Comprehensive Identification and Expression Profiling of Circular RNAs During Nodule Development in Phaseolus vulgaris.

Zhihua Wu,Erdai Qin,Hong Liu,Rui Qin,Huan Liu,Wen Huang,Aleel K Grennan,Shuo Liu

doi:10.3389/fpls.2020.587185

Abstract

Symbiotic nitrogen fixation by legume nodules provides an abundant nitrogen source for plants, and understanding this process is key for developing green agriculture. Circular RNA (circRNA), a type of endogenous RNA produced by reverse splicing of mRNA precursors, plays important regulatory roles in plants at the transcriptional and post-transcriptional levels. However, the relationship between circRNAs and legume–rhizobium is unknown. Here, we performed comprehensive identification and expression profiling of circRNAs during nodulation in common bean (Phaseolus vulgaris) compared to uninoculated roots of corresponding ages by constructing circRNA-seq and mRNA-seq libraries. We identified 8,842 high-confident circRNAs, 3,448 of which were specifically produced during symbiosis, with the highest number at the nitrogen-fixing stage. Significantly, more circRNAs were derived from exons than from intergenic regions or introns in all samples. The lengths and GC contents of the circRNAs were similar in roots and nodules. However, circRNAs showed specific spatiotemporal expression patterns during nodule and root development. GO and other functional annotation of parental genes of differentially expressed circRNAs indicated their potential involvement in different biological processes. The expression of major circRNAs during symbiosis is independent of parental genes’ expression to a certain degree, while expression of the remaining minor circRNAs showed positive correlation to parental genes. Functional annotation of the targeted mRNAs in the circRNA–miRNA–mRNA network showed that circRNAs may be involved in transmembrane transport and positive regulation of kinase activity during nodulation and nitrogen fixation as miRNA sponges. Our comprehensive analysis of the expression profile of circRNAs and their potential functions suggests that circRNAs may function as new post-transcriptional regulators in legume–rhizobium symbiosis.

Highlights

The economically and ecologically important Leguminosae family, the third largest family of angiosperms, is widely distributed in diverse environments worldwide
A total of 8842 high-confident circular RNA (circRNA) produced from 4155 parental genes were identified, most with GC contents of 25–35% (Supplementary Figure 2B and Supplementary Table 2)
To analyze the relationships between DEcircRNAs and expression of their parental genes, we identified the intersections of the parental genes of DEcircRNAs and all differentially expressed mRNAs (DEmRNAs)

Summary

Introduction

The economically and ecologically important Leguminosae family, the third largest family of angiosperms, is widely distributed in diverse environments worldwide. 88% of legume species form specialized symbiotic nitrogen-fixing nodules, which convert inorganic nitrogen in the atmosphere into organic ammonium via symbiosis with rhizobia. This process plays important roles in maintaining ecosystem function and sustainable agriculture (Doyle and Luckow, 2003). From the perspective of symbiosis, common bean is promiscuous in that it forms nitrogen-fixing nodules with a wide diversity of rhizobia from the Rhizobium and Sinorhizobium genera (Velazquez et al, 2001). Common bean is an ideal model diploid for studying gene regulation and evolution of legume–rhizobium symbiosis in the phaseoloid group (McClean et al, 2008)

Methods

Results

Conclusion