Description
Isolated cultures and environmental metagenomic sequencing data using a target DNA markers ITS region for Fungi
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 1,197 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.
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:
Dames J (2020): FBIP: Mycorrhizal and root endophytic fungi associated with Orchids. v1.1. South African National Biodiversity Institute. Dataset/Occurrence. http://ipt.sanbi.org.za/iptsanbi/resource?r=dames_ru_2017_v2&v=1.1
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: f703b08e-008e-438c-ad2d-58d544825692. 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
Occurrence; Specimen
Contacts
- Metadata Provider ●
- Originator ●
- Point Of Contact
- Distributor
Geographic Coverage
South Africa (Eastern Cape, KwaZulu-Natal)
| Bounding Coordinates | South West [-33.334, 26.493], North East [-28.234, 31.191] |
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Taxonomic Coverage
The isolates and metagenomic sequences are mycorrhizal and other root endophytic fungi that are found within orchid roots
| Phylum | Fungi |
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Temporal Coverage
| Start Date / End Date | 2017-05-01 / 2018-11-29 |
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Project Data
Isolated cultures and environmental metagenomic sequencing data using a target DNA markers ITS region for Fungi
| Title | FBIP: Mycorrhizal and root endophytic fungi associated with Orchids |
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| Identifier | FBIS170410226411 |
| Funding | Foundational Biodiversity Information Programme |
| Study Area Description | South Africa (Eastern Cape, KwaZulu-Natal) |
The personnel involved in the project:
- Principal Investigator
Sampling Methods
1 g of orchid root material was collected from each orchid species, replicated 6 times, roots were surface sterilized and were etiher stored in RNA Later and frozen for molecular analysis or they were were sliced into smaller segments and placed onto suitable media to isolate endophytic fungi.
| Study Extent | South Africa (Eastern Cape, KwaZulu-Natal) |
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| Quality Control | The coordinates of the location where samples were collected was recorded |
Method step description:
- Fungal isolates: Sampled root sections were surface sterilized and plated onto Malt Extract Agar. After incubation sub-cultures were made to ensure pure cultures were maintained. DNA was extracted from the cultures and the ITS region was amplified using ITS1 and ITS 4 primers. After purification amplicons were sent for Sanger Sequencing and submitted to GenBank for identification. Root samples: Genomic DNA was extracted from root samples, followed by polymerase chain reaction (PCR) amplification of the ITS region using Miseq tagged primers. Amplicon were submitted to SAIAB for Illumina Next Generation Sequencing.Data was analysed using Mothur software.
Additional Metadata
| Alternative Identifiers | http://ipt.sanbi.org.za/iptsanbi/resource?r=dames_ru_2017_v2 |
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