email: chengg@berkeley.edu / gaochengaob@126.com
The codes were used in the analysis of Mycobiome data generated from EPICON project.
EPICON is a DOE funded project conceived of by Peggy G. Lemaux, Devin Coleman-Derr, Elizabeth Purdom, John Vogel, Jeffery A. Dahlberg and John W. Taylor, with Peggy G. Lemaux as director. EPICON aimed at understanding responses of sorghum to drought, from host gene expression to host-associated microbiome.
For detailed descriptions of experimental design, please see associated publications:
Gao et al Nature Communications 2019 Fungal community assembly in drought stressed sorghum shows stochasticity, selection, and universal ecological dynamics (Accepted)
Gao et al ISMEJ 2019 Strong succession in arbuscular mycorrhizal fungal communities https://www.nature.com/articles/s41396-018-0264-0
Varoquaux#, Cole#, Gao# et al PNAS 2019 Transcriptomic analysis of field-droughted sorghum from seedling to maturity reveals biotic and metabolic responses www.pnas.org/cgi/doi/10.1073/pnas.1907500116
Xu et al PNAS 2018 Drought delays development of the sorghum root microbiome and enriches for monoderm bacteria https://www.pnas.org/content/115/18/E4284
Briefly, we collected 1026 sample from three treatments, two sorghum culrivars, 17 time points and four compartments.
Three treatments: control, pre-flowering drought and post-flowering drought
Two sorghum cultivars: the pre-flowering, drought tolerant sorghum cultivar RTx430, and the post-flowering, drought tolerant (or ‘stay green’) cultivar BTx642
Four compartments: Leaf, Root, Rhizosphere, Soil
Fungal community compositon and abundance was recognized by:
Illumina Miseq sequencing of fungal ITS2 rDNA region using 5.8SFun and ITS4Fun primers of the leaf, root, rhizosphere and soil
Illumina Miseq sequencing of fungal ITS2 region for 26 air samples.
qPCR of fungal 18S rRNA region using FF2 and FR1 primers of leaf and root samples
Fungal transcripts in transcriptomes containing both sorghum plants and their fungi generated from leaf and root samples
Fungal community assembly was explored by:
Multivariate analysis such as PCoA, adonis, betadispersion
Raup-Crick index and Beta Nearest Taxon Index
Dissimilarity Overlap Curve
etc...