FBIP: Mycorrhizal and root endophytic fungi associated with Orchids

Joanna Dames1, Mahlatse Kgatla2

1 Rhodes University, Mycorrhizal Research Laboratory, Lab 215; Biological Sciences Building; Department of Biochemistry and Microbiology; Cnr of University Rd & Artillery Rd , 6140, Grahamstown, South Africa; 2 SANBI, 2 Cussonia Avenue, Brummeria, 0184, Pretoria, South Africa

Corresponding author(s): Joanna Dames (j.dames@ru.ac.za)

Received {date}; Revised {date}; Accepted {date}; Published {date}

Citation: Combination of authors, year of data paper publication (in parentheses), Title, Journal Name, Volume, Issue number (in parentheses), and doi of the data paper.

Resource Citation

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

Abstract

Isolated cultures and environmental metagenomic sequencing data using a target DNA markers ITS region for Fungi

Keywords: Occurrence, Specimen

Project details

Project title: FBIP: Mycorrhizal and root endophytic fungi associated with Orchids
Personnel: Joanna Dames
Funding: Foundational Biodiversity Information Programme
Study area descriptions/descriptor: South Africa (Eastern Cape, KwaZulu-Natal)

Data published through GBIF: http://ipt.sanbi.org.za/iptsanbi/resource?r=dames_ru_2017_v2

Taxonomic coverage

General taxonomic coverage description: The isolates  and metagenomic sequences are mycorrhizal and other root endophytic fungi that are found within orchid roots
Taxonomic ranks
Phylum: Fungi

Spatial coverage

General spatial coverage: South Africa (Eastern Cape, KwaZulu-Natal)
Coordinates: 33°20'2.5''S and 28°14'3.12''S Latitude; 26°29'35.63''E and 31°11'28.68''E Longitude 

Temporal coverage: 01 May 2017 - 29 November 2018

Methods

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.
Study extent description: South Africa (Eastern Cape, KwaZulu-Natal)
Sampling description: 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 description: The coordinates of the location where samples were collected was recorded

Datasets

Dataset description
Object name: Darwin Core Archive FBIP: Mycorrhizal and root endophytic fungi associated with Orchids
Character encoding: UTF-8
Format name: Darwin Core Archive format
Format version: 1.0
Distribution: http://ipt.sanbi.org.za/iptsanbi/archive.do?r=dames_ru_2017_v2
Publication date of data: 2020-09-30
Language: English
Licences of use: Creative Commons Attribution (CC-BY) 4.0 License

Metadata language: English
Date of metadata creation: 2020-09-27
Hierarchy level: Dataset