Analysis codes for Ushio et al. (2023) eLife "An ecological network approach for detecting and validating influential organisms for rice growth"

This repository contains analysis codes to reproduce the results in Ushio et al. (2023) eLife https://doi.org/10.7554/eLife.87202. bioRxiv version is here: https://doi.org/10.1101/2023.02.19.529115.

License

See LICENSE.

Analysis workflow

Step 1. Detection of causal relationships between ecological community members and rice growth in 2017

• 01_2017_DNAxRice/: Codes for Unified Information-theoretic Causality (UIC) analysis of quantitative environmental DNA data and rice growth in 2017.
  

Step 2. Summary of rice growth data in 2019

• 02_2019_Rice/: Codes for summarizing and visualizing rice growth in 2019
  

Step 3. Processing of environmental DNA sequence data in 2019

• 03_2019_eDNA/: Codes for sequence data processing of quantitative environmental DNA data in 2019
  

Step 4. Detection of differentially expressed genes in rice in 2019

• 04_2019_riceRNA/: Codes for RNA sequence data processing and detection of differentially expressed genes in rice leaves in 2019
  

Step 5. Format figures

• FigCode/: Format figures
  
• FigCode/Fig_Combine.Rmd: Combine figures
  

Package versions

see text files in 00_SessionInfo/

Data availablity

Sequence data are deposited in DDBJ Sequence Read Archives (DRA). The accession numbers are as follows: DRA009658 (16S), DRA009659 (ITS), DRA009660 (COI), and DRA009661 (18S) for eDNA data of ecological communities in 2017 (Ushio 2022 Proceedings of the Royal Society B https://doi.org/10.1098/rspb.2021.2690), DRA015682 (16S), DRA015683 (ITS), DRA015685 (COI), and DRA015686 (18S) for eDNA data of ecological communities in 2019, and DRA015706 (Rice RNA-seq) for rice RNA expression data.

Get sequence data

You may download sequence data (*.fastq.bz2) from DDBJ Sequence Read Archives (DRA) by executing the following commands. DRAXXXXXX should be DRA accession number. Alternatively, you can access https:/ddbj.nig.ac.jp/DRASearch/submission?acc=DRAXXXXXX.

# Prepare folders
cd ~/Desktop
mkdir temp
mkdir temp/xml
cd temp

# Specify DRA accession number
DRA_ACCESSION="DRAXXXXXX"

# Download data (downlaod only *.bz2 and *.xml files)
wget -r --no-parent -A "*.bz2","*.xml" "ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/fastq/DRA015/${DRA_ACCESSION}/"

# If you need to specify the proxy:
#wget -r --no-parent -A "*.bz2","*.xml" -e FTP_PROXY=proxy.xxx.xx:xxxx "ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/fastq/DRA015/${DRA_ACCESSION}/"

# Move files
mv ftp.ddbj.nig.ac.jp/ddbj_database/dra/fastq/DRA015/${DRA_ACCESSION}/*/*.fastq.bz2 ./
mv ftp.ddbj.nig.ac.jp/ddbj_database/dra/fastq/DRA015/${DRA_ACCESSION}/*.xml xml

# Delete temporal folder
rm -r ftp.ddbj.nig.ac.jp

# Convert bz2 to gz format (if you wish)
#for f in *.bz2; do
#  bzcat "$f" | gzip -c >"${f%.bz2}.gz"
#  rm $f
#done