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Plant Taxonomy

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https://www.readbyqxmd.com/read/28925170/-analysis-of-projects-funded-by-nsfc-in-field-of-chinese-material-medica-resource-in-recent-three-years
#1
Wei Gao, Shu-Zhen Guo, Li-Wei Han, Feng-Zhu Zhang
The paper reviewed the sponsorship and final reports of projects focus on Science of Chinese materia medica resource in Medical Science Department, National Natural Science Foundation of China. The applicant and supportive organizations were analyzed. The progress and results of some projects were summarized by research fields including formation mechanism of Dao-di herbs, research of plant taxonomy, breeding and cultivation of medical plants, ecological and environmental adaptability of Chinese materia medica resource, quality assessment of Chinese materia medica resource, and biosynthesis and regulation of active compounds...
October 2016: Zhongguo Zhong Yao za Zhi, Zhongguo Zhongyao Zazhi, China Journal of Chinese Materia Medica
https://www.readbyqxmd.com/read/28920414/metagenomic-analysis-of-bacterial-community-structure-and-diversity-of-lignocellulolytic-bacteria-in-vietnamese-native-goat-rumen
#2
Huyen Thi Do, Khoa Trong Dao, Viet Khanh Hoang Nguyen, Giang Ngoc Le, Phuong Thi Mai Nguyen, Lam Tung Le, Nguyet Thu Phung, Nico van Straalen, Dick Roelofs, Hai Nam Truong
Objective: In a previous study, analysis of Illumina sequenced metagenomic DNA data of bacteria in Vietnamese goats' rumen showed a high diversity of putative lignocellulolytic genes. In this study, taxonomy speculation of microbial community and lignocellulolytic bacteria population in the rumen was conducted to elucidate a role of bacterial structure for effective degradation of plant materials. Methods: The metagenomic data had been subjected into Basic Local Alignment Search Tool (BLASTX) algorithm and the National Center for Biotechnology Information (NCBI) non-redundant (NR) sequence database...
September 18, 2017: Asian-Australasian Journal of Animal Sciences
https://www.readbyqxmd.com/read/28913573/genetic-analysis-of-japanese-and-american-specimens-of-scirpus-hattorianus-suggests-its-introduction-from-north-america
#3
Kohei Satoh, Kohtaroh Shutoh, Takahide Kurosawa, Eisuke Hayasaka, Shingo Kaneko
Scirpus hattorianus is a possible alien species in Japan, and a clarification of its unclear taxonomy is required to reveal its origin. It is not known whether the plants initially described from Japan represent the same species distributed in North America. To clarify the origin of the species, we attempted to sequence old specimens collected about 80 years ago using newly designed primer pairs specific for short sequences, including the variable sites. Chloroplast sequences of ndhF were compared among Japanese and North American S...
September 14, 2017: Journal of Plant Research
https://www.readbyqxmd.com/read/28910606/multivariate-analysis-as-a-key-tool-in-chemotaxonomy-of-brinjal-eggplant-african-eggplants-and-wild-related-species
#4
Łukasz P Haliński, John Samuels, Piotr Stepnowski
The brinjal eggplant (Solanum melongena L.) is an important vegetable species worldwide, while African eggplants (S. aethiopicum L., S. macrocarpon L.) are indigenous vegetable species of local significance. Taxonomy of eggplants and their wild relatives is complicated and still unclear. Hence, the objective of the study was to clarify taxonomic position of cultivars and landraces of brinjal, its wild relatives and African eggplant species and their wild ancestors using chemotaxonomic markers and multivariate analysis techniques for data processing, with special attention paid to the recognition of markers characteristic for each group of the plants...
