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Researchers should cite this work as follows:
Jacobs A (2019): FBIP: Barcoding of the national collection of fungi: with special Emphasis on Hypocrealean fungi. v1.0. South African National Biodiversity Institute. Dataset/Occurrence. http://ipt.sanbi.org.za/iptsanbi/resource?r=barcoding&v=1.0
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The publisher and rights holder of this work is South African National Biodiversity Institute. This work is licensed under a Creative Commons Attribution (CC-BY) 4.0 License.
This resource has been registered with GBIF, and assigned the following GBIF UUID: b5cd47e0-0039-4092-a77f-7493b586a3e1. South African National Biodiversity Institute publishes this resource, and is itself registered in GBIF as a data publisher endorsed by South African Biodiversity Information Facility.
Barcoding; Hypocrealean; Fungi; DNA; BLAST; Specimen
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Limpopo, Norther West, Gauteng, Mpumalanga, KwaZulu Natal, Eastern Cape, Free State, Western Cape
|Bounding Coordinates||South West [-34.886, 16.348], North East [-22.106, 32.959]|
Most specimen have been identified to Genus and Species level, some are identified to Phylum and Class level
|Start Date / End Date||1993-06-01 / 2017-07-23|
The main aim of this study is to expand the current knowledge basis on soil fungi by generating DNA barcodes for isolates in the NCF that has not been identified to species level as they could represent new species. The focus will be on the large portion of strains. representing the plant pathogenic and beneficial genera Fusarium and Trichoderma, respectively.
|Title||Barcoding of the national collection of fungi: with special Emphasis on Hypocrealean fungi|
|Funding||Funding from Foundational Biodiversity Information Programme (FBIP)|
|Study Area Description||Limpopo, Norther West, Gauteng, Mpumalanga, KwaZulu Natal, Eastern Cape, Free State, Western Cape|
The personnel involved in the project:
samples where sourced from Agricultural Reasearch Council collection of living specimens.
|Study Extent||South Africa|
Method step description:
- Strain selection: Strains representing the order Hypocreales will be selected based on the following criteria: a)No Sequence data available for the strain b) Morphological identification done to genus level or higher and c) Isolate obtained from soil . These will include strains from the MRC PROMEC collection as the ARC is now the custodians of this world renowned collection of fungi of medical importance. Amplicon generation: DNA extractions and amplification of target gene. The target gene will be genus specific as the ITS gene region doesn't provide species level identification for this group of fungi. For the genera Fusarium and Trichoderma it will be the translation elongation factor 1a gene as (Geiser et al., 2004; European Journal of Plant Pathology 110: 473-479; O’ Donnell et al., 2012; Mycologia, 104: 427–445; Druzhinina et al., Microbiology (2008), 154, 3447–3459. Data analyses: BLAST analyses will be done on the obtained sequence data using a number of international mycological databases such as TrichoMARK, Fusarium MLST and Fusarium ID, MycoBank and NCBI GenBank. The DNA based identification will be used to update the information in the NCF's database. This will also ensure that data is available on these selected strains that would be incorporated in taxonomic re-evaluations of orders, species complexes etc., and will be available for research sectors in agriculture, health, and industry. Population of databases: The newly generated data will be incorporate in the soil and phytopathogenic databases' BLAST tool which will also consult existing data in CBS, NCF and NCBI GenBank. The data will also be deposited in the BOLD database. Collaborative research: The barcoded species will be included in taxonomic and phylogenetic revisions that are currently being performed by the researchers located at the NCF (ARC-PPR) and both national and internationally.