https://cbs.umn.edu/sites/cbs.umn.edu/files/public/downloads/Nguyenetal2015b.pdf

FUNGuild: An open annotation tool for parsing fungal community datasets by ecological guild

The nuclear ribosomal internal transcribed spacer (ITS) region is the formal fungal barcode and in most cases the marker of choice for the exploration of fungal diversity in environmental samples. Two problems are particularly acute in the pursuit of satisfactory taxonomic assignment of newly generated ITS sequences: (i) the lack of an inclusive, reliable public reference data set and (ii) the lack of means to refer to fungal species, for which no Latin name is available in a standardized stable way. Here, we report on progress in these regards through further development of the UNITE database (http://unite.ut.ee) for molecular identification of fungi. All fungal species represented by at least two ITS sequences in the international nucleotide sequence databases are now given a unique, stable name of the accession number type (e.g. Hymenoscyphus pseudoalbidus|GU586904|SH133781.05FU), and their taxonomic and ecological annotations were corrected as far as possible through a distributed, third-party annotation effort. We introduce the term ‘species hypothesis’ (SH) for the taxa discovered in clustering on different similarity thresholds (97–99%). An automatically or manually designated sequence is chosen to represent each such SH. These reference sequences are released (http://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and in the QIIME pipeline. The system and the data will be updated automatically as the number of public fungal ITS sequences grows. We invite everybody in the position to improve the annotation or metadata associated with their particular fungal lineages of expertise to do so through the new Web-based sequence management system in UNITE.

http://web.stanford.edu/~kpeay/papers/Koljalg_2013_MEC.pdf

Towards a unified paradigm for sequence-based identification of fungi

https://nph.onlinelibrary.wiley.com/doi/epdf/10.1111/j.1469-8137.2009.03160.x

The UNITE database for molecular identification of fungi - recent updates and future perspectives

The National Center for Biotechnology Information (NCBI) Taxonomy includes organism names and classifications for every sequence in the nucleotide and protein sequence databases of the International Nucleotide Sequence Database Collaboration. Since the last review of this resource in 2012, it has undergone several improvements. Most notable is the shift from a single SQL database to a series of linked databases tied to a framework of data called NameBank. This means that relations among data elements can be adjusted in more detail, resulting in expanded annotation of synonyms, the ability to flag names with specific nomenclatural properties, enhanced tracking of publications tied to names and improved annotation of scientific authorities and types. Additionally, practices utilized by NCBI Taxonomy curators specific to major taxonomic groups are described, terms peculiar to NCBI Taxonomy are explained, external resources are acknowledged and updates to tools and other resources are documented. Database URL: https://www.ncbi.nlm.nih.gov/taxonomy.

/pdf/ncbi-taxonomy-a-comprehensive-update-on-curation-resources-5elwmr30fn.pdf

NCBI Taxonomy: a comprehensive update on curation, resources and tools.

Bacterial wilt caused by Pseudomonas solanacearum is widely distributed in tropical, subtropical and some warm temperate regions of the world, and is a major constraint on production of many crop plants. Major sections of this review are on: phylogeny (particularly using molecular biology), properties, relationships and geographical distribution; host range; modes of dispersal and sources of inoculum (including root-to-root transmission, movement of soil and dissemination by farm implements, and insect transmission); some environmental interactions (temperature - the most important factor affecting the host-pathogen interaction as well as survival in soils, light intensity, soil moisture (preferably high), soil type, and synergism with nematodes); and control strategies, especially development of host-plant resistance, appropriate cropping systems, soil amendment, disease avoidance, integrated control, and biological control using antagonistic rhizobacteria and avirulent mutants. -P.J.Jarvis

Biology and epidemiology of bacterial wilt caused by pseudomonas solanacearum

Patterns of urediniospores release and development of rose apple rust Abstract†n†This research was conducted to evaluate some epidemiological features of the rose apple (Syzygium jambos) rust (Puccinia psidii Winter) under field conditions at the Universidade de BrasIlia, BrasIlia, DF, Brazil, from March 29 through December 31, 1988. Data for the amount of airborne urediniospores were collected in ten plants, using a Burkardis seven-day volumetric spore trap set between two rose apple trees. Most of the airborne urediniospores were collected between June 23 and July 6, from 10†a.m. to 1†p.m. The†major quantity of S.†jambos affected shoots occurred between April 28 and July 20. There was a positive correlation between the amount of trapped urediniospores and infected young shoots. A†negative correlation was shown between temperature (12h) and number of airborne urediniospores. The number of days with relative humidity (RH)†‡80% was positively corre- lated to the amount of deformed shoots. Also, the amount of urediniospores and infected young shoots were positively correlated to the number of days with night (24h) temperature £20 o C or night RH‡80%. These data show that this disease was favored by low temperatures (£20 o C), high night RH†(‡80%) and high levels of airborne urediniospores.

/pdf/padroes-de-liberacao-de-urediniosporos-e-desenvolvimento-da-4aq1u8sict.pdf

Padrões de liberação de urediniósporos e desenvolvimento da ferrugem do jambeiro

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Padrões de liberação de urediniósporos e desenvolvimento da ferrugem do jambeiro