September 11, 2017: Phytochemistry
https://www.readbyqxmd.com/read/28895519/parapedobacter-lycopersici-sp-nov-isolated-from-the-rhizosphere-soil-of-tomato-plants-solanum-lycopersicum-l
#5
Jeong Myeong Kim, Shin Ae Lee, Hayoung Cho, Soo-Jin Kim, Jae-Ho Joa, Soon-Wo Kwon, Hang-Yeon Weon
A novel Gram-stain-negative bacterial strain, designated T16R-256T, was isolated from the rhizosphere soil of tomato plants grown in a greenhouse in Yecheon-gun, Gyeongsangbuk-do, Republic of Korea and characterized using polyphasic taxonomy. Cells were aerobic, non-flagellated and rod-shaped. Colonies were light yellow, convex and round. The strain grew in the temperature range of 15-37 °C (optimally at 28-30 °C) and pH range of 7.0-9.0 (optimally at 7.0-8.0) and in 4 % NaCl (w/v). A comparison of 16S rRNA gene sequences showed that strain T16R-256T is a member of the genus Parapedobacter, exhibiting high sequence similarity with Parapedobacter pyrenivorans P-4T (94...
September 12, 2017: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/28878756/analysis-of-microbial-functions-in-the-rhizosphere-using-a-metabolic-network-based-framework-for-metagenomics-interpretation
#6
Shany Ofaim, Maya Ofek-Lalzar, Noa Sela, Jiandong Jinag, Yechezkel Kashi, Dror Minz, Shiri Freilich
Advances in metagenomics enable high resolution description of complex bacterial communities in their natural environments. Consequently, conceptual approaches for community level functional analysis are in high need. Here, we introduce a framework for a metagenomics-based analysis of community functions. Environment-specific gene catalogs, derived from metagenomes, are processed into metabolic-network representation. By applying established ecological conventions, network-edges (metabolic functions) are assigned with taxonomic annotations according to the dominance level of specific groups...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28859638/should-dna-sequence-be-incorporated-with-other-taxonomical-data-for-routine-identifying-of-plant-species
#7
Tanakorn Suesatpanit, Kitisak Osathanunkul, Panagiotis Madesis, Maslin Osathanunkul
BACKGROUND: A variety of plants in Acanthaceae have long been used in traditional Thai ailment and commercialised with significant economic value. Nowadays medicinal plants are sold in processed forms and thus morphological authentication is almost impossible. Full identification requires comparison of the specimen with some authoritative sources, such as a full and accurate description and verification of the species deposited in herbarium. Intake of wrong herbals can cause adverse effects...
August 31, 2017: BMC Complementary and Alternative Medicine
https://www.readbyqxmd.com/read/28854055/powdery-mildew-of-chrysanthemum-%C3%A3-morifolium-phylogeny-and-taxonomy-in-the-context-of-golovinomyces-species-on-asteraceae-hosts
#8
Michael Bradshaw, Uwe Braun, Monika Götz, Jamjan Meeboon, Susumu Takamatsu
The taxonomic history of the common powdery mildew of Chrysanthemum × morifolium (chrysanthemum, florist's daisy), originally described in Germany as Oidium chrysanthemi, is discussed. The position of O. chrysanthemi was investigated on the basis of morphological traits and molecular phylogenetic analyses. Based on the results of this study, this species, which is closely related to Golovinomyces artemisae, was reassessed and reallocated to Golovinomyces. The phylogenetic analysis and taxonomic reassessment of the chrysanthemum powdery mildew is supplemented by a morphological description, a summary of its worldwide distribution data, and a brief discussion of the introduction of this fungus to North America...
May 2017: Mycologia
https://www.readbyqxmd.com/read/28846186/puccinia-coronata-f-sp-avenae-a-threat-to-global-oat-production
#9
Eric S Nazareno, Feng Li, Madeleine Smith, Robert F Park, Shahryar F Kianian, Melania Figueroa
Puccinia coronata f. sp. avenae (Pca) causes crown rust disease in cultivated and wild oat (Avena spp.). The significant yield losses inflicted by this pathogen makes crown rust the most devastating disease in the oat industry. Puccinia coronata f. sp. avenae is a basidiomycete fungus with an obligate biotrophic lifestyle and is classified as a typical macrocyclic and heteroecious fungus. The asexual phase in the life cycle of Pca occurs in oat while the sexual phase occurs primarily in Rhamnus species as the alternate host...
