Abstract
Circular RNAs (circRNAs), a class of recently discovered non-coding RNAs, play a role in biological and developmental processes. A recent study showed that circRNAs exist in plants and play a role in their environmental stress responses. However, cotton circRNAs and their role in Verticillium wilt response have not been identified up to now. In this study, two CSSLs (chromosome segment substitution lines) of G.barbadense introgressed into G. hirsutum, CSSL-1 and CSSL-4 (a resistant line and a susceptible line to Verticillium wilt, respectively), were inoculated with V. dahliae for RNA-seq library construction and circRNA analysis. A total of 686 novel circRNAs were identified. CSSL-1 and CSSL-4 had similar numbers of circRNAs and shared many circRNAs in common. However, CSSL-4 differentially expressed approximately twice as many circRNAs as CSSL-1, and the differential expression levels of the common circRNAs were generally higher in CSSL-1 than in CSSL-4. Moreover, two C-RRI comparisons, C-RRI-vs-C-RRM and C-RRI-vs-C-RSI, possessed a large proportion (approximately 50%) of the commonly and differentially expressed circRNAs. These results indicate that the differentially expressed circRNAs may play roles in the Verticillium wilt response in cotton. A total of 280 differentially expressed circRNAs were identified. A Gene Ontology analysis showed that most of the ‘stimulus response’ term source genes were NBS family genes, of which most were the source genes from the differentially expressed circRNAs, indicating that NBS genes may play a role in Verticillium wilt resistance and might be regulated by circRNAs in the disease-resistance process in cotton.
Highlights
In contrast with messenger RNA, non-coding RNAs comprise the majority of the RNA world and include rRNA, lncRNA, snRNA, tRNA and miRNA, which function in various biological regulatory processes
To analyse the role of circular RNA (circRNA) in Verticillium wilt response, the two Chromosome segment substitution lines (CSSLs) of G. barbadense introgressed in G. hirsutum, CSSL-1 and CSSL-4, were inoculated with V. dahliae, and the root and stem of the inoculated plants and the plants in the control group were harvested to construct RNA-seq libraries
To elucidate the role of circRNAs in cotton Verticillium wilt response, two CSSLs of G. barbadense introgressed in G. hirsutum, CSSL-1 and CSSL-4, were used to construct an RNA-seq library and to analyse circRNA based on V. dahliae inoculation
Summary
In contrast with messenger RNA (mRNA), non-coding RNAs comprise the majority of the RNA world and include rRNA, lncRNA, snRNA, tRNA and miRNA, which function in various biological regulatory processes. CircRNAs are observed in a diverse range of life forms, including archaea (Danan et al, 2012), mammals such as humans (Salzman et al, 2012), mice (Jiang et al, 2014; Pei et al, 2017), mosquitos (Gruner et al, 2016), sheep (Li et al, 2017), and plants such as rice (Lu et al, 2015; Ye et al, 2015), Arabidopsis (Ye et al, 2015; Sun et al, 2016; Pan et al, 2018; Dou et al, 2017), barley (Darbani, Noeparvar & Borg, 2016), and maize (Chen et al, 2018) This diversity suggests conserved biological functions and distinct properties. Very recent studies have shown that circRNAs function as protein-coding sequences in vitro or vivo (Legnini et al, 2017; Pamudurti et al, 2017; Yang et al, 2017)
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