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Plant Taxonomy

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https://www.readbyqxmd.com/read/28330330/a-combined-chloroplast-atpb-rbcl-and-trnl-f-phylogeny-unveils-the-ancestry-of-balsams-impatiens-spp-in-the-western-ghats-of-india
#1
P P Shajitha, N R Dhanesh, P J Ebin, Joseph Laly, Devassy Aneesha, John Reshma, Jomy Augustine, Mathew Linu
Only a few Impatiens spp. from South India (one of the five centers of diversity for Impatiens species) were included in the published datum of molecular phylogeny of the family Balsaminaceae. The present investigation is a novel attempt to reveal the phylogenetic association of Impatiens species of South India, by placing them in the global phylogeny of Impatiens based on a combined analysis of two chloroplast genes. Thirty species of genus Impatiens were collected from different locations of South India. Total genomic DNA was extracted from fresh plant leaf, and polymerase chain reaction was carried out using atpB-rbcL and trnL-F intergenic spacer-specific forward and reverse primers...
December 2016: 3 Biotech
https://www.readbyqxmd.com/read/28298348/a-phylogenetic-perspective-on-the-association-between-ants-hymenoptera-formicidae-and-black-yeasts-ascomycota-chaetothyriales
#2
Marie Vasse, Hermann Voglmayr, Veronika Mayer, Cécile Gueidan, Maximilian Nepel, Leandro Moreno, Sybren de Hoog, Marc-André Selosse, Doyle McKey, Rumsaïs Blatrix
The frequency and the geographical extent of symbiotic associations between ants and fungi of the order Chaetothyriales have been highlighted only recently. Using a phylogenetic approach based on seven molecular markers, we showed that ant-associated Chaetothyriales are scattered through the phylogeny of this order. There was no clustering according to geographical origin or to the taxonomy of the ant host. However, strains tended to be clustered according to the type of association with ants: strains from ant-made carton and strains from plant cavities occupied by ants ('domatia') rarely clustered together...
March 15, 2017: Proceedings. Biological Sciences
https://www.readbyqxmd.com/read/28284246/ictv-virus-taxonomy-profile-ourmiavirus
#3
Massimo Turina, Brad I Hillman, Keramat Izadpanah, Mina Rastgou, Cristina Rosa, Ictv Report Consortium
Members of the plant virus genus Ourmiavirus are characterized by having non-enveloped bacilliform virions with a series of discrete lengths from 30 to 62 nm composed of a single coat protein (CP). The genome consists of three positive-sense single-stranded RNAs, each encoding a single protein. The RNA-dependent RNA polymerase (RdRp) has closest similarity to that of viruses from the family Narnaviridae; the movement protein (MP) is similar to the MPs of tombusviruses; the CP shows limited similarity to the CPs of several plant and animal viruses...
February 2017: Journal of General Virology
https://www.readbyqxmd.com/read/28284245/ictv-virus-taxonomy-profile-geminiviridae
#4
F Murilo Zerbini, Rob W Briddon, Ali Idris, Darren P Martin, Enrique Moriones, Jesús Navas-Castillo, Rafael Rivera-Bustamante, Philippe Roumagnac, Arvind Varsani, Ictv Report Consortium
The geminiviruses are a family of small, non-enveloped viruses with single-stranded, circular DNA genomes of 2500-5200 bases. Geminiviruses are transmitted by various types of insect (whiteflies, leafhoppers, treehoppers and aphids). Members of the genus Begomovirus are transmitted by whiteflies, those in the genera Becurtovirus, Curtovirus, Grablovirus, Mastrevirus and Turncurtovirus are transmitted by specific leafhoppers, the single member of the genus Topocuvirus is transmitted by a treehopper and one member of the genus Capulavirus is transmitted by an aphid...
February 2017: Journal of General Virology
https://www.readbyqxmd.com/read/28272844/performance-of-iucn-proxies-for-generation-length
#5
Han Chi Fung, Robin S Waples
One of the criteria used by the International Union for Conservation of Nature (IUCN) to assess threat status is the rate of decline in abundance over 3 generations or 10 years, whichever is longer. The traditional method for calculating generation length (T) uses age-specific survival and fecundity, but these data are rarely available. Consequently, proxies that require less information are often used, which introduces potential biases. The IUCN recommends 2 proxies based on adult mortality rate, T̂d = α + 1/d, and reproductive life span, T̂z = α + z(*) RL, where α is age at first reproduction, d is adult mortality rate, RL is reproductive life span, and z is a coefficient derived from data for comparable species...
