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

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.

In silico identification and characterization of AGO, DCL and RDR gene families and their associated regulatory elements in sweet orange (Citrus sinensis L.)

“…In our analysis, we have identified four CsRDR genes, while CsRDR4/5 were found to be absent in C. sinensis genome indicating their evolutionary structure and functional effectiveness may be substituted or changed in C. sinensis. The DCL4 and AGO1 are two common and effective RNAi related genes found in all monocots and dicots [45] that have also been identified in our analysis.…”

“…For instance, 4 DCLs for Arabidopsis , 8 for rice, millet, and B . napus , 5 for Barley, 4 for sugarcane and many more were reported for different monocots and dicot species [ 14 , 40 – 42 , 44 , 45 ]. The number of identified AGO proteins exhibited a wide range of clades across the plant lineage.…”

“…The number of identified AGO proteins exhibited a wide range of clades across the plant lineage. The maximum number of AGO proteins and their clades were observed in the flowering plants, for example, 22 AGO proteins in soybean ( Glycine max , a paleopolyploid) [ 87 ], 21 in sugarcane [ 45 ], 19 in rice [ 14 ], and 17 in maize [ 40 ]. Although the genomic diversity exists among the AGO proteins in flowering plant, the three common clades can be observed through phylogenetic analysis: the AGO1/5/10, AGO2/3/7, and AGO4/6/8/9 clades [ 88 ].…”

“…32 genes in rice [14], 28 genes in maize [39] and tomato [33], 38 genes in foxtail millet [40], 22 genes in grapevine [41] and pepper [42] and 20 genes in cucumber [43]. Recently 23 genes in Barley (Hordeum vulgare L.) [44], 36 genes in sugarcane (Saccharum spontaneum) [45] and 25 genes in sweet orange (Citrus sinensis) [46] belonging to DCL, AGO and RDR genes have been identified and characterized. Besides, their expression pattern was also investigated under various conditions.…”

“…Recently 23 genes in Barley ( Hordeum vulgare L .) [ 44 ], 36 genes in sugarcane ( Saccharum spontaneum ) [ 45 ] and 25 genes in sweet orange ( Citrus sinensis) [ 46 ] belonging to DCL , AGO and RDR genes have been identified and characterized. Besides, their expression pattern was also investigated under various conditions.…”