Transcriptomic atlas in Pisum sativum

We integrated a total of 149 publicly available RNA-seq libraries from 7 international studies (see atlas_info). These transcriptomes were generated from 10 different pea varieties and covered a wide range of biological conditions, including a comprehensive collection of plant organs, various modalities of abiotic stress (mineral nutrition, water supply and temperature) and biotic interactions (nodule). The raw expression data from the source RNA-seq libraries were re-assembled to the reference genome (Kreplak et al., 2019) and the mean expression value was computed between biological replicates produced in individual studies (see atlas_info), thus providing a transcriptomic atlas of the 44.756 genes in the pea genome across 81 biological conditions. Method : RNA-seq data (sequenced reads and fastq files) generated from P. sativum were downloaded from the Sequence Read Archive publicly available at NCBI (Bioproject numbers listed in table info) using SRAtools v3.0.1 (SRA toolkit). A fastp v0.22.0 (Chen et al., 2018) analysis was performed to trim the adapters and filter out reads with a low-quality score, followed by a quality assessment performed using FastQC v0.12.1 (Babraham Bioinformatics). The RNA-seq reads were mapped to the P. sativum reference genome v1a (Kreplak et al., 2019) using STAR v2.7.10b (Dobin et al., 2012). Gene expression table counts were generated using FeatureCounts v2.0.1 (Liao et al., 2013) and normalized by median ratio using the DESeq2 R-package. The transcriptomic atlas comprises expression data of 44.756 genes of the pea genome across 81 biological conditions.