Quantitative Analysis of Transcripts of the Open Reading Frames of <i>Sugarcane Yellow Leaf Virus</i> Genome By One‐multiplex <scp>RT</scp>‐<scp>PCR</scp>: Evidence for a High Transcript Level of Suppressor Gene in Sink Leaves

ElSayed, Abdelaleim Ismail; Komor, Ewald

doi:10.1111/jph.12131

Cited by 3 publications

(1 citation statement)

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“…The AGO1 protein cannot function and is degraded by the ubiquitin degradation system of plants. The ORF3 encodes a capsid protein CP or P3, while ORF5 encodes a read-through protein and the genomic RNA of the YLV is coated with these two structural proteins to form an icosahedron with a diameter of 22–23 nm regular sphere observed under an electron microscope ( ElSayed and Komor, 2013 ). On the surface of intact virions, most of them are CP and a few are CP-RTP.…”

Section: Introductionmentioning

confidence: 99%

Transcriptome Analysis of Sugarcane Response to Sugarcane Yellow Leaf Virus Infection Transmitted by the Vector Melanaphis sacchari

et al. 2022

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Sugarcane yellow leaf disease severely affects sugarcane production. As a viral disease, the pathogen sugarcane yellow leaf virus can only be transmitted by aphid vectors rather than mechanical means. To understand the sugarcane responses to ScYLV infection, the corresponding transcriptomic profile of ScYLV-infected and ScYLV-free plants were analyzed with RNA-Seq technology. In this study, Melanaphis sacchari was used as the vector to transmit ScYLV to the susceptible sugarcane cultivar CP72-1210 and transcriptome was sequenced as well as differentially expressed genes between disease-infected and non-infected sugarcane plants were investigated. A total of 1,22,593 genes were assembled, of which 1,630 genes were differentially expressed. Among DEGs, 1,622 were upregulated and eight were downregulated that were further annotated with GO, KEGG, KOG, PFAM, SwissProt, and Nr databases. The expression levels of DEGs in the three KEGG pathways, namely endocytosis, PEX protein synthesis, and endoplasmic reticulum stress response to viral protein synthesis were observed. Interestingly, it was found that the yellow leaf virus could induce the formation of autophagosomes by LC3, promoted by ER stress, and may be related to the replication of viral RNA. We tested 63 DEGs in this research. The qRT-PCR results showed that two were downregulated and 45 were upregulated in response to the ScYLV infection. This study will not only offer an overall comprehension of sugarcane responses to ScYLV infection at the gene expression level but also increase the chances to block the transmission of ScYLV for use in further molecular biology techniques and will aid in increasing the resistance of plants against ScYLV.

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Section: Introductionmentioning

confidence: 99%

Transcriptome Analysis of Sugarcane Response to Sugarcane Yellow Leaf Virus Infection Transmitted by the Vector Melanaphis sacchari

et al. 2022

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Molecular Evolutionary History of Sugarcane yellow leaf virus Based on Sequence Analysis of RNA-Dependent RNA Polymerase and Putative Aphid Transmission Factor-Coding Genes

2014

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RNA-dependent RNA polymerase (RdRp) encoded by ORF2 and putative aphid transmission factor (PATF) encoded by ORF5 of Sugarcane yellow leaf virus (SCYLV) were detected in six sugarcane cultivars affected by yellow leaf using RT-PCR and real-time RT-PCR assays. Expression of both genes varied among infected plants, but overall expression of RdRp was higher than expression of PATF. Cultivar H87-4094 from Hawaii yielded the highest transcript levels of RdRp, whereas cultivar C1051-73 from Cuba exhibited the lowest levels. Sequence comparisons among 25 SCYLV isolates from various geographical locations revealed an amino acid similarity of 72.1-99.4 and 84.7-99.8 % for the RdRp and PATF genes, respectively. The 25 SCYLV isolates were separated into three (RdRp) and two (PATF) phylogenetic groups using the MEGA6 program that does not account for genetic recombination. However, the SCYLV genome contained potential recombination signals in the RdRp and PATF coding genes based on the GARD genetic algorithm. Use of this later program resulted in the reconstruction of phylogenies on the left as well as on the right sides of the putative recombination breaking points, and the 25 SCYLV isolates were distributed into three distinct phylogenetic groups based on either RdRp or PATF sequences. As a result, recombination reshuffled the affiliation of the accessions to the different clusters. Analysis of selection pressures exerted on RdRp and PATF encoded proteins revealed that ORF 2 and ORF 5 underwent predominantly purifying selection. However, a few sites were also under positive selection as assessed by various models such as FEL, IFEL, REL, FUBAR, MEME, GA-Branch, and PRIME.

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Genome characterization of Sugarcane Yellow Leaf Virus with special reference to RNAi based molecular breeding

Khalil

Yueyu

Naiyan

et al. 2018

Microbial Pathogenesis

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Quantitative Analysis of Transcripts of the Open Reading Frames of Sugarcane Yellow Leaf Virus Genome By One‐multiplex RT‐PCR: Evidence for a High Transcript Level of Suppressor Gene in Sink Leaves

Cited by 3 publications

References 24 publications

Transcriptome Analysis of Sugarcane Response to Sugarcane Yellow Leaf Virus Infection Transmitted by the Vector Melanaphis sacchari

Transcriptome Analysis of Sugarcane Response to Sugarcane Yellow Leaf Virus Infection Transmitted by the Vector Melanaphis sacchari

Molecular Evolutionary History of Sugarcane yellow leaf virus Based on Sequence Analysis of RNA-Dependent RNA Polymerase and Putative Aphid Transmission Factor-Coding Genes

Genome characterization of Sugarcane Yellow Leaf Virus with special reference to RNAi based molecular breeding

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