Expression atlas of chickpea during development

In this study, we aim to present a global view of transcriptome dynamics in different tissues/organs/developmental stage in chickpea. We generated about ~31-95 million reads from each of 94 libraries representing 32 different tissues/organs using Illumina platform. We generated a hybrid assembly of these data along with PacBio data to produce full-length transcriptome assembly. We mapped the reads to the transcriptome assembly for estimation of the abundance of coding and long non-coding transcripts in different tissue samples. The transcriptome dynamics was studied by differential and tissue-specific expression analyses, and co-expression network and transcriptional regulatory network analyses. Overall design: We collected different tissues/organs from vegetative and reproductive stages of development. Total RNA isolated from these tissue samples was subjected to Illumina sequencing. The sequenced data was further filtered using NGS QC Toolkit to obtain high-quality reads. The filtered reads were mapped to the chickpea transcriptome assembly using Bowtie and fragments per exon kilobase per million (FPKM) was calculated using RSEM for each gene in all the samples to measure their gene expression.本研究旨在全面解析鹰嘴豆不同组织/器官及发育阶段的转录组动态变化特征。本研究依托Illumina测序平台，对涵盖32种不同组织/器官的94个文库分别进行测序，每个文库产出约3100万至9500万条读段（reads）。本研究将该测序数据与PacBio测序数据进行混合组装，构建得到全长转录组（transcriptome）组装序列。将测序读段比对至该转录组组装序列，以估算不同组织样本中编码转录本与长链非编码转录本的表达丰度。本研究通过差异表达分析、组织特异性表达分析，以及共表达网络与转录调控网络分析，对转录组动态变化特征展开研究。 实验设计概述：本研究采集了鹰嘴豆营养生长与生殖生长阶段的不同组织/器官样本。从上述组织样本中提取的总RNA经Illumina平台完成测序，测序所得原始数据通过NGS QC Toolkit进行过滤，以获得高质量读段。使用Bowtie工具将过滤后的读段比对至鹰嘴豆转录组组装序列，并通过RSEM工具计算所有样本中每个基因的每百万片段每外显子千碱基（FPKM）值，以量化其基因表达水平。