March 8, 2017: Conservation Biology: the Journal of the Society for Conservation Biology
https://www.readbyqxmd.com/read/28271979/toward-a-taxonomy-for-multi-omics-science-terminology-development-for-whole-genome-study-approaches-by-omics-technology-and-hierarchy
#6
Nina Pirih, Tanja Kunej
Omics is a form of high-throughput systems science. However, taxonomies for omics studies are limited, inviting us to rethink new ways in which we classify, prioritize, and rank various omics systems science studies. In this overarching context, the genome-wide study approaches have proliferated in number and popularity over the past decade. However, their hierarchy is not well organized and the development of attendant terminology is not controlled. In the present study, we searched the literature in PubMed and the Web of Science databases published from March 1999 to September 2016 using the keywords, including genome-wide, association, whole genome, transcriptome-wide, metabolome, epigenome, and phenome...
January 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28262809/data-integration-aids-understanding-of-butterfly-host-plant-networks
#7
Ai Muto-Fujita, Kazuhiro Takemoto, Shigehiko Kanaya, Takeru Nakazato, Toshiaki Tokimatsu, Natsushi Matsumoto, Mayo Kono, Yuko Chubachi, Katsuhisa Ozaki, Masaaki Kotera
Although host-plant selection is a central topic in ecology, its general underpinnings are poorly understood. Here, we performed a case study focusing on the publicly available data on Japanese butterflies. A combined statistical analysis of plant-herbivore relationships and taxonomy revealed that some butterfly subfamilies in different families feed on the same plant families, and the occurrence of this phenomenon more than just by chance, thus indicating the independent acquisition of adaptive phenotypes to the same hosts...
March 6, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28260703/streptomyces-cameroonensis-sp-nov-a-geldanamycin-producer-that-promotes-theobroma-cacao-growth
#8
Thaddée Boudjeko, Romaric Armel Mouafo Tchinda, Mina Zitouni, Joëlle Aimée Vera Tchatchou Nana, Sylvain Lerat, Carole Beaulieu
The taxonomy of an actinobacterial strain, designated JJY4(T), was established using a polyphasic approach. JJY4(T) was isolated from the rhizosphere of Chromolaena odorata in Yaoundé (Cameroon) during a project for the selection of biological control agents. Strain JJY4(T) exhibited antimicrobial activities against bacteria, fungi, and oomycetes. Strain JJY4(T) also exhibited the traits of plant growth-promoting rhizobacteria such as the solubilization of inorganic phosphate, production of siderophores and indole-3-acetic acid, and 1-aminocyclopropane-1-carboxylate deaminase activity...
March 4, 2017: Microbes and Environments
https://www.readbyqxmd.com/read/28260113/stomatal-co2-responsiveness-and-photosynthetic-capacity-of-tropical-woody-species-in-relation-to-taxonomy-and-functional-traits
#9
Thomas B Hasper, Mirindi E Dusenge, Friederike Breuer, Félicien K Uwizeye, Göran Wallin, Johan Uddling
Stomatal CO2 responsiveness and photosynthetic capacity vary greatly among plant species, but the factors controlling these physiological leaf traits are often poorly understood. To explore if these traits are linked to taxonomic group identity and/or to other plant functional traits, we investigated the short-term stomatal CO2 responses and the maximum rates of photosynthetic carboxylation (V cmax) and electron transport (J max) in an evolutionary broad range of tropical woody plant species. The study included 21 species representing four major seed plant taxa: gymnosperms, monocots, rosids and asterids...
March 4, 2017: Oecologia
https://www.readbyqxmd.com/read/28257464/integrative-taxonomy-of-root-knot-nematodes-reveals-multiple-independent-origins-of-mitotic-parthenogenesis
#10
Toon Janssen, Gerrit Karssen, Olivera Topalović, Danny Coyne, Wim Bert
During sampling of several Coffea arabica plantations in Tanzania severe root galling, caused by a root-knot nematode was observed. From pure cultures, morphology and morphometrics of juveniles and females matched perfectly with Meloidogyne africana, whereas morphology of the males matched identically with those of Meloidogyne decalineata. Based on their Cox1 sequence, however, the recovered juveniles, females and males were confirmed to belong to the same species, creating a taxonomic conundrum. Adding further to this puzzle, re-examination of M...
