This repository contains all code related to the manuscript "Plasticity in the dual mycorrhizal associations of tea tree, Melaleuca alternifolia"
Melaleuca alternifolia, commonly known as tea tree, is a commercially important crop plant native to Australia. Tea tree is delineated by two ecotypes, coastal and upland. Our project investigates the mycorrhizal associations of tea tree in coastal and upland populations, utilising ITS2 metabarcoding and root colonisation measurements. We aimed to determine mycorrhizal type of tea tree using microscopy and characterise the mycorrhizal fungal communities associated with tea tree ecotypes using metabarcoding.
- Luke Florence: Department of Environment and Genetics, La Trobe University, Melbourne, VIC, 3086, Australia
- Terry J. Rose: Faculty of Science and Engineering, Southern Cross University, Lismore, NSW, 2480, Australia
- Michael T. Rose: Faculty of Science and Engineering, Southern Cross University, Lismore, NSW, 2480, Australia
- Camille Truong: Royal Botanic Gardens Victoria, Melbourne, VIC, 3004, Australia
- Correspondence: [email protected]
The data from this study are available from the figshare repository (https://doi.org/10.26181/25241788) in nine files: an information file, sample metadata that includes root colonisation measurements, OTU sequences in fasta format, OTU-by-sample matrix and taxonomy table for all eukaryotes, as well as OTU-by-sample matrices and taxonomy tables for both arbuscular mycorrhizal and ectomycorrhizal fungi.
The fungal traits data used for ECM assignment are from the following publication:
- Põlme et al. (2020). FungalTraits: a user-friendly traits database of fungi and fungus-like stramenopiles. Fungal diversity, 105, 1-16.
ECM lineage thresholds for assigning OTU to ECM are from the following publication:
- Tedersoo et al. (2022). Best practices in metabarcoding of fungi: From experimental design to results. Molecular ecology, 31(10), 2769-2795.
This project is conducted using shell and R computing environments and the following software:
- R version 4.3.1 -- "Beagle Scouts"
- Trimmomatic version 0.36
- ITSxpress v2.0.0
- VSEARCH v2.22.1
- ITSx version 1.1.3
- Perl version 5.32.1
- BLAST version 2.14.1
- tidyverse version 2.0.0
- lme4 version 1.1.31
- emmeans version 1.8.2
- parameters version 0.21.3
- DHARMa version 0.4.6
- performance version 0.10.1
- adespatial version 0.3.20
- vegan version 2.6.4
- phyloseq version 1.42.0
- ANCOMBC version 2.0.1
- writexl version 1.4.2
- cowplot version 1.1.1
- patchwork version 1.2.0