README Paper Abies vs ozone

This repository contains the scripts, data, metadata, and results to perform the transcriptomic, the genetic, and the metabolic analysis to "Abies vs Ozone's Project".

In these directories you will find analyses to answer the project's particular aims:

• To quantify the secondary metabolite relative abundance in the tolerant and the damaged trees during two ozone concentration periods: Metabolomic analysis

• To identify the tolerance sacred fir's origins: Genomic analysis

• To evaluate the tolerant and the damaged trees differential expression in the two ozone concentration periods: Transcriptomic analysis

GENERAL directory structure:

+----- Abies_vs_ozone/
|   +--1_Sampling/
|   +--2_Metabolomics/
|   +--3_Genomics/
|   +--4_Transcriptomics/
|   +--5_INFO_PROJECT/
|   +--README.md

README.md: a markdown file about this project. This file includes the repository's disposition.

1_Sampling: samples field metadata and scripts to perform maps.

2_Metabolomics: metabolite-generated analyses with a gas chromatograph spectrum mass (GC-SM). Data from the html files were loaded into the tables. Subsequently, the relative abundance was calculated. Finally, all the samples' values were compared using a barplot, ANOVA, and PCA analysis.

3_Genomics: genomic analyses from the GBS sequencing. ipyRAD was used to assemble de novo, VCFTools and plink were used to make more specific filters. The relatedness was calculated using a single SNP per locus. The mantel test, PCA, and admixture were performed in order to identify samples' local origin.

4_Transcriptomics: transcriptomic analysis from RNAseq data. Samples were cut with Trimmomatic and they were mapped to a reference transcriptome with BWA. R allowed to evaluate differential expression between the samples with the packages edgeR and DESeq2. Subsequently, a volcanoplot was performed to show overexpressed and underexpressed genes.

5_INFO_PROJECT: slide-shows, summaries, and final analyses.

Workfolow of main analyses:

METABOLOMICS

To quantify the secondary metabolite relative abundance in the healthy and the damaged trees during the two ozone concenrations periods.

Check more information about this pipeline in README_metabolomics.

To see a short summary about the final metabolomics analysis click here.

GENOMICS

To identify the geographic origin of tolerant invididuals.

Check more information about this pipeline in README_genomics.

To see a short summary about the final genomic analysis click here.

TRANSCRIPTOMICS

To evaluate the healthy and the damaged trees differential expression in the two periods with contrasting ozone concentrations.

Check more information about this pipeline in README_transcriptomics.

To see a short summary about the final transcriptomic analysis click here.

Contact

Verónica Reyes Galindo
veronica.rg.pb@gmail.com