Transcriptome-Wide Identification and Characterization of Potato Circular RNAs in Response to Pectobacterium carotovorum Subspecies brasiliense Infection

Abstract

Little information about the roles of circular RNAs (circRNAs) during potato-Pectobacterium carotovorum subsp. brasiliense (Pcb) interaction is currently available. In this study, we conducted the systematic identification of circRNAs from time series samples of potato cultivars Valor (susceptible) and BP1 (disease tolerant) infected by Pcb. A total of 2098 circRNAs were detected and about half (931, 44.38%) were intergenic circRNAs. And differential expression analysis detected 429 significantly regulated circRNAs. circRNAs play roles by regulating parental genes and sponging miRNAs. Gene Ontology (GO) enrichment of parental genes and miRNAs targeted mRNAs revealed that these differentially expressed (DE) circRNAs were involved in defense response (GO:0006952), cell wall (GO:0005199), ADP binding (GO:0043531), phosphorylation (GO:0016310), and kinase activity (GO:0016301), suggesting the roles of circRNAs in regulating potato immune response. Furthermore, weighted gene co-expression network analysis (WGCNA) found that circRNAs were closely related with coding-genes and long intergenic noncoding RNAs (lincRNAs). And together they were cultivar-specifically regulated to strengthen immune response of potato to Pcb infection, implying the roles of circRNAs in reprogramming disease responsive transcriptome. Our results will provide new insights into the potato-Pcb interaction and may lead to novel disease control strategy in the future.

Transcriptome-wide identification of novel circular RNAs in soybean in response to low-phosphorus stress

“…Recently, although the involvement of circRNAs in plant tolerance to abiotic stress has been reported in several species [19][20][21]26], their role has rarely been reported in soybean [30], especially under LP stress. In the present study, to identify and explore how circRNAs respond to LP stress in soybean, root samples of two representative soybean genotypes, NN94156 and Bogao, which present significant differences in their traits related to P-use efficiency, were used to construct RNA-seq libraries under LP (5 μM, -P) and HP (500 μM, +P, control) conditions.…”

“…Unlike traditional linear RNAs, circRNAs are generated from head-to-tail back-splicing; thus, they do not have the terminal 5 0 cap and the 3 0 polyadenylated tail structures found in linear genes [18]. Increasing amounts of evidence have indicated that circRNAs are commonly produced by thousands of genes and have substantial functions in regulating gene expression at multiple levels in eukaryotic cells [19]. For example, circRNAs can function as transcriptional and posttranscriptional regulators, miRNA sponges, small nucleolar RNAs (snoRNAs), RNA processing intermediates, and transcriptional cis-regulators [19][20][21].…”

“…Increasing amounts of evidence have indicated that circRNAs are commonly produced by thousands of genes and have substantial functions in regulating gene expression at multiple levels in eukaryotic cells [19]. For example, circRNAs can function as transcriptional and posttranscriptional regulators, miRNA sponges, small nucleolar RNAs (snoRNAs), RNA processing intermediates, and transcriptional cis-regulators [19][20][21]. Moreover, increasing amounts of evidence have indicated that circRNAs play a key role in plant responses to abiotic stress [20,[22][23][24][25][26].…”

“…Moreover, increasing amounts of evidence have indicated that circRNAs play a key role in plant responses to abiotic stress [20,[22][23][24][25][26]. For example, cir-cRNAs are involved in plant dehydration and immune responses [26], chilling stress [27], heat stress [20], dehydration [28], infection by pathogenic bacteria [19,21], and LP stress [29]. These findings indicate that circRNAs are abundant in plants and have important functions in response to abiotic stresses.…”

circRNAs Are Involved in the Rice-Magnaporthe oryzae Interaction

“…Plant circRNAs have been found to function during fiber development, flowering, and fruit coloration based on spatial-and/or tissue-specific expression patterns (Tan et al, 2017;Wang et al, 2017c;Tong et al, 2018). The expression of plant circRNAs also responds to abiotic and biotic stimuli, including pathogen invasion (Zuo et al, 2016;Wang et al, 2017c;Zhou et al, 2017;Ghorbani et al, 2018;Xiang et al, 2018;Gao et al, 2019). For example, the accumulation of a set of circR-NAs is altered in kiwifruit upon canker pathogen infection (Wang et al, 2017c).…”