Abstract
RNA silencing is a conserved mechanism in eukaryotic organisms to regulate gene expression. Argonaute (AGO), Dicer-like (DCL) and RNA-dependent RNA polymerase (RDR) proteins are critical components of RNA silencing, but how these gene families’ functions in sugarcane were largely unknown. Most stress-resistance genes in modern sugarcane cultivars (Saccharum spp.) were originated from wild species of Saccharum, for example S. spontaneum. Here, we used genome-wide analysis and a phylogenetic approach to identify four DCL, 21 AGO and 11 RDR genes in the S. spontaneum genome (termed SsDCL, SsAGO and SsRDR, respectively). Several genes, particularly some of the SsAGOs, appeared to have undergone tandem or segmental duplications events. RNA-sequencing data revealed that four SsAGO genes (SsAGO18c, SsAGO18b, SsAGO10e and SsAGO6b) and three SsRDR genes (SsRDR2b, SsRDR2d and SsRDR3) tended to have preferential expression in stem tissue, while SsRDR5 was preferentially expressed in leaves. qRT-PCR analysis showed that SsAGO10c, SsDCL2 and SsRDR6b expressions were strongly upregulated, whereas that of SsAGO18b, SsRDR1a, SsRDR2b/2d and SsRDR5 was significantly depressed in S. spontaneum plants exposed to PEG-induced dehydration stress or infected with Xanthomonas albilineans, causal agent of leaf scald disease of sugarcane, suggesting that these genes play important roles in responses of S. spontaneum to biotic and abiotic stresses.
Highlights
RNA silencing, known as RNA interference (RNAi), plays an important role in multiple processes in plants, including growth and development, epigenetic modifications and responses to and defenses against abiotic and biotic stresses[1,2,3]
In this study we identified and classified protein members of the DCL, AGO and RNA-dependent RNA polymerase (RDR) gene families in the S. spontaneum genome, and analyzed the functions of these genes to understand their roles in responses to polyethylene glycol (PEG)-induced dehydration stress and X. albilineans infection
To identify the AGO, DCL, and RDR gene families in S. spontaneum, we gathered the previously characterized and conserved domains of the three gene families and used HMMER software to search for corresponding domains in the S. spontaneum genome database
Summary
RNA silencing, known as RNA interference (RNAi), plays an important role in multiple processes in plants, including growth and development, epigenetic modifications and responses to and defenses against abiotic and biotic stresses[1,2,3]. The RISC binds complementary mRNAs guided by single-stranded sRNAs to mediate processes such as translational inhibition, RNA degradation or chromosome modification[8,9] These sRNAs are amplified from the targeted RNA by cellular host RNA-dependent RNA polymerases (RDRs) to produce additional dsRNAs that will be processed into secondary siRNAs that amplify the silencing s ignal[10,11]. Different members of DCL, AGO, and RDR families play different roles in RNA silencing in plants, but they share partially redundant functions[20]. In this study we identified and classified protein members of the DCL, AGO and RDR gene families in the S. spontaneum genome, and analyzed the functions of these genes to understand their roles in responses to polyethylene glycol (PEG)-induced dehydration stress and X. albilineans infection. Our findings will provide important information for exploration of molecular resistance mechanisms in S. spontaneum
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