Transcriptome Analysis of Stem and Globally Comparison with Other Tissues in Brassica napus.

Liyun Miao,Jun Xiang,Chunhua Fu,Xuekun Zhang,Jianping Gan,Maoteng Li,Nadia Raboanatahiry,Guangyuan Lu,Libin Zhang

doi:10.3389/fpls.2016.01403

Abstract

Brassica napus is one of the most important oilseed crops in the world. However, there is currently no enough stem transcriptome information and comparative transcriptome analysis of different tissues, which impedes further functional genomics research on B. napus. In this study, the stem transcriptome of B. napus was characterized by RNA-seq technology. Approximately 13.4 Gb high-quality clean reads with an average length of 100 bp were generated and used for comparative transcriptome analysis with the existing transcriptome sequencing data of roots, leaves, flower buds, and immature embryos of B. napus. All the transcripts were annotated against GO and KEGG databases. The common genes in five tissues, differentially expressed genes (DEGs) of the common genes between stems and other tissues, and tissue-specific genes were detected, and the main biochemical activities and pathways implying the common genes, DEGs and tissue-specific genes were investigated. Accordingly, the common transcription factors (TFs) in the five tissues and tissue-specific TFs were identified, and a TFs-based regulation network between TFs and the target genes involved in ‘Phenylpropanoid biosynthesis’ pathway were constructed to show several important TFs and key nodes in the regulation process. Collectively, this study not only provided an available stem transcriptome resource in B. napus, but also revealed valuable comparative transcriptome information of five tissues of B. napus for future investigation on specific processes, functions and pathways.

Highlights

Brassica napus as one of the world’s most important oilseed crops provides edible oil and raw materials for livestock feed and biofuel applications (Cai et al, 2015; Wood et al, 2015)
Total RNA was extracted from the stems of ZY821 at initial flowering stage, and cDNA libraries were prepared and sequenced with Illumina HiSeq sequencing instrument
The stem clean reads were mapped to the reference genome of B. napus Darmor-bzh3 (Chalhoub et al, 2014), and 121,415,423 (90.60%) of the clean reads had perfect match to the reference genome, in which 73.50, 3.19, and 23.31% of them were mapped to exonic regions, intronic regions and intergenic regions, respectively

Summary

Introduction

Brassica napus as one of the world’s most important oilseed crops provides edible oil and raw materials for livestock feed and biofuel applications (Cai et al, 2015; Wood et al, 2015). Multiple copies of most genes in B. napus resulted in generating a highly complex and redundant transcriptome (Parkin et al, 2010), which precluded accurate transcript differentiation (Trick et al, 2009), limited the ability to elucidate the genetic mechanisms controlling a trait (Parkin et al, 2010), and imposed a huge challenge in high-throughput genotyping with sequencing and array. That can capture millions of long sequence tags, have been proved to revolutionize genetic analysis (Mardis, 2008) and possess the ability to comprehensively catalog gene expression in polyploid species (Parkin et al, 2010)

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Discussion

Conclusion