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Plant Taxonomy

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https://www.readbyqxmd.com/read/28635587/ictv-virus-taxonomy-profile-ophioviridae
#1
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 21, 2017: Journal of General Virology
https://www.readbyqxmd.com/read/28611840/deep-learning-for-plant-identification-in-natural-environment
#2
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
https://www.readbyqxmd.com/read/28606445/multilocus-coalescent-species-delimitation-to-evaluate-traditionally-defined-morphotypes-in-hydrangea-sect-asperae-hydrangeaceae
#3
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
https://www.readbyqxmd.com/read/28598568/managing-biological-control-services-through-multi-trophic-trait-interactions-review-and-guidelines-for-implementation-at-local-and-landscape-scales
#4
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
https://www.readbyqxmd.com/read/28597444/endoreduplication-as-a-part-of-flower-ontogeny-in-trifolium-pratense-cultivars
#5
Valéria Kocová, Nikola Straková, Vladislav Kolarčik, Albert Rákai, Pavol Mártonfi
BACKGROUND: Endoreduplication appears in numerous plant species and plays a vital role during ontogeny. The presence of polyploid cells in an otherwise diploid organism is tied specifically to the taxonomy, ecology and physiology of the studied specimen. Little is known about the changes in endopolyploidy levels of floral organs during their development. In order to uncover the workings of endoreduplication in polysomatic species, our study examines flowers of T. pratense in three ontogenetic stages by means of flow cytometry...
December 2016: Botanical Studies (Taipei, Taiwan)
https://www.readbyqxmd.com/read/28597435/micro-morphological-study-of-evolvulus-spp-convolvulaceae-the-old-world-medicinal-plants
#6
Kanapol Ketjarun, George W Staples, Sasivimon C Swangpol, Paweena Traiperm
BACKGROUND: Several medicinal properties have been reported for plants in the genus Evolvulus, such as a brain tonic and antifungal from Evolvulus alsinoides, and a sedative and an anthelmintic from Evolvulus nummularius. Therefore, the correct identification of the source plants is critically important. The aim of this research was to investigate the micromorphology of two Evolvulus taxa used for herbal medicines compared with one worldwide ornamental species by using peeling, paraffin embedding, acetolysis, and SEM methods in order to support species identification...
December 2016: Botanical Studies (Taipei, Taiwan)
https://www.readbyqxmd.com/read/28595622/the-evolution-of-trypanosomatid-taxonomy
#7
REVIEW
Alexa Kaufer, John Ellis, Damien Stark, Joel Barratt
Trypanosomatids are protozoan parasites of the class Kinetoplastida predominately restricted to invertebrate hosts (i.e. possess a monoxenous life-cycle). However, several genera are pathogenic to humans, animals and plants, and have an invertebrate vector that facilitates their transmission (i.e. possess a dixenous life-cycle). Phytomonas is one dixenous genus that includes several plant pathogens transmitted by phytophagous insects. Trypanosoma and Leishmania are dixenous genera that infect vertebrates, including humans, and are transmitted by hematophagous invertebrates...
June 8, 2017: Parasites & Vectors
https://www.readbyqxmd.com/read/28579999/development-of-chloroplast-and-nuclear-dna-markers-for-chinese-oaks-quercus-subgenus-quercus-and-assessment-of-their-utility-as-dna-barcodes
#8
Jia Yang, Lucía Vázquez, Xiaodan Chen, Huimin Li, Hao Zhang, Zhanlin Liu, Guifang Zhao
Chloroplast DNA (cpDNA) is frequently used for species demography, evolution, and species discrimination of plants. However, the lack of efficient and universal markers often brings particular challenges for genetic studies across different plant groups. In this study, chloroplast genomes from two closely related species (Quercus rubra and Castanea mollissima) in Fagaceae were compared to explore universal cpDNA markers for the Chinese oak species in Quercus subgenus Quercus, a diverse species group without sufficient molecular differentiation...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28559960/medicinal-plants-for-the-treatment-of-obesity-ethnopharmacological-approach-and-chemical-and-biological-studies
#9
REVIEW
Luciano Mamede de Freitas Junior, Eduardo B de Almeida
Obesity is a global epidemic that has shown a steady increase in morbimortality indicators; it is considered a social problem and entails serious health risks. One of the alternatives in the treatment of obesity is the traditional use of medicinal plants, which supports the research and development of obesity phytotherapy. In this article, we provide information about ethnopharmacological species used to treat obesity, through an electronic search of the periodical databases Web of Science, Scopus, PubMed and Scielo, considering the period 1996-2015 and using the descriptors "plants for obesity", "ethnopharmacology for obesity" and "anti-obesity plants" in both Portuguese and English...
