Identification of Submergence-Responsive MicroRNAs and Their Targets Reveals Complex MiRNA-Mediated Regulatory Networks in Lotus (Nelumbo nucifera Gaertn).

Qijiang Jin,Neil Mattson,Yanjie Wang,Xiaojing Liu,Hongwei Jiang,Xin Li,Xiao Zhang,Dongrui Yao,Bei Wang,Yingchun Xu

doi:10.3389/fpls.2017.00006

Abstract

MicroRNAs (miRNAs) are endogenous non-coding RNAs with important regulatory functions in plant development and stress responses. However, their population abundance in lotus (Nelumbo nucifera Gaertn) has so far been poorly described, particularly in response to stresses. In this work, submergence-related miRNAs and their target genes were systematically identified, compared, and validated at the transcriptome-wide level using high-throughput sequencing data of small RNA, Mrna, and the degradome. A total of 128 known and 20 novel miRNAs were differentially expressed upon submergence. We identified 629 target transcripts for these submergence-responsive miRNAs. Based on the miRNA expression profiles and GO and KEGG annotation of miRNA target genes, we suggest possible molecular responses and physiological changes of lotus in response to submergence. Several metabolic, physiological and morphological adaptations-related miRNAs, i.e., NNU_far-miR159, NNU_gma-miR393h, and NNU_aly-miR319c-3p, were found to play important regulatory roles in lotus response to submergence. This work will contribute to a better understanding of miRNA-regulated adaption responses of lotus to submergence stress.

Highlights

Lotus (Nelumbo nucifera Gaertn), a basal eudicot belonging to the plant family Nelumbonaceae, is a commercially important crop
Two sets of total RNA obtained from combined samples with (Sub) or without (Ck) submergence-treatment were used for cDNA library construction and sequencing at the Total Genomics Solution (TGS) company (Shenzhen, China), according to the manufacturer’s instructions
Some previously reported stress-related miRNAs, i.e., miR393, miR397b, and miR402, that are known to be important for plant response to abscisic acid (ABA), cold, dehydration and salt stress, exhibited no significant changes in lotus upon submergence (Sunkar and Zhu, 2004). The inconsistency of these miRNAs’ expression patterns suggested that a set of specific miRNAs might involve in lotus submergence response. In accordance with this suggestion, we found 20 novel miRNAs (25.97%) that were differentially expressed in control and submergence treatment seedlings

Summary

Introduction

Lotus (Nelumbo nucifera Gaertn), a basal eudicot belonging to the plant family Nelumbonaceae, is a commercially important crop. In Asia, lotus is cultivated as an edible and ornamental plants and has high demand (Ming et al, 2013). It is a source of herbal medicine because of strong antipyretic, antioxidant, anti-HIV, and anti-inflammatory properties. While lotus is an aquatic plant, it is sensitive to submergence due to rapid water level fluctuations. An urgent need exists to improve the submergence tolerance of lotus varieties to address damage from flooding and to enhance the potential growing range within the littoral zone of lakes/ponds

Methods

Results

Conclusion