Asha Srinivasan, Mohammad Sumayya, Makeshkumar T
Division of Crop Protection, ICAR-Central Tuber Crops Research Institute, Sreekaryam, Thiruvananthapuram, Kerala 695017 India.
Department of Molecular Biology and Biotechnology, College of Agriculture, Kerala Agricultural University, Vellayani, Thiruvananthapuram, 695522 India.
3 Biotech. 2023 Mar;13(3):95. doi: 10.1007/s13205-023-03494-2. Epub 2023 Feb 23.
Small RNA (sRNA) mediated gene regulation during (SLCMV) infection was studied from the Indian Cassava Cultivar H226. Our study generated high throughput sRNA dataset of 23.64 million reads from the control and SLCMV infected H226 leaf libraries. mes-miR9386 was detected as the most prominent miRNA expressed in control and infected leaf. Among the differentially expressed miRNAs, mes-miR156, mes- miR395 and mes-miR535a/b showed significant down regulation in the infected leaf. Genome-wide analysis of the three small RNA profiles revealed critical role of virus-derived small RNAs (vsRNAs) from the infected leaf tissues of H226. The vsRNAs were mapped to the bipartite SLCMV genome and high expression of siRNAs generated from the virus genomic region encoding genes in the infected leaf pointed towards the susceptibility of H226 cultivars to SLCMV. Furthermore, the sRNA reads mapped to the antisense strand of the SLCMV ORFs was higher than the sense strand. These vsRNAs were potential to target key host genes involved in virus interaction such as aldehyde dehydrogenase, ADP-ribosylation factor1 and ARF1-like GTP-binding proteins. The sRNAome-assisted analysis also revealed the origin of virus-encoded miRNAs from the SLCMV genome in the infected leaf. These virus-derived miRNAs were predicted to have hair-pin like secondary structures, and have different isoforms. Moreover, our study revealed that the pathogen sRNAs play a critical role in the infection process in H226 plants.
The online version contains supplementary material available at 10.1007/s13205-023-03494-2.
从印度木薯品种H226研究了木薯潜隐花叶病毒（SLCMV）感染期间小RNA（sRNA）介导的基因调控。我们的研究从对照和感染SLCMV的H226叶片文库中生成了2364万个读段的高通量sRNA数据集。mes-miR9386被检测为在对照和感染叶片中表达最显著的miRNA。在差异表达的miRNA中，mes-miR156、mes-miR395和mes-miR535a/b在感染叶片中表现出显著下调。对这三种小RNA图谱的全基因组分析揭示了来自H226感染叶片组织的病毒衍生小RNA（vsRNA）的关键作用。vsRNA被定位到双分体SLCMV基因组，并且在感染叶片中从编码基因的病毒基因组区域产生的siRNA的高表达表明H226品种对SLCMV易感。此外，映射到SLCMV ORF反义链的sRNA读段高于正义链。这些vsRNA有可能靶向参与病毒相互作用的关键宿主基因，如醛脱氢酶、ADP-核糖基化因子1和ARF1样GTP结合蛋白。sRNA组辅助分析还揭示了感染叶片中SLCMV基因组中病毒编码miRNA的起源。这些病毒衍生的miRNA被预测具有发夹样二级结构，并且具有不同的异构体。此外，我们的研究表明病原体sRNA在H226植物的感染过程中起关键作用。
在线版本包含可在10.1007/s13205-023-03494-2获取的补充材料。
