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. 2020 Aug 6;10(1):13202.
doi: 10.1038/s41598-020-70061-7.

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

Dong-Li Cui  1 , Jian-Yu Meng  1 , Xiao-Yan Ren  2 , Jing-Jing Yue  3 , Hua-Ying Fu  1 , Mei-Ting Huang  1 , Qing-Qi Zhang  4 , San-Ji Gao  5
Affiliations

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

Dong-Li Cui et al. Sci Rep. .

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.

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Conflict of interest statement

The authors declare no competing interests.

Figures

Figure 1
Figure 1
Structural domains of dicer-like protein (SsDCL) (a), argonaute protein (SsAGO) (b), and RNA-dependent RNA polymerase (SsRDR) (c) from S. spontaneum. Domains are indicated by colored boxes. The scale bars at the bottom represent the length of proteins in aa (amino acid).
Figure 2
Figure 2
Analysis of putative cis-acting elements related to response to drought or wound and pathogen stresses in S. spontaneum promoter sequences (1 kb) of SsDCL, SsAGO, and SsRDR genes. Numbers of elements present are indicated with darker blue shading representing higher numbers.
Figure 3
Figure 3
Phylogenetic analysis of S. spontaneum SsAGO(a), SsDCL(b), and SsRDR(c) genes. Neighbor-Joining (NJ) trees were constructed using MEGA 7 software based on the protein sequences for each family member. Bootstrap support values from 1,000 replications are indicated above the branches. S. spontaneum genes are indicated by a red circle.
Figure 4
Figure 4
Chromosome localization of SsDCL (in blue), SsAGO (in black), and SsRDR (in green) genes. The chromosome number is shown at the top of each bar. Horizontal bars represent the gene locations on each chromosome with positions in Mb (megabases) shown. Genes having tandem duplications are indicated by solid circles, whereas segmental duplication genes are joined by blue (SsDCLs), black (SsAGOs), and green lines (SsRDRs).
Figure 5
Figure 5
Schematic representation of protein–protein interaction (PPI) networks between SsDCLs, SsAGOs, and SsRDRs from S. spontaneum. Nodes having different colors indicate different proteins. Gray lines connect proteins within the PPI networks with darker colors and thicker lines indicating higher core PPI values.
Figure 6
Figure 6
Heat map showing spatiotemporal expression patterns of genes encoding SsDCL, SsAGO, and SsRDR in various S. spontaneum tissues including mature leaf, mature stem, pre-mature leaf, pre-mature stem, seedling leaf, and seedling stem. The size of the circles represents normalized expression level wherein larger circles correspond to higher expression levels.
Figure 7
Figure 7
Quantitative real time PCR (qRT-PCR) analysis of relative transcript expression of 18 candidate genes encoding SsDCL, SsAGO, and SsRDR in S. spontaneum clone SES208 exposed to dehydration treatment (PEG-6000) for 0, 3, 6, and 12 h. The x-axis indicates the time points of PEG-6000 exposure, whereas the y-axis indicates the relative expression level. The top young leaves were sampled and used for qRT-PCR assay. Relative transcript expression values are presented as means ± standard errors based on three biological replicates with three technical replicates. Significant differential expression is indicated by an asterisk (*, p < 0.05; **, p < 0.01).
Figure 8
Figure 8
Quantitative real time PCR (qRT-PCR) analysis of relative transcript expression of 18 candidate genes encoding SsDCL, SsAGO, and SsRDR in S. spontaneum clone SES208 inoculated with X. albilineans strain Xa-FJ1 at 0, 24, 48, and 72 h post-infection (hpi). The x-axis indicates the time points of experimental treatment, while the y-axis indicates the relative expression level. The top young leaves were sampled and used for qRT-PCR assay. Relative transcript expression values are presented as means ± standard errors based on three biological replicates with three technical replicates. Significant differential expression is indicated by an asterisk (*, p < 0.05; **, p < 0.01).
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