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Plant Taxonomy

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https://www.readbyqxmd.com/read/29322929/ontology-based-systematic-representation-and-analysis-of-traditional-chinese-drugs-against-rheumatism
#1
Qingping Liu, Jiahao Wang, Yan Zhu, Yongqun He
BACKGROUND: Rheumatism represents any disease condition marked with inflammation and pain in the joints, muscles, or connective tissues. Many traditional Chinese drugs have been used for a long time to treat rheumatism. However, a comprehensive information source for these drugs is still missing, and their anti-rheumatism mechanisms remain unclear. An ontology for anti-rheumatism traditional Chinese drugs would strongly support the representation, analysis, and understanding of these drugs...
December 21, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/29300934/effects-of-sample-preservation-and-dna-extraction-on-enumeration-of-antibiotic-resistance-genes-in-wastewater
#2
An-Dong Li, Jacob W Metch, Yulin Wang, Emily Garner, An Ni Zhang, Maria V Riquelme, Peter J Vikesland, Amy Pruden, Tong Zhang
With the growing application of high-throughput sequencing-based metagenomics for profiling antibiotic resistance genes (ARGs) in wastewater treatment plants (WWTPs), comparison of sample pretreatment and DNA extraction methods are needed to move towards standardized comparisons among laboratories. Three widely employed DNA extraction methods (FastDNA® Spin Kit for Soil, PowerSoil® DNA Isolation Kit, and ZR Fecal DNA MiniPrep™), with and without preservation in 50% ethanol and freezing, were applied to the influent, activated sludge and effluent of two WWTPs, in Hong Kong and in the USA...
December 27, 2017: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/29298729/grapevine-rootstocks-shape-underground-bacterial-microbiome-and-networking-but-not-potential-functionality
#3
Ramona Marasco, Eleonora Rolli, Marco Fusi, Grégoire Michoud, Daniele Daffonchio
BACKGROUND: The plant compartments of Vitis vinifera, including the rhizosphere, rhizoplane, root endosphere, phyllosphere and carposphere, provide unique niches that drive specific bacterial microbiome associations. The majority of phyllosphere endophytes originate from the soil and migrate up to the aerial compartments through the root endosphere. Thus, the soil and root endosphere partially define the aerial endosphere in the leaves and berries, contributing to the terroir of the fruit...
January 3, 2018: Microbiome
https://www.readbyqxmd.com/read/29297332/taxonomic-assessment-of-allium-species-from-kazakhstan-based-on-its-and-matk-markers
#4
Saule Abugalieva, Lyubov Volkova, Yuliya Genievskaya, Anna Ivaschenko, Yuri Kotukhov, Gulzhahan Sakauova, Yerlan Turuspekov
BACKGROUND: As part of nation-wide project to infer the genetic variation of the native flora in Kazakhstan, a study was attempted to assess phylogenetic relationships of endemic and rare Allium species. In total, 20 Allium species were collected in field trips in five different regions of Kazakhstan during 2015-2016. Most species (9) were collected in the southern part of the country along of Karatau mountains, followed by Altai mountains (5) in eastern Kazakhstan. The ITS and matK DNA regions were applied in order to assess the taxonomic relationships among species...
December 28, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/29288361/genome-sequence-and-comparative-analysis-of-jiangella-alba-yim-61503t-isolated-from-a-medicinal-plant-maytenus-austroyunnanensis
#5
Jian-Yu Jiao, Nimaichand Salam, Lan Liu, Manik Prabhu Narsing Rao, Xiao-Tong Zhang, Bao-Zhu Fang, Ming-Xian Han, Zi-Tong Zhang, Jing Chen, Jiao Zhao, Yu Zhou, Dalal Hussien M Alkhalifah, Qing Liu, Min Xiao, Hans-Peter Klenk, Wen-Jun Li
A draft genome sequence of Jiangella alba YIM 61503T revealed a genome size of 7,664,864 bp arranged in 33 scaffolds. The genome was predicted to contain 7196 predicted genes, including 51 coding for RNA. Phylogenetic and comparative analyses of the draft genome of J. alba YIM 61503T with the available genomes of other Jiangella species suggested a proximal similarity between strains J. alba YIM 61503T and J. muralis DSM 45357T, while indicating a high divergence between J. gansuensis YIM 002T and other Jiangella species...
