keyword
MENU ▼
Read by QxMD icon Read
search

Plant Taxonomy

keyword
https://www.readbyqxmd.com/read/28533898/reconstructing-a-herbivore-s-diet-using-a-novel-rbcl-dna-mini-barcode-for-plants
#1
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
#2
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-behaviors-in-nuclear-power-plant-control-rooms-during-emergencies
#3
Dunxing Wang, Qin Gao, Zhizhong Li, Fei Song, Liang Ma
This study aims to develop a taxonomy of coordination behaviors during emergencies in nuclear power plants (NPPs). We summarized basic coordination behaviors from literature in aviation, healthcare, and nuclear field and identified coordination behaviors specific to the nuclear domain by interviewing and surveying control crew operators. The established taxonomy includes seven workflow stages and 24 basic coordination behaviors. To evaluate the reliability and feasibility of the taxonomy, we analyzed 12 videos of operators' training sessions by coding coordination behaviors with the taxonomy and the inter-rater reliability was acceptable...
May 10, 2017: Ergonomics
https://www.readbyqxmd.com/read/28486689/the-phytoclust-tool-for-metabolic-gene-clusters-discovery-in-plant-genomes
#4
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
#5
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
#6
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
#7
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
#8
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
#9
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
#10
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
https://www.readbyqxmd.com/read/28434019/recent-developments-in-olive-olea-europaea-l-genetics-and-genomics-applications-in-taxonomy-varietal-identification-traceability-and-breeding
#11
REVIEW
L Sebastiani, M Busconi
The latest results in DNA markers application and genomic studies in olive. Olive (Olea europaea L.) is among the most ancient tree crops worldwide and the source of oil beneficial for human health. Despite this, few data on olive genetics are available in comparison with other cultivated plant species. Molecular information is mainly linked to molecular markers and their application to the study of DNA variation in the Olea europaea complex. In terms of genomic research, efforts have been made in sequencing, heralding the era of olive genomic...
April 22, 2017: Plant Cell Reports
https://www.readbyqxmd.com/read/28414633/genome-wide-analysis-provides-evidence-on-the-genetic-relatedness-of-the-emergent-xylella-fastidiosa-genotype-in-italy-to-isolates-from-central-america
#12
Annalisa Giampetruzzi, Maria Saponari, Giuliana Loconsole, Donato Boscia, Vito Nicola Savino, Rodrigo Almeida, Stefania Zicca, Blanca Landa, Carlos Chacon Diaz, Pasquale Saldarelli
Xylella fastidiosa is a plant pathogenic bacterium recently introduced in Europe that is causing decline in olive trees in the South of Italy. Genetic studies have consistently shown that the bacterial genotype recovered from infected olive trees belongs to the sequence type ST53 within subspecies pauca. This genotype, ST53, has also been reported to occur in Costa Rica. The ancestry of ST53 was recently clarified, showing it contains alleles which are monophyletic with those of subsp. pauca in South America...
April 17, 2017: Phytopathology
https://www.readbyqxmd.com/read/28412534/isolation-and-identification-of-culturable-bacteria-capable-of-heterotrophic-growth-from-rapid-sand-filters-of-drinking-water-treatment-plants
#13
Johanna Vandermaesen, Bart Lievens, Dirk Springael
The microbial community in sand filters (SFs) of drinking water treatment plants (DWTPs) likely contributes to SF functionalities, such as organic carbon removal through heterotrophic metabolism. However, the dynamics and functionality of the SF microbiome and microbial communities in oligotrophic freshwater environments in general, are poorly understood. Therefore, the availability of bacterial strains from these oligotrophic environments is of great interest, but such organisms are currently underrepresented in culture collections...
April 12, 2017: Research in Microbiology
https://www.readbyqxmd.com/read/28406446/is-there-any-alternative-to-canonical-dna-barcoding-of-multicellular-eukaryotic-species-a-case-for-the-tubulin-gene-family
#14
Diego Breviario
Modern taxonomy is largely relying on DNA barcoding, a nucleotide sequence-based approach that provides automated species identification using short orthologous DNA regions, mainly of organellar origin when applied to multicellular Eukaryotic species. Target DNA loci have been selected that contain a minimal amount of nucleotide sequence variation within species while diverging among species. This strategy is quite effective for the identification of vertebrates and other animal lineages but poses a problem in plants where different combinations of two or three loci are constantly used...
