BDATA

BIODIVERSITY DATA

FBIP: Barcoding of the national collection of fungi: with special Emphasis on Hypocrealean fungi

Latest version published by South African National Biodiversity Institute on Jun 28, 2019 South African National Biodiversity Institute

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.

Data Records

The data in this occurrence resource has been published as a Darwin Core Archive (DwC-A), which is a standardized format for sharing biodiversity data as a set of one or more data tables. The core data table contains 450 records.

This IPT archives the data and thus serves as the data repository. The data and resource metadata are available for download in the downloads section. The versions table lists other versions of the resource that have been made publicly available and allows tracking changes made to the resource over time.

Downloads

Download the latest version of this resource data as a Darwin Core Archive (DwC-A) or the resource metadata as EML or RTF:

Data as a DwC-A file download 450 records in English (13 KB) - Update frequency: unknown
Metadata as an EML file download in English (10 KB)
Metadata as an RTF file download in English (9 KB)

Versions

The table below shows only published versions of the resource that are publicly accessible.

How to cite

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

Rights

Researchers should respect the following rights statement:

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.

GBIF Registration

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.

Keywords

Barcoding; Hypocrealean; Fungi; DNA; BLAST; Specimen

Contacts

Who created the resource:

Adriaana Jacobs
Researcher
Agricultural Research Council Private Bag X134 121 Pretoria Gauteng ZA 012 8088256

Who can answer questions about the resource:

Adriaana Jacobs
Researcher
Agricultural Research Council Private Bag X134 121 Pretoria Gauteng ZA 012 8088256

Who filled in the metadata:

Adriaana Jacobs
Researcher
Agricultural Research Council Private Bag X134 121 Pretoria Gauteng ZA 012 8088256

Who else was associated with the resource:

Content Provider
Mahlatse Kgatla
FBIP Data Specialist
SANBI 2 Cussonia Avenue, Brummeria 0184 Pretoria Gauteng ZA 0128435196
http://fbip.co.za/contact/

Geographic Coverage

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]

Taxonomic Coverage

Most specimen have been identified to Genus and Species level, some are identified to Phylum and Class level

Phylum  Fungi

Temporal Coverage

Start Date / End Date 1993-06-01 / 2017-07-23

Project Data

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
Identifier FBIS150520118174
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:

Principal Investigator
Adriaana Jacobs

Sampling Methods

samples where sourced from Agricultural Reasearch Council collection of living specimens.

Study Extent South Africa

Method step description:

  1. 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.

Additional Metadata

Alternative Identifiers http://ipt.sanbi.org.za/iptsanbi/resource?r=barcoding