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.本研究整合了来自7项国际研究（详见atlas_info）的共计149条公开可用的RNA测序（RNA-seq）文库。这些转录组样本来自10个不同的豌豆品种，涵盖了广泛的生物学条件，包括完整的植物器官集合、多种非生物胁迫类型（矿质营养、水分供给与温度胁迫）以及生物互作（根瘤）。本研究将原始RNA-seq文库的测序数据比对至参考基因组（Kreplak等，2019），并计算了各独立研究中生物学重复的平均表达量（详见atlas_info），最终构建了覆盖81种生物学条件的豌豆基因组44756个基因的转录组图谱。 实验方法：利用SRA工具包（SRA Toolkit）v3.0.1，从NCBI公开的序列读取档案（Sequence Read Archive, SRA）下载了豌豆（P. sativum）的RNA-seq数据（测序读段与FASTQ文件），相关生物项目编号详见附表信息。使用fastp v0.22.0（Chen等，2018）对测序读段进行接头修剪与低质量读段过滤，随后通过FastQC v0.12.1（Babraham生物信息学平台）完成质量评估。使用STAR v2.7.10b（Dobin等，2012）将RNA-seq读段比对至豌豆参考基因组v1a（Kreplak等，2019）。通过FeatureCounts v2.0.1（Liao等，2013）生成基因表达计数表，并使用DESeq2 R包通过中位数比率法完成表达量标准化。本转录组图谱涵盖了豌豆基因组中44756个基因在81种生物学条件下的表达数据。