Occurrence

FBIP: Mycorrhizal and root endophytic fungi associated with Orchids

Latest version published by South African National Biodiversity Institute on 30 September 2020 South African National Biodiversity Institute
Isolated cultures and environmental metagenomic sequencing data using a target DNA markers ITS region for Fungi
Publication date:
30 September 2020
License:
CC-BY 4.0

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.

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 1,197 records in English (61 kB) - Update frequency: unknown
Metadata as an EML file download in English (9 kB)
Metadata as an RTF file download in English (8 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:

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

Who created the resource:

Joanna Dames
Associate Professor
Rhodes University
Mycorrhizal Research Laboratory, Lab 215; Biological Sciences Building; Department of Biochemistry and Microbiology; Cnr of University Rd & Artillery Rd
6140 Grahamstown
Eastern Cape
ZA
+27466038443

Who can answer questions about the resource:

Joanna Dames
Associate Professor
Rhodes University
Mycorrhizal Research Laboratory, Lab 215; Biological Sciences Building; Department of Biochemistry and Microbiology; Cnr of University Rd & Artillery Rd
6140 Grahamstown
Eastern Cape
ZA
+27466038443

Who filled in the metadata:

Joanna Dames
Associate Professor
Rhodes University
Mycorrhizal Research Laboratory, Lab 215; Biological Sciences Building; Department of Biochemistry and Microbiology; Cnr of University Rd & Artillery Rd
6140 Grahamstown
Eastern Cape
ZA
+27466038443

Who else was associated with the resource:

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

Geographic Coverage

South Africa (Eastern Cape, KwaZulu-Natal)

Bounding Coordinates South West [-33.334, 26.493], North East [-28.234, 31.191]

Taxonomic Coverage

The isolates and metagenomic sequences are mycorrhizal and other root endophytic fungi that are found within orchid roots

Phylum  Fungi

Temporal Coverage

Start Date / End Date 2017-05-01 / 2018-11-29

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
Identifier FBIS170410226411
Funding Foundational Biodiversity Information Programme
Study Area Description South Africa (Eastern Cape, KwaZulu-Natal)

The personnel involved in the project:

Principal Investigator
Joanna Dames

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)
Quality Control The coordinates of the location where samples were collected was recorded

Method step description:

  1. 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