Investigation of ORF0 as a sensitive alternative diagnostic segment to detect Sugarcane yellow leaf virus

ElSayed, Abdelaleim Ismail; Komor, Ewald

doi:10.1007/s10327-012-0370-1

Cited by 9 publications

(1 citation statement)

References 26 publications

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“…In addition, it was shown that ORF3‐4 could be multiplied by PCR in sufficient quantities for sequencing purposes in several cultivars from Hawaii and Cuba, in contrast to some other ORFs (ElSayed, unpubl.). But, the ORF0‐1 gene may be a better diagnostic tool because of its high sensitivity, in case that the sequence is exactly known and the infection levels were to be followed over time or on a cellular scale (ElSayed and Komor ).…”

Section: Discussionmentioning

confidence: 99%

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

ElSayed

Komor

2013

Journal of Phytopathology

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The transcript levels of four genome parts of the Sugarcane yellow leaf virus representing the different open reading frames were determined in sink leaves, source leaves and mature internodes of two SCYLV‐susceptible and one SCYLV‐resistant Hawaiian sugarcane cultivar. Amplification products were resolved by capillary gel electrophoresis and detected by fluorescence spectrophotometry. Sink leaves had higher transcript levels of ORF0‐1, which codes for a suppressor protein, than source leaves and internodes. The transcript levels for ORF3‐4, which code for capsid protein and movement protein, were significantly lower in source leaves in two of the three cultivars than in sink leaves and internodes. The differences between the cultivars could not be related to SCYLV resistance, however. We propose the transcription of the viral open reading frames, especially of the gene for the suppressor protein, is modulated in the plant.

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Section: Discussionmentioning

confidence: 99%

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

ElSayed

Komor

2013

Journal of Phytopathology

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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 from China reveals a novel recombinant genotype

Lin

Gao

Damaj³

et al. 2014

Arch Virol

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Sugarcane yellow leaf virus (SCYLV; genus Polerovirus, family Luteoviridae) is a recombinant virus associated with yellow leaf disease, a serious threat to sugarcane in China and worldwide. Among the nine known SCYLV genotypes existing worldwide, COL, HAW, REU, IND, CHN1, CHN2, BRA, CUB and PER, the last five have been reported in China. In this study, the complete genome sequences (5,880 nt) of GZ-GZ18 and HN-CP502 isolates from the Chinese provinces of Guizhou and Hainan, respectively, were cloned, sequenced and characterized. Phylogenetic analysis showed that, among 29 SCYLV isolates described worldwide, the two Chinese isolates clustered together into an independent clade based on the near-complete genome nucleotide (ORF0-ORF5) or amino acid sequences of individual genes, except for the MP protein (ORF4). We propose that the two isolates represent a novel genotype, CHN3, diverging from other genotypes by 1.7-13.6 % nucleotide differences in ORF0-ORF5, and 2.7-28.1 %, 1.8-20.4 %, 0.5-5.1 % and 2.7-15.9 % amino acid differences in P0 (ORF0), RdRp (RNA-dependent RNA polymerase) (ORF1+2), CP (coat protein) (ORF3) and RT (readthrough protein) (ORF3+5), respectively. CHN3 was closely related to the BRA, HAW and PER genotypes, differing by 1.7-3.8 % in the near-complete genome nucleotide sequence. Recombination analysis further identified CHN3 as a new recombinant strain, arising from the major parent CHN-HN1 and the minor parent CHN-GD-WY19. Recombination breakpoints were distributed mostly within the RdRp region in CHN3 and the four significant recombinant genotypes, IND, REU, CUB and BRA. Recombination is considered to contribute significantly to the evolution and emergence of such new SCYLV variants.

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Investigation of ORF0 as a sensitive alternative diagnostic segment to detect Sugarcane yellow leaf virus

Cited by 9 publications

References 26 publications

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

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

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 from China