2017: PloS One
https://www.readbyqxmd.com/read/28243951/the-current-status-of-cyanobacterial-nomenclature-under-the-prokaryotic-and-the-botanical-code
#11
Aharon Oren, Stefano Ventura
Cyanobacterial taxonomy developed in the botanical world because Cyanobacteria/Cyanophyta have traditionally been identified as algae. However, they possess a prokaryotic cell structure, and phylogenetically they belong to the Bacteria. This caused nomenclature problems as the provisions of the International Code of Nomenclature for algae, fungi, and plants (ICN; the "Botanical Code") differ from those of the International Code of Nomenclature of Prokaryotes (ICNP; the "Prokaryotic Code"). While the ICN recognises names validly published under the ICNP, Article 45(1) of the ICN has not yet been reciprocated in the ICNP...
February 27, 2017: Antonie Van Leeuwenhoek
https://www.readbyqxmd.com/read/28239373/variations-of-soil-microbial-community-structures-beneath-broadleaved-forest-trees-in-temperate-and-subtropical-climate-zones
#12
Sihang Yang, Yuguang Zhang, Jing Cong, Mengmeng Wang, Mengxin Zhao, Hui Lu, Changyi Xie, Caiyun Yang, Tong Yuan, Diqiang Li, Jizhong Zhou, Baohua Gu, Yunfeng Yang
Global warming has shifted climate zones poleward or upward. However, understanding the responses and mechanism of microbial community structure and functions relevant to natural climate zone succession is challenged by the high complexity of microbial communities. Here, we examined soil microbial community in three broadleaved forests located in the Wulu Mountain (WLM, temperate climate), Funiu Mountain (FNM, at the border of temperate and subtropical climate zones), or Shennongjia Mountain (SNJ, subtropical climate)...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28230521/micromonospora-terminaliae-sp-nov-an-endophytic-actinobacterium-isolated-from-the-surface-sterilized-stem-of-the-medicinal-plant-terminalia-mucronata
#13
Onuma Kaewkla, Arinthip Thamchaipinet, Christopher Milton Mathew Franco
An endophytic actinobacterium, strain TMS7T, was isolated from the stem of a Thai medicinal plant collected from the grounds of the Phujong-Nayoa National park, Ubon Ratchathani province, Thailand. As a result of a polyphasic taxonomy study, this strain was identified as a member of the genus Micromonospora. This strain was a Gram-stain-positive, aerobic actinobacterium with well-developed substrate mycelium with hyphae forming a single microspore was non-motile. Stran TMS7T was identified according to its 16S rRNA gene sequence as a new member of the genus Micromonospora...
February 24, 2017: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/28222171/metabolite-profiling-of-the-carnivorous-pitcher-plants-darlingtonia-and-sarracenia
#14
Hannu Hotti, Peddinti Gopalacharyulu, Tuulikki Seppänen-Laakso, Heiko Rischer
Sarraceniaceae is a New World carnivorous plant family comprising three genera: Darlingtonia, Heliamphora, and Sarracenia. The plants occur in nutrient-poor environments and have developed insectivorous capability in order to supplement their nutrient uptake. Sarracenia flava contains the alkaloid coniine, otherwise only found in Conium maculatum, in which its biosynthesis has been studied, and several Aloe species. Its ecological role and biosynthetic origin in S. flava is speculative. The aim of the current research was to investigate the occurrence of coniine in Sarracenia and Darlingtonia and to identify common constituents of both genera, unique compounds for individual variants and floral scent chemicals...
2017: PloS One
https://www.readbyqxmd.com/read/28216196/hypericum-perforatum-st-john-s-wort-beyond-depression-a-therapeutic-perspective-for-pain-conditions
#15
REVIEW
Nicoletta Galeotti
ETHNOPHARMACOLOGICAL RELEVANCE: Hypericum perforatum L. (Hypericaceae), popularly called St. John's wort (SJW), has a rich historical background being one of the oldest used and most extensively investigated medicinal herbs. Many bioactivities and applications of SJW are listed in popular and in scientific literature, including antibacterial, antiviral, anti-inflammatory. In the last three decades many studies focused on the antidepressant activity of SJW extracts. However, several studies in recent years also described the antinociceptive and analgesic properties of SJW that validate the traditional uses of the plant in pain conditions...
