FBIP: Mycorrhizal and root endophytic fungi associated with Orchids
Citation
Dames J (2020). FBIP: Mycorrhizal and root endophytic fungi associated with Orchids. South African National Biodiversity Institute. Occurrence dataset https://doi.org/10.15468/hrhfap accessed via GBIF.org on 2024-09-01.Description
Isolated cultures and environmental metagenomic sequencing data using a target DNA markers ITS region for FungiSampling Description
Study Extent
South Africa (Eastern Cape, KwaZulu-Natal)Sampling
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.Quality Control
The coordinates of the location where samples were collected was recordedMethod steps
- 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.
Taxonomic Coverages
The isolates and metagenomic sequences are mycorrhizal and other root endophytic fungi that are found within orchid roots
-
Fungirank: phylum
Geographic Coverages
South Africa (Eastern Cape, KwaZulu-Natal)
Bibliographic Citations
Contacts
Joanna Damesoriginator
position: Associate Professor
Rhodes University
Mycorrhizal Research Laboratory, Lab 215; Biological Sciences Building; Department of Biochemistry and Microbiology; Cnr of University Rd & Artillery Rd
Grahamstown
6140
Eastern Cape
ZA
Telephone: +27466038443
email: j.dames@ru.ac.za
Joanna Dames
metadata author
position: Associate Professor
Rhodes University
Mycorrhizal Research Laboratory, Lab 215; Biological Sciences Building; Department of Biochemistry and Microbiology; Cnr of University Rd & Artillery Rd
Grahamstown
6140
Eastern Cape
ZA
Telephone: +27466038443
email: j.dames@ru.ac.za
Mahlatse Kgatla
distributor
position: FBIP Data Specialist
SANBI
2 Cussonia Avenue, Brummeria
Pretoria
0184
Gauteng
ZA
Telephone: 0128435196
email: m.kgatla@sanbi.org.za
homepage: http://fbip.co.za/contact/
Joanna Dames
administrative point of contact
position: Associate Professor
Rhodes University
Mycorrhizal Research Laboratory, Lab 215; Biological Sciences Building; Department of Biochemistry and Microbiology; Cnr of University Rd & Artillery Rd
Grahamstown
6140
Eastern Cape
ZA
Telephone: +27466038443
email: j.dames@ru.ac.za