August 28, 2017: Molecular Plant Pathology
https://www.readbyqxmd.com/read/28841664/frequent-gene-flow-blurred-taxonomic-boundaries-of-sections-in-lilium-l-liliaceae
#10
Xun Gong, Kuo-Hsiang Hung, Yu-Wei Ting, Tsai-Wen Hsu, Lenka Malikova, Huyen Trang Tran, Chao-Li Huang, Shih-Hui Liu, Tzen-Yuh Chiang
Gene flow between species may last a long time in plants. Reticulation inevitably causes difficulties in phylogenetic reconstruction. In this study, we looked into the genetic divergence and phylogeny of 20 Lilium species based on multilocus analyses of 8 genes of chloroplast DNA (cpDNA), the internally transcribed nuclear ribosomal DNA (nrITS) spacer and 20 loci extracted from the expressed sequence tag (EST) libraries of L. longiflorum Thunb. and L. formosanum Wallace. The phylogeny based on the combined data of the maternally inherited cpDNA and nrITS was largely consistent with the taxonomy of Lilium sections...
2017: PloS One
https://www.readbyqxmd.com/read/28839166/the-impact-of-immigration-on-microbial-community-composition-in-full-scale-anaerobic-digesters
#11
Rasmus H Kirkegaard, Simon J McIlroy, Jannie M Kristensen, Marta Nierychlo, Søren M Karst, Morten S Dueholm, Mads Albertsen, Per H Nielsen
Anaerobic digestion is widely applied to treat organic waste at wastewater treatment plants. Characterisation of the underlying microbiology represents a source of information to develop strategies for improved operation. Hence, we investigated microbial communities of thirty-two full-scale anaerobic digesters over a six-year period using 16S rRNA gene amplicon sequencing. Sampling of the sludge fed into these systems revealed that several of the most abundant populations were likely inactive and immigrating with the influent...
August 24, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28829803/evaluation-of-single-and-multilocus-dna-barcodes-towards-species-delineation-in-complex-tree-genus-terminalia
#12
Priyanka Mishra, Amit Kumar, Akshitha Nagireddy, Ashutosh K Shukla, Velusamy Sundaresan
DNA barcoding is used as a universal tool for delimiting species boundaries in taxonomically challenging groups, with different plastid and nuclear regions (rbcL, matK, ITS and psbA-trnH) being recommended as primary DNA barcodes for plants. We evaluated the feasibility of using these regions in the species-rich genus Terminalia, which exhibits various overlapping morphotypes with pantropical distribution, owing to its complex taxonomy. Terminalia bellerica and T. chebula are ingredients of the famous Ayurvedic Rasayana formulation Triphala, used for detoxification and rejuvenation...
2017: PloS One
https://www.readbyqxmd.com/read/28776041/hiding-in-plain-sight-mining-bacterial-species-records-for-phenotypic-trait-information
#13
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
https://www.readbyqxmd.com/read/28731473/ninety-nine-de-novo-assembled-genomes-from-the-moose-alces-alces-rumen-microbiome-provide-new-insights-into-microbial-plant-biomass-degradation
#14
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
https://www.readbyqxmd.com/read/28725360/a-geometrical-model-for-testing-bilateral-symmetry-of-bamboo-leaf-with-a-simplified-gielis-equation
#15
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
https://www.readbyqxmd.com/read/28714846/ictv-virus-taxonomy-profile-benyviridae
#16
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
https://www.readbyqxmd.com/read/28713409/phylogenetic-resolution-in-juglans-based-on-complete-chloroplast-genomes-and-nuclear-dna-sequences
#17
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
https://www.readbyqxmd.com/read/28706324/didymellaceae-revisited
#18
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
https://www.readbyqxmd.com/read/28691341/divergence-is-not-enough-the-use-of-ecological-niche-models-for-the-validation-of-taxa-boundaries
#19
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
https://www.readbyqxmd.com/read/28690801/single-nucleotide-polymorphism-barcoding-of-cytochrome-c-oxidase-i-sequences-for-discriminating-17-species-of-columbidae-by-decision-tree-algorithm
#20
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
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