December 29, 2017: Antonie Van Leeuwenhoek
https://www.readbyqxmd.com/read/29274498/species-delimitation-within-the-bothryorrhynchapion-weevils-multiple-evidence-from-genetics-morphology-and-ecological-associations
#6
Łukasz Kajtoch, Matteo Montagna, Marek Wanat
Curculionidae is a hyperdiverse group of beetles, whose taxonomy and phylogenetics is still poorly understood, especially at the genus level. The latest work on the evolution of Apionini showed a noticeable "mess" in the subtribe Oxystomatina, where most of the morphology-based genera were found to be polyphyletic or paraphyletic. These discrepancies between classical taxonomy and molecular phylogenetics implied the need for further taxonomic revision of these groups. Here, we used sets of morphological, molecular and ecological characters to verify the taxonomic statuses and disentangle the phylogenetic relations among the Bothryorrhynchapion apionids, which are classified as a subgenus of Cyanapion...
December 20, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/29260329/recognition-of-six-additional-cystoviruses-pseudomonas-virus-phi6-is-no-longer-the-sole-species-of-the-family-cystoviridae
#7
Sari Mäntynen, Lotta-Riina Sundberg, Minna M Poranen
Cystoviridae is a family of bacterial viruses (bacteriophages) with a tri-segmented dsRNA genome. It includes a single genus Cystovirus, which has presently only one recognised virus species, Pseudomonas virus phi6. However, a large number of additional dsRNA phages have been isolated from various environmental samples, indicating that such viruses are more widespread and abundant than previously recognised. Six of the additional dsRNA phage isolates (Pseudomonas phages phi8, phi12, phi13, phi2954, phiNN and phiYY) have been fully sequenced...
December 19, 2017: Archives of Virology
https://www.readbyqxmd.com/read/29245492/european-species-of-the-aphid-genus-i-eulachnus-i-del-guercio-1909%C3%A2-hemiptera-aphididae-lachninae-revision-and-molecular-phylogeny
#8
Mariusz Kanturski, Łukasz Kajtoch, Karina Wieczorek
The aphid genus Eulachnus in Europe is revised to include 12 species, using an integrative taxonomy approach, based on morphometric, molecular and biological traits. Fundatrix, apterous and alate viviparous female of a new species-Eulachnus stekolshchikovi Kanturski sp. nov. are described. Neotypes are designated for E. agilis, E. brevipilosus and E. nigricola. Lectotypes are designated for E. alticola, E. cembrae, E. rileyi and E. tuberculostemmatus. New synonyms are proposed: E. abameleki syn. nov. (= Cinara pini), E...
November 27, 2017: Zootaxa
https://www.readbyqxmd.com/read/29242781/ima-genome-f-8-draft-genome-of-cercospora-zeina-fusarium-pininemorale-hawksworthiomyces-lignivorus-huntiella-decipiens-and-ophiostoma-ips
#9
Brenda D Wingfield, Dave K Berger, Emma T Steenkamp, Hye-Jin Lim, Tuan A Duong, Burton H Bluhm, Z Wilhelm de Beer, Lieschen De Vos, G Fourie, Kershney Naidoo, Nicky Olivier, Yao-Cheng Lin, Yves Van de Peer, Fourie Joubert, Bridget G Crampton, Velushka Swart, Nicole Soal, Catherine Tatham, Magriet A van der Nest, Nicolaas A van der Merwe, Stephanie van Wyk, P Markus Wilken, Michael J Wingfield
The genomes of Cercospora zeina, Fusarium pininemorale, Hawksworthiomyces lignivorus, Huntiella decipiens, and Ophiostoma ips are presented in this genome announcement. Three of these genomes are from plant pathogens and otherwise economically important fungal species. Fusarium pininemorale and H. decipiens are not known to cause significant disease but are closely related to species of economic importance. The genome sizes range from 25.99 Mb in the case of O. ips to 4.82 Mb for H. lignivorus. These genomes include the first reports of a genome from the genus Hawksworthiomyces...
December 2017: IMA Fungus
https://www.readbyqxmd.com/read/29236867/karyotype-analysis-in-bignonieae-bignoniaceae-chromosome-numbers-and-heterochromatin
#10
Joel M P Cordeiro, Miriam Kaehler, Gustavo Souza, Leonardo P Felix
Chromosome numbers and heterochromatin banding pattern variability have been shown to be useful for taxonomic and evolutionary studies of different plant taxa. Bignonieae is the largest tribe of Bignoniaceae, composed mostly by woody climber species whose taxonomies are quite complicated. We reviewed and added new data concerning chromosome numbers in Bignonieae and performed the first analyses of heterochromatin banding patterns in that tribe based on the fluorochromes chromomycin A3 (CMA) and 4'-6-diamidino-2-phenylindole (DAPI)...
December 11, 2017: Anais da Academia Brasileira de Ciências
https://www.readbyqxmd.com/read/29236853/pollen-morphology-and-viability-in-bromeliaceae
#11
Everton H Souza, Fernanda V D Souza, Mônica L Rossi, Renan M Packer, Maria Amelia V Cruz-Barros, Adriana P Martinelli
Pollen morphology characterization is important in taxonomy, conservation and plant breeding, and pollen viability studies can support breeding programs. This study investigated pollen morphology and male fertility in 18 species of Bromeliaceae with ornamental potential. For morphological characterization, pollen grains were acetolyzed and characterization of exine was done using scanning and transmission electron microscopy. Pollen viability was investigated by in vitro germination and histochemical tests...
December 7, 2017: Anais da Academia Brasileira de Ciências
https://www.readbyqxmd.com/read/29228286/cut-and-paste-transposons-in-fungi-with-diverse-lifestyles
#12
Anna Muszewska, Kamil Steczkiewicz, Marta Stepniewska-Dziubinska, Krzysztof Ginalski
Transposons (TEs) shape genomes via recombination and transposition, lead to chromosomal rearrangements, create new gene neighbourhoods and alter gene expression. They play key roles in adaptation either to symbiosis in Amanita genus or to pathogenicity in Pyrenophora tritici-repentis. Despite growing evidence of their importance, the abundance and distribution of mobile elements replicating in a "cut and paste" fashion is barely described so far. In order to improve our knowledge on this old and ubiquitous class of transposable elements, 1,730 fungal genomes were scanned using both de novo and homology-based approaches...
December 8, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29218421/cistus-ladanifer-cistaceae-a-natural-resource-in-mediterranean-type-ecosystems
#13
REVIEW
David F Frazão, Joana R Raimundo, Joana L Domingues, Celestino Quintela-Sabarís, José C Gonçalves, Fernanda Delgado
Cistus ladanifer has a well-defined taxonomic identity. 2,2,6-trimethylcyclohexanone may be an authenticity and taxonomic marker. Its traits and applications make it a possible economic resource fitted for Mediterranean areas. Cistus ladanifer is a dominant shrub species endemic to the western Mediterranean region. Due to its dominant nature and its potential ecological, aromatic or pharmacological applications, C. ladanifer has been the object of numerous studies. In this review current knowledge on different aspects of this species is summarized, from its taxonomy to its chemical characterisation or its competitive traits...
December 7, 2017: Planta
https://www.readbyqxmd.com/read/29214972/ictv-virus-taxonomy-profile-partitiviridae
#14
Eeva J Vainio, Sotaro Chiba, Said A Ghabrial, Edgar Maiss, Marilyn Roossinck, Sead Sabanadzovic, Nobuhiro Suzuki, Jiatao Xie, Max Nibert, Ictv Report Consortium
The Partitiviridae is a family of small, isometric, non-enveloped viruses with bisegmented double-stranded (ds) RNA genomes of 3-4.8 kbp. The two genome segments are individually encapsidated. The family has five genera, with characteristic hosts for members of each genus: either plants or fungi for genera Alphapartitivirus and Betapartitivirus, fungi for genus Gammapartitivirus, plants for genus Deltapartitivirus and protozoa for genus Cryspovirus. Partitiviruses are transmitted intracellularly via seeds (plants), oocysts (protozoa) or hyphal anastomosis, cell division and sporogenesis (fungi); there are no known natural vectors...
December 7, 2017: Journal of General Virology
https://www.readbyqxmd.com/read/29180830/mycosphaerellaceae-chaos-or-clarity
#15
S I R Videira, J Z Groenewald, C Nakashima, U Braun, R W Barreto, P J G M de Wit, P W Crous
The Mycosphaerellaceae represent thousands of fungal species that are associated with diseases on a wide range of plant hosts. Understanding and stabilising the taxonomy of genera and species of Mycosphaerellaceae is therefore of the utmost importance given their impact on agriculture, horticulture and forestry. Based on previous molecular studies, several phylogenetic and morphologically distinct genera within the Mycosphaerellaceae have been delimited. In this study a multigene phylogenetic analysis (LSU, ITS and rpb2) was performed based on 415 isolates representing 297 taxa and incorporating ex-type strains where available...
June 2017: Studies in Mycology
https://www.readbyqxmd.com/read/29180374/diazotroph-community-characterization-via-a-high-throughput-nifh-amplicon-sequencing-and-analysis-pipeline
#16
John Christian Gaby, Lavanya Rishishwar, Lina C Valderrama-Aguirre, Stefan J Green, Augusto Valderrama-Aguirre, I King Jordan, Joel E Kostka
The dinitrogenase reductase (nifH) gene is the most widely established molecular marker for the study of nitrogen-fixing prokaryotes in nature. A large number of PCR primer sets have been developed for nifH amplification, and the effective deployment of these approaches should be guided by a rapid, easy-to-use analysis protocol. Bioinformatic analysis of marker gene sequences also requires considerable expertise. In this study, we advance the state of the art for nifH analysis by evaluating nifH primer set performance, developing an improved amplicon sequencing workflow, and implementing a user-friendly bioinformatics pipeline...
November 27, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29170851/the-complete-chloroplast-genome-sequence-of-dodonaea-viscosa-comparative-and-phylogenetic-analyses
#17
Josphat K Saina, Andrew W Gichira, Zhi-Zhong Li, Guang-Wan Hu, Qing-Feng Wang, Kuo Liao
The plant chloroplast (cp) genome is a highly conserved structure which is beneficial for evolution and systematic research. Currently, numerous complete cp genome sequences have been reported due to high throughput sequencing technology. However, there is no complete chloroplast genome of genus Dodonaea that has been reported before. To better understand the molecular basis of Dodonaea viscosa chloroplast, we used Illumina sequencing technology to sequence its complete genome. The whole length of the cp genome is 159,375 base pairs (bp), with a pair of inverted repeats (IRs) of 27,099 bp separated by a large single copy (LSC) 87,204 bp, and small single copy (SSC) 17,972 bp...
November 23, 2017: Genetica
https://www.readbyqxmd.com/read/29166661/ultraconserved-elements-uces-resolve-the-phylogeny-of-australasian-smurf-weevils
#18
Matthew H Van Dam, Athena W Lam, Katayo Sagata, Bradley Gewa, Raymond Laufa, Michael Balke, Brant C Faircloth, Alexander Riedel
Weevils (Curculionoidea) comprise one of the most diverse groups of organisms on earth. There is hardly a vascular plant or plant part without its own species of weevil feeding on it and weevil species diversity is greater than the number of fishes, birds, reptiles, amphibians and mammals combined. Here, we employ ultraconserved elements (UCEs) designed for beetles and a novel partitioning strategy of loci to help resolve phylogenetic relationships within the radiation of Australasian smurf-weevils (Eupholini)...
2017: PloS One
https://www.readbyqxmd.com/read/29153402/phylogenetics-and-phylogenomics-of-rust-fungi
#19
M Catherine Aime, Alistair R McTaggart, Stephen J Mondo, Sébastien Duplessis
Rust fungi (Pucciniales) are the most speciose and the most complex group of plant pathogens. Historically, rust taxonomy was largely influenced by host and phenotypic characters, which are potentially plastic. Molecular systematic studies suggest that the extant diversity of this group was largely shaped by host jumps and subsequent shifts. However, it has been challenging to reconstruct the evolutionary history for the order, especially at deeper (family-level) nodes. Phylogenomics offer a potentially powerful tool to reconstruct the Pucciniales tree of life, although researchers working at this vanguard still face unprecedented challenges working with nonculturable organisms that possess some of the largest and most repetitive genomes now known in kingdom fungi...
2017: Advances in Genetics
https://www.readbyqxmd.com/read/29152185/naming-diversity-in-an-evolutionary-context-phylogenetic-definitions-of-the-roucela-clade-campanulaceae-campanuloideae-and-the-cryptic-taxa-within
#20
Andrew A Crowl, Nico Cellinese
In recent times, evolution has become a central tenet of taxonomy, but nomenclature has consistently been decoupled from the tree-thinking process, often leading to significant issues in reconciling traditional (Linnaean) names with clades in the Tree of Life. Recent evolutionary studies on the Roucela clade, a group of endemic plants found in the Mediterranean Basin, motivated the establishment of phylogenetic concepts to formally anchor clade names on the Campanuloideae (Campanulaceae) tree. These concepts facilitate communication of clades that approximate traditionally defined groups, in addition to naming newly discovered cryptic diversity in a phylogenetic framework...
November 2017: Ecology and Evolution
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