2017: American Journal of Translational Research
https://www.readbyqxmd.com/read/28552970/genetic-structuring-dispersal-and-taxonomy-of-the-high-alpine-populations-of-the-geranium-arabicum-kilimandscharicum-complex-in-tropical-eastern-africa
#10
Tigist Wondimu, Abel Gizaw, Felly M Tusiime, Catherine A Masao, Ahmed A Abdi, Yan Hou, Sileshi Nemomissa, Christian Brochmann
The scattered eastern African high mountains harbor a renowned and highly endemic flora, but the taxonomy and phylogeographic history of many plant groups are still insufficiently known. The high-alpine populations of the Geranium arabicum/kilimandscharicum complex present intricate morphological variation and have recently been suggested to comprise two new endemic taxa. Here we aim to contribute to a clarification of the taxonomy of these populations by analyzing genetic (AFLP) variation in range-wide high-alpine samples, and we address whether hybridization has contributed to taxonomic problems...
2017: PloS One
https://www.readbyqxmd.com/read/28533898/reconstructing-a-herbivore-s-diet-using-a-novel-rbcl-dna-mini-barcode-for-plants
#11
David L Erickson, Elizabeth Reed, Padmini Ramachandran, Norman A Bourg, William J McShea, Andrea Ottesen
Next Generation Sequencing and the application of metagenomic analyses can be used to answer questions about animal diet choice and study the consequences of selective foraging by herbivores. The quantification of herbivore diet choice with respect to native versus exotic plant species is particularly relevant given concerns of invasive species establishment and their effects on ecosystems. While increased abundance of white-tailed deer (Odocoileus virginianus) appears to correlate with increased incidence of invasive plant species, data supporting a causal link is scarce...
May 2017: AoB Plants
https://www.readbyqxmd.com/read/28515782/ecotypic-differentiation-under-farmers-selection-molecular-insights-into-the-domestication-of-pachyrhizus-rich-ex-dc-fabaceae-in-the-peruvian-andes
#12
Marc Delêtre, Beatriz Soengas, Prem Jai Vidaurre, Rosa Isela Meneses, Octavio Delgado Vásquez, Isabel Oré Balbín, Monica Santayana, Bettina Heider, Marten Sørensen
Understanding the distribution of crop genetic diversity in relation to environmental factors can give insights into the eco-evolutionary processes involved in plant domestication. Yam beans (Pachyrhizus Rich. ex DC.) are leguminous crops native to South and Central America that are grown for their tuberous roots but are seed-propagated. Using a landscape genetic approach, we examined correlations between environmental factors and phylogeographic patterns of genetic diversity in Pachyrhizus landrace populations...
June 2017: Evolutionary Applications
https://www.readbyqxmd.com/read/28490255/developing-a-taxonomy-of-coordination-behaviours-in-nuclear-power-plant-control-rooms-during-emergencies
#13
Dunxing Wang, Qin Gao, Zhizhong Li, Fei Song, Liang Ma
This study aims to develop a taxonomy of coordination behaviours during emergencies in nuclear power plants (NPPs). We summarised basic coordination behaviours from literature in aviation, health care and nuclear field and identified coordination behaviours specific to the nuclear domain by interviewing and surveying control crew operators. The established taxonomy includes 7 workflow stages and 24 basic coordination behaviours. To evaluate the reliability and feasibility of the taxonomy, we analysed 12 videos of operators' training sessions by coding coordination behaviours with the taxonomy and the inter-rater reliability was acceptable...
May 19, 2017: Ergonomics
https://www.readbyqxmd.com/read/28486689/the-phytoclust-tool-for-metabolic-gene-clusters-discovery-in-plant-genomes
#14
Nadine Töpfer, Lisa-Maria Fuchs, Asaph Aharoni
The existence of Metabolic Gene Clusters (MGCs) in plant genomes has recently raised increased interest. Thus far, MGCs were commonly identified for pathways of specialized metabolism, mostly those associated with terpene type products. For efficient identification of novel MGCs, computational approaches are essential. Here, we present PhytoClust; a tool for the detection of candidate MGCs in plant genomes. The algorithm employs a collection of enzyme families related to plant specialized metabolism, translated into hidden Markov models, to mine given genome sequences for physically co-localized metabolic enzymes...
