Genome-wide identification and characterization of DCL, AGO and RDR gene families in Saccharum spontaneum

• Published in: Scientific reports Vol. 10; no. 1; p. 13202
• Main Authors: Cui, Dong-Li, Meng, Jian-Yu, Ren, Xiao-Yan, Yue, Jing-Jing, Fu, Hua-Ying, Huang, Mei-Ting, Zhang, Qing-Qi, Gao, San-Ji
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 06.08.2020; Nature Publishing Group
• Subjects: 631/449/2661; 631/61/191; Argonaute Proteins - genetics; Chromosomes, Plant - genetics; Computer Simulation; Cultivars; Dehydration; DNA-directed RNA polymerase; Gene expression; Gene families; Genome-Wide Association Study; Genomes; Humanities and Social Sciences; Leaves; multidisciplinary; Phylogeny; Promoter Regions, Genetic - genetics; Protein Interaction Mapping; Ribonuclease III - genetics; RNA polymerase; RNA-Dependent RNA Polymerase - genetics; RNA-directed RNA polymerase; RNA-mediated interference; Saccharum; Saccharum - enzymology; Saccharum - genetics; Saccharum - metabolism; Saccharum spontaneum; Scald; Science; Science (multidisciplinary); Sugarcane
• ISSN: 2045-2322; 2045-2322
• DOI: 10.1038/s41598-020-70061-7

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.