April 13, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28402790/plant-diversity-and-plant-identity-influence-fusarium-communities-in-soil
#15
Nicholas LeBlanc, Linda Kinkel, H Corby Kistler
Fusarium communities play important functional roles in soil and in plants as pathogens, endophytes, and saprotrophs. This study tests how rhizosphere Fusarium communities may vary with plant species, changes in the diversity of the surrounding plant community, and soil physiochemical characteristics. Fusarium communities in soil associated with the roots of two perennial prairie plant species maintained as monocultures or growing within polyculture plant communities were characterized using targeted metagenomics...
2017: Mycologia
https://www.readbyqxmd.com/read/28400766/function-and-structural-organization-of-the-replication-protein-of-bamboo-mosaic-virus
#16
REVIEW
Menghsiao Meng, Cheng-Cheng Lee
The genus Potexvirus is one of the eight genera belonging to the family Alphaflexiviridae according to the Virus Taxonomy 2015 released by International Committee on Taxonomy of Viruses (www.ictvonline.org/index.asp). Currently, the genus contains 35 known species including many agricultural important viruses, e.g., Potato virus X (PVX). Members of this genus are characterized by flexuous, filamentous virions of 13 nm in diameter and 470-580 nm in length. A potexvirus has a monopartite positive-strand RNA genome, encoding five open-reading frames (ORFs), with a cap structure at the 5' end and a poly(A) tail at the 3' end...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28389925/plant-dehydrins-shedding-light-on-structure-and-expression-patterns-of-dehydrin-gene-family-in-barley
#17
Raha Abedini, Farzan GhaneGolmohammadi, Reihaneh PishkamRad, Ehsan Pourabed, Ahad Jafarnezhad, Zahra-Sadat Shobbar, Maryam Shahbazi
Dehydrins, an important group of late embryogenesis abundant proteins, accumulate in response to dehydration stresses and play protective roles under stress conditions. Herein, phylogenetic analysis of the dehydrin family was performed using the protein sequences of 108 dehydrins obtained from 14 plant species based on plant taxonomy and protein subclasses. Sub-cellular localization and phosphorylation sites of these proteins were also predicted. The protein features distinguishing these dehydrins categories were identified using various attribute weighting and decision tree analyses...
April 7, 2017: Journal of Plant Research
https://www.readbyqxmd.com/read/28388878/medium-term-water-deficit-elicits-distinct-transcriptome-responses-in-eucalyptus-species-of-contrasting-environmental-origin
#18
Antanas V Spokevicius, Josquin Tibbits, Philippe Rigault, Marc-Alexandre Nolin, Caroline Müller, Andrew Merchant
BACKGROUND: Climatic and edaphic conditions over geological timescales have generated enormous diversity of adaptive traits and high speciation within the genus Eucalyptus (L. Hér.). Eucalypt species occur from high rainfall to semi-arid zones and from the tropics to latitudes as high as 43°S. Despite several morphological and metabolomic characterizations, little is known regarding gene expression differences that underpin differences in tolerance to environmental change. Using species of contrasting taxonomy, morphology and physiology (E...
April 7, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28373739/phylogeny-and-taxonomy-of-the-scab-and-spot-anthracnose-fungus-elsino%C3%A3-myriangiales-dothideomycetes
#19
X L Fan, R W Barreto, J Z Groenewald, J D P Bezerra, O L Pereira, R Cheewangkoon, L Mostert, C M Tian, P W Crous
Species of Elsinoë are phytopathogens causing scab and spot anthracnose on many plants, including some economically important crops such as avocado, citrus, grapevines, and ornamentals such as poinsettias, field crops and woody hosts. Disease symptoms are often easily recognisable, and referred to as signature-bearing diseases, for the cork-like appearance of older infected tissues with scab-like appearance. In some Elsinoë-host associations the resulting symptoms are better described as spot anthracnose...
June 2017: Studies in Mycology
https://www.readbyqxmd.com/read/28366187/ictv-virus-taxonomy-profile-potyviridae
#20
Stephen J Wylie, Mike Adams, Celia Chalam, Jan Kreuze, Juan José López-Moya, Kazusato Ohshima, Shelly Praveen, Frank Rabenstein, Drake Stenger, Aiming Wang, F Murilo Zerbini, Ictv Report Consortium
The Potyviridae is the largest family of RNA plant viruses, members of which have single-stranded, positive-sense RNA genomes and flexuous filamentous particles 680-900 nm long and 11-20 nm wide. There are eight genera, distinguished by the host range, genomic features and phylogeny of the member viruses. Genomes range from 8.2 to 11.3 kb, with an average size of 9.7 kb. Most genomes are monopartite but those of members of the genus Bymovirus are bipartite. Some members cause serious disease epidemics in cultivated plants...
March 2017: Journal of General Virology
keyword
keyword
90058
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"