Illumina sequencing data from fungal (ITS) and bacterial (16S) endophyte meta-communities associated with Parkinsonia spp. in North America and Australia

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General
Title
Illumina sequencing data from fungal (ITS) and bacterial (16S) endophyte meta-communities associated with Parkinsonia spp. in North America and Australia
Type
Dataset
Date Record Created
2017-05-03
Date Record Modified
Not provided
Language
English
Embargo
Embargo
Not embargoed.
Embargo date
Not provided
Embargo comment
Not provided
Coverage
Date Coverage
2013-05-01 to 2017-05-01
Time Period
Not provided
Geospatial Location
  1. Text: Australian samples were collected around northern and central Queensland (Charters Towers, Mount Isa, Cloncurry, Gropers Creek, Caerphilly), Western Australia (Kununurra), and the Northern Territory (Snake Creek Station and Newcastle Waters Station). DNA was extracted at the Ecosciences Precinct in Brisbane, QLD.
  2. Text: North American samples were collected near Tucson and Phoenix in Arizona and near Austin and San Antonio in Texas.
  3. Text: Remaining DNA extractions and sequencing of all samples was performed at UC Berkeley in California USA.
Description
  1. This dataset contains the raw FASTQ files from multiplex dual-index Illumina sequencing of fungal, bacterial and oomycete communities associated with Parkinsonia spp. in North America and Australia. Fungal reads were obtained via sequencing of the ITS amplicon using ITS1F and ITS2 primers, bacterial reads were obtained via sequencing of the 16s rRNA gene using primers 515F and 806R primers, and oomycete reads were obtained via sequencing of the ITS region using ITS6 and ITS7 primers. Samples were taken from multiple plant parts of healthy and dieback-affected Parkinsonia aculeata in Australia (QLD, WA, NT), and healthy P. aculeata, P. microphylla and P. florida in the USA (AZ, TX). FASTQ files can be cleaned up and curated after Bissett et al. (2016). The quality of all Illumina R1 and R2 reads can be assessed visually using FastQC (Andrews 2016), merged using FLASH (Magoč & Salzberg 2011), and converted to FASTA format. For 16S rRNA sequences, extract and edit using MOTHUR v1.34.1 (Schloss et al. 2009). For ITS region sequences, extract and edit using ITSx (Bengtsson-Palme et al. 2013). For a more detailed protocol, refer to Chapter 5 and Appendix C of the forthcoming PhD thesis “Investigating the cause of dieback in the invasive plant, Parkinsonia aculeata”, by Tracey V. Steinrucken (2017).

    • Type: full
Related Publications
  1. Bengtsson-Palme J, Ryberg M, Hartmann M, Branco S, Wang Z, Godhe A et al 2013, ‘Improved software detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and other eukaryotes for analysis of environmental sequencing data’, Methods in Ecology and Evolution, vol. 4, no. 10, pp. 914-919.
  2. Bissett A, Fitzgerald A, Meintjes T, Mele PM, Reith F, Dennis PG et al. 2016, ‘Introducing BASE: the Biomes of Australian Soil Environments soil microbial diversity database’, GigaScience, vol. 5, no. 1, pp. 1-11.
  3. Magoč T & Salzberg SL 2011, ‘FLASH: fast length adjustment of short reads to improve genome assemblies’, Bioinformatics, vol. 27, no. 21, pp. 2957-2963.
  4. Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB et al. 2009’, Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities’, Applied and Environmental Microbiology, vol. 75, no. 23, pp. 7537-7541.
Related Websites
  1. Download HIE data
  2. HIE | Hawkesbury Institute for the Environment
  3. Multiplex Illumina Sequencing of Invasive Plant Endophytes
  4. Andrews S 2016, FastQC a quality control tool for high throughput sequence data
Related Data
Not provided
Related Services
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Technical metadata
Not provided
People
Creators
  1. Tracey Steinrucken , Hawkesbury Institute for the Environment (HIE) [PI]
  2. Dr. Andrew Bissett
  3. Assoc. Prof. Jeffrey Powell , Hawkesbury Institute for the Environment (HIE)
  4. Dr Matteo Garbelotto
  5. Dr Rieks Van Klinken
  6. Dylan Smith
Primary Contact
Tracey Steinrucken, t.steinrucken@westernsydney.edu.au
Supervisors
Not provided
Subject
Fields of Research
Not provided
Socio-Economic Objective
Not provided
Keywords
  1. Parkinsonia aculeata
  2. NGS
  3. Illumina
  4. Endophytes
  5. Dieback
  6. Invasive Plant
  7. Community Analysis
  8. Metacommunity
Research Activity
Pure basic research
Rights
License
CC BY 4.0: Attribution 4.0 International
License - Other
Not provided
Access Rights/Conditions
Dataset is available via the Western Sydney University ResearchDirect record via Related Website under Description section.
Type
open
Rights
Not provided
Attachments
No files currently attached.
Citation
Sending Citation
on
Identifier Type
useCuration
Creators
  1. Tracey Steinrucken
  2. Dr Andrew Bissett
  3. Dr Jeffrey Powell
  4. Dr Matteo Garbelotto
  5. Dr Rieks Van Klinken
  6. Dylan Smith
Title
Illumina sequencing data from fungal (ITS) and bacterial (16S) endophyte meta-communities associated with Parkinsonia spp. in North America and Australia
Edition
Not provided
Publisher
Western Sydney University
Place of Publication
Not provided
Dates
  1. 2017-05-03 {missing: "dc:type.skos:prefLabel" }
  2. 2017-05-03 Date Created
URL
http://research-data.westernsydney.edu.au/redbox/default/detail/db298ed8934ffc71cec7813408670767
Context
Steinrucken, Tracey; Bissett, Andrew; Powell, Jeffrey; Garbelotto, Matteo; Van Klinken, Rieks; Smith, Dylan (2017): Illumina sequencing data from fungal (ITS) and bacterial (16S) endophyte meta-communities associated with Parkinsonia spp. in North America and Australia. Western Sydney University. http://doi.org/10.4225/35/5909643c91a9c