May 9, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28480020/the-distribution-diversity-and-conservation-status-of-cycas-in-china
#15
REVIEW
Ying Zheng, Jian Liu, Xiuyan Feng, Xun Gong
As ancient gymnosperm and woody plants, cycads have survived through dramatic tectonic activities, climate fluctuation, and environmental variations making them of great significance in studying the origin and evolution of flora biodiversity. However, they are among the most threatened plant groups in the world. The principal aim of this review is to outline the distribution, diversity, and conservation status of Cycas in China and provide suggestions for conservation practices. In this review, we describe the taxonomy, distribution, and conservation status of Cycas in China...
May 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/28460071/interactive-microbial-distribution-analysis-using-bioatlas
#16
Jesper Beltoft Lund, Markus List, Jan Baumbach
Massive amounts of 16S rRNA sequencing data have been stored in publicly accessible databases, such as GOLD, SILVA, GreenGenes (GG), and the Ribosomal Database Project (RDP). Many of these sequences are tagged with geo-locations. Nevertheless, researchers currently lack a user-friendly tool to analyze microbial distribution in a location-specific context. BioAtlas is an interactive web application that closes this gap between sequence databases, taxonomy profiling and geo/body-location information. It enables users to browse taxonomically annotated sequences across (i) the world map, (ii) human body maps and (iii) user-defined maps...
April 29, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28452295/ictv-virus-taxonomy-profile-secoviridae
#17
Jeremy R Thompson, Indranil Dasgupta, Marc Fuchs, Toru Iwanami, Alexander V Karasev, Karel Petrzik, Hélène Sanfaçon, Ioannis Tzanetakis, René van der Vlugt, Thierry Wetzel, Nobuyuki Yoshikawa, Ictv Report Consortium
Members of the family Secoviridae are non-enveloped viruses with mono- or bipartite (RNA-1 and RNA-2) linear positive-sense ssRNA genomes with the size of the RNAs combined ranging from 9 to 13.7 kb. They are related to picornaviruses and are classified in the order Picornavirales. The majority of known members infect dicotyledonous plants and many are important plant pathogens (e.g. grapevine fanleaf virus and rice tungro spherical virus). This is a summary of the current International Committee on Taxonomy of Viruses (ICTV) report on the taxonomy of the family Secoviridae available at www...
April 2017: Journal of General Virology
https://www.readbyqxmd.com/read/28448771/geosmithia-associated-with-bark-beetles-and-woodborers-in-the-western-usa-taxonomic-diversity-and-vector-specificity
#18
Miroslav Kolařík, Jiri Hulcr, Ned Tisserat, Wilhelm De Beer, Martin Kostovčík, Zuzana Kolaříková, Steven J Seybold, David M Rizzo
Fungi in the genus Geosmithia (Ascomycota: Hypocreales) are frequent associates of bark beetles and woodborers that colonize hardwood and coniferous trees. One species, Geosmithia morbida, is an economically damaging invasive species. The authors surveyed the Geosmithia species of California and Colorado, USA, to (i) provide baseline data on taxonomy of Geosmithia and beetle vector specificity across the western USA; (ii) investigate the subcortical beetle fauna for alternative vectors of the invasive G. morbida; and (iii) interpret the community composition of this region within the emerging global biogeography of Geosmithia...
April 24, 2017: Mycologia
https://www.readbyqxmd.com/read/28444200/the-mediterranean-the-cradle-of-anthoxanthum-poaceae-diploid-diversity
#19
Zuzana Chumová, Eliška Záveská, Terezie Mandáková, Karol Krak, Pavel Trávnícek
Background and Aims: Knowledge of diploid phylogeny and ecogeography provide a foundation for understanding plant evolutionary history, diversification patterns and taxonomy. The genus Anthoxanthum (vernal grasses, Poaceae) represents a taxonomically intricate polyploid complex with large phenotypic variation and poorly resolved evolutionary relationships. The aims of the study were to reveal: (1) evolutionary lineages of the diploid taxa and their genetic differentiation; (2) the past distribution of the rediscovered 'Mediterranean diploid'; and (3) possible migration routes of diploids in the Mediterranean...
April 21, 2017: Annals of Botany
https://www.readbyqxmd.com/read/28437778/strengthening-governance-for-intertidal-ecosystems-requires-a-consistent-definition-of-boundaries-between-land-and-sea
#20
Stefanie M Rog, Carly N Cook
The protection of intertidal ecosystems is complex because they straddle both marine and terrestrial realms. This leads to inconsistent characterisation as marine and/or terrestrial systems, or neither. Vegetated intertidal ecosystems are especially complex to classify because they can have an unclear border with terrestrial vegetation, causing confusion around taxonomy (e.g., mangrove-like plants). This confusion and inconsistency in classification can impact these systems through poor governance and incomplete protection...
April 21, 2017: Journal of Environmental Management
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