February 12, 2017: Journal of Ethnopharmacology
https://www.readbyqxmd.com/read/28213104/isolation-and-characterization-of-a-virulent-bacteriophage-infecting-acinetobacter-johnsonii-from-activated-sludge
#16
Niansi Fan, Rong Qi, Min Yang
A double-stranded DNA phage named AJO1, infecting Acinetobacter johnsonii, which plays an important role in wastewater treatment, was isolated from activated sludge in a full-scale municipal wastewater treatment plant. Based on morphological taxonomy, AJO1, with an icosahedral head 55 ± 2 nm in diameter and a non-contractile tail 8 ± 2 nm in length, was classified as a member of the Podoviridae family. Bacterial infection characteristics were as follows: no polyvalent infectivity, optimal multiplicity of infection of 10(-2); eclipse and burst size of 30 min and 51...
February 14, 2017: Research in Microbiology
https://www.readbyqxmd.com/read/28194307/vascular-plant-biodiversity-of-the-lower-coppermine-river-valley-and-vicinity-nunavut-canada-an-annotated-checklist-of-an-arctic-flora
#17
Jeffery M Saarela, Paul C Sokoloff, Roger D Bull
The Coppermine River in western Nunavut is one of Canada's great Arctic rivers, yet its vascular plant flora is poorly known. Here, we report the results of a floristic inventory of the lower Coppermine River valley and vicinity, including Kugluk (Bloody Falls) Territorial Park and the hamlet of Kugluktuk. The study area is approximately 1,200 km(2), extending from the forest-tundra south of the treeline to the Arctic coast. Vascular plant floristic data are based on a review of all previous collections from the area and more than 1,200 new collections made in 2014...
2017: PeerJ
https://www.readbyqxmd.com/read/28193550/genetic-characterization-molecular-epidemiology-and-phylogenetic-relationships-of-insect-specific-viruses-in-the-taxon-negevirus
#18
Marcio R T Nunes, María Angélica Contreras-Gutierrez, Hilda Guzman, Livia C Martins, Mayla Feitoza Barbirato, Chelsea Savit, Victoria Balta, Sandra Uribe, Rafael Vivero, Juan David Suaza, Hamilton Oliveira, Joaquin P Nunes Neto, Valeria L Carvalho, Sandro Patroca da Silva, Jedson F Cardoso, Rodrigo Santo de Oliveira, Poliana da Silva Lemos, Thomas G Wood, Steven G Widen, Pedro F C Vasconcelos, Durland Fish, Nikos Vasilakis, Robert B Tesh
The recently described taxon Negevirus is comprised of a diverse group of insect-specific viruses isolated from mosquitoes and phlebotomine sandflies. In this study, a comprehensive genetic characterization, molecular, epidemiological and evolutionary analyses were conducted on nearly full-length sequences of 91 new negevirus isolates obtained in Brazil, Colombia, Peru, Panama, USA and Nepal. We demonstrated that these arthropod restricted viruses are clustered in two major phylogenetic groups with origins related to three plant virus genera (Cilevirus, Higrevirus and Blunevirus)...
February 10, 2017: Virology
https://www.readbyqxmd.com/read/28187589/palaearctic-i-protosmia-i-bees-of-the-subgenus-i-chelostomopsis%C3%A2-i-megachilidae-osmiini-biology-taxonomy-and-key-to-species
#19
Andreas Müller
Chelostomopsis represents a subgenus of the osmiine bee genus Protosmia (Megachilidae) containing three Palaearctic and one Nearctic species. Analysis of female pollen loads and literature data indicate that all Chelostomopsis species are broad pollen generalists exploiting the flowers of numerous plant families, such as Fabaceae, Asteraceae, Lamiaceae, Cistaceae and Brassicaceae. Preexisting linear cavities in dead wood or pine cones serve as nesting sites and pure resin is used to construct cell partitions and nest plug...
February 2, 2017: Zootaxa
https://www.readbyqxmd.com/read/28182623/evaluation-of-dna-barcodes-in-codonopsis-campanulaceae-and-in-some-large-angiosperm-plant-genera
#20
De-Yi Wang, Qiang Wang, Ying-Li Wang, Xiao-Guo Xiang, Lu-Qi Huang, Xiao-Hua Jin
DNA barcoding is expected to be one of the most promising tools in biological taxonomy. However, there have been no agreements on which core barcode should be used in plants, especially in species-rich genera with wide geographical distributions. To evaluate their discriminatory power in large genera, four of the most widely used DNA barcodes, including three plastid regions (matK, rbcL, trnH-psbA) and nuclear internal transcribed spacer (nrITS), were tested in seven species-rich genera (Ficus, Pedicularis, Rhodiola, Rhododendron,Viburnum, Dendrobium and Lysimachia) and a moderate size genus, Codonopsis...
2017: PloS One
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