Comparative analysis of circular RNAs between soybean cytoplasmic male-sterile line NJCMS1A and its maintainer NJCMS1B by high-throughput sequencing

Abstract

BackgroundCytoplasmic male sterility (CMS) is a natural phenomenon of pollen abortion caused by the interaction between cytoplasmic genes and nuclear genes. CMS is a simple and effective pollination control system, and plays an important role in crop heterosis utilization. Circular RNAs (circRNAs) are a vital type of non-coding RNAs, which play crucial roles in microRNAs (miRNAs) function and post-transcription control. To explore the expression profile and possible functions of circRNAs in the soybean CMS line NJCMS1A and its maintainer NJCMS1B, high-throughput deep sequencing coupled with RNase R enrichment strategy was conducted.ResultsCircRNA libraries were constructed from flower buds of NJCMS1A and its maintainer NJCMS1B with three biological replicates. A total of 2867 circRNAs were identified, with 1009 circRNAs differentially expressed between NJCMS1A and NJCMS1B based on analysis of high-throughput sequencing. Of the 12 randomly selected circRNAs with different expression levels, 10 showed consistent expression patterns based on high-throughput sequencing and quantitative real-time PCR analyses. Tissue specific expression patterns were also verified with two circRNAs by quantitative real-time PCR. Most parental genes of differentially expressed circRNAs were mainly involved in biological processes such as metabolic process, biological regulation, and reproductive process. Moreover, 83 miRNAs were predicted from the differentially expressed circRNAs, some of which were strongly related to pollen development and male fertility; The functions of miRNA targets were analyzed using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG), and the target mRNAs were significantly enriched in signal transduction and programmed cell death. Furthermore, a total of 165 soybean circRNAs were predicted to contain at least one internal ribosome entry site (IRES) element and an open reading frame, indicating their potential to encode polypeptides or proteins.ConclusionsOur study indicated that the circRNAs might participate in the regulation of flower and pollen development, which could provide a new insight into the molecular mechanisms of CMS in soybean.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-5054-6) contains supplementary material, which is available to authorized users.

CircRNA Expression Pattern and ceRNA and miRNA–mRNA Networks Involved in Anther Development in the CMS Line of Brassica campestris

“…Recently, several differentially expressed (DE) circRNAs that are involved in programmed cell death (PCD) and might play an important role in CMS have been found among the soybean CMS line NJCMS1A, and its maintainer NJCMS1B. It indicates that circRNAs may play a role in regulating flower and pollen development, and provide novel insights into the mechanisms of CMS [18]. However, the circRNA–miRNA–mRNA network was not established in the abovementioned study, and the clear interactions of circRNAs, miRNAs, and mRNAs among male reproductive development need further study.…”

Characterization and Function of Circular RNAs in Plants

“…Considering circular structures and relatively low expression levels of circRNAs, an additional protocol that using linear RNase R for library preparation has become the preferred method for greatly enriching circRNAs. This method has been widely used in plant circRNA studies and yielded high confidence circRNAs in maize, soybean, bamboo, tomato, and grape (Zuo et al, 2016;Chen L. F. et al, 2018;Gao et al, 2019;Luo et al, 2019;.…”

Male sterility in soybean: Occurrence, molecular basis and utilization

“…Besides this, circular RNAs (circRNAs) are crucial non‐coding RNAs, which play imperative roles in miRNAs function and post‐transcription control. Chen et al () found that 83 miRNAs were predicted from the differentially expressed circRNAs, some of which were strongly related to pollen development and male fertility in soybean. Further, 165 new circRNAs were reported and it was predicted that they at least contain one internal ribosome entry site element and an open reading frame, indicating their potential to encode polypeptides or proteins, it is assumed that there may be some relation to MS in soybean.…”

“…Besides this, circular RNAs (circRNAs) are crucial non-coding RNAs, which play imperative roles in miRNAs function and post-transcription control. Chen et al (2018) found that 83 miR-NAs were predicted from the differentially expressed circRNAs, some of which were strongly related to pollen development and It is widely accepted that CMS in the plant is closely related to mitochondrial genome rearrangement, and many trait-determining mitochondrial genes could be suppressed or activated by Rf-genes (Bentolila & Stefanov, 2012;Chen et al, 2017;Zheng et al, 2012). In fact, some specific CMS-related genes have been identified as direct or indirect MS due to damage or abnormalities in the mitochondrial genome (Kazama et al, 2019).…”