zhang
Plant image identification has become an interdisciplinary focus in both botanical taxonomy and computer vision. The first plant image dataset collected by mobile phone in natural scene is presented, which contains 10,000 images of 100 ornamental plant species in Beijing Forestry University campus. A 26-layer deep learning model consisting of 8 residual building blocks is designed for large-scale plant classification in natural environment. The proposed model achieves a recognition rate of 91.78% on the BJFU100 dataset, demonstrating that deep learning is a promising technology for smart forestry...
2017: Computational Intelligence and Neuroscience
Yannick De Smet, Olivier De Clerck, Tatsuya Uemachi, Carolina Granados Mendoza, Stefan Wanke, Paul Goetghebeur, Marie-Stéphanie Samain
The number of species recognized in section Asperae of the flowering plant genus Hydrangea differs widely between subsequent revisions. This variation is largely centered around the H. aspera species complex, with numbers of recognized species varying from one to nearly a dozen. Despite indications of molecular variation in this complex, no sequence-based species delimitation methods have been employed to evaluate the primarily morphology-based species boundaries. In the present study, a multi-locus coalescent-based approach to species delimitation is employed in order to identify separate evolutionary lines within H...
June 9, 2017: Molecular Phylogenetics and Evolution
Geonho Cho, Daniel Burckhardt, Seunghwan Lee
The taxonomy of jumping plant-lice from South Korea is revised based on extensive, recently collected material and specimens preserved in several collections. Three species are described as new (Craspedolepta yongjungi, Cacopsylla baccatae and Cyamophila floribundae spp. nov.) and 11 species are recorded from South Korea for the first time (Aphalaridae 2, Homotomidae 1, Liviidae 1, Psyllidae 6, Triozidae 1). One genus and 13 species are synonymised, two species are removed from synonymy and two species are recombined...
March 6, 2017: Zootaxa
David J Perović, Sagrario Gámez-Virués, Douglas A Landis, Felix Wäckers, Geoff M Gurr, Stephen D Wratten, Min-Sheng You, Nicolas Desneux
Ecological studies are increasingly moving towards trait-based approaches, as the evidence mounts that functions, as opposed to taxonomy, drive ecosystem service delivery. Among ecosystem services, biological control has been somewhat overlooked in functional ecological studies. This is surprising given that, over recent decades, much of biological control research has been focused on identifying the multiple characteristics (traits) of species that influence trophic interactions. These traits are especially well developed for interactions between arthropods and flowers - important for biological control, as floral resources can provide natural enemies with nutritional supplements, which can dramatically increase biological control efficiency...
June 9, 2017: Biological Reviews of the Cambridge Philosophical Society
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