Integrating long noncoding RNAs and mRNAs expression profiles of response to Plasmodiophora brassicae infection in Pakchoi (Brassica campestris ssp. chinensis Makino).

Hongfang Zhu,Zhaohui Zhang,Xiaofeng Li,Wen Zhai,Yuying Zhu,Dandan Xi,Serena Aceto

doi:10.1371/journal.pone.0224927

Abstract

The biotrophic protist Plasmodiophora brassicae causes serious damage to Brassicaceae crops grown worldwide. However, the molecular mechanism of the Brassica rapa response remains has not been determined. Long noncoding RNA and mRNA expression profiles in response to Plasmodiophora brassicae infection were investigated using RNA-seq on the Chinese cabbage inbred line C22 infected with P. brassicae. Approximately 5,193 mRNAs were significantly differentially expressed, among which 1,345 were upregulated and 3,848 were downregulated. The GO enrichment analysis shows that most of these mRNAs are related to the defense response. Meanwhile, 114 significantly differentially expressed lncRNAs were identified, including 31 upregulated and 83 downregulated. Furthermore, a total of 2,344 interaction relationships were detected between 1,725 mRNAs and 103 lncRNAs with a correlation coefficient greater than 0.8. We also found 15 P. brassicaerelated mRNAs and 16 lncRNA interactions within the correlation network. The functional annotation showed that 15 mRNAs belong to defense response proteins (66.67%), protein phosphorylation (13.33%), root hair cell differentiation (13.33%) and regulation of salicylic acid biosynthetic process (6.67%). KEGG annotation showed that the vast majority of these genes are involved in the biosynthesis of secondary metabolism pathways and plant-pathogen interactions. These results provide a new perspective on lncRNA-mRNA network function and help to elucidate the molecular mechanism of P. brassicae infection.

Highlights

Clubroot, a soil-borne disease, has caused considerable damage to Brassicaceae crops [1, 2]
To elucidate long noncoding RNAs (lncRNAs) and mRNA expression patterns in response to Plasmodiophora brassicae infection in Brassica rapa L., 6 libraries were constructed from control and clubroot tissues (CS22A) (Fig 1) for three biological replicates and sequenced using the Illumina platform [52]
The Gene Ontology (GO) annotation of the potential lncRNA targets showed that most upregulated significantly differentially expressed mRNAs were involved in the regulation of gene expression, and the downregulated significantly expressed mRNAs were closely related to stimulus, response to stress, defense response and response to biotic stimulus

Summary

Introduction

A soil-borne disease, has caused considerable damage to Brassicaceae crops [1, 2]. This disease is caused by the protist Plasmodiophora brassicae (P. brassicae), which can survive for up to 20 years in soil [3]. The two stages of P. brassicae, root-hair infection and cortical. Gene expression profiles of response to Plasmodiophora brassicae infection in Pakchoi accession number PRJNA528807. The Brassica rapa reference genome and gene model annotation files were downloaded from the Genome Database (http://brassicadb.org/)

Methods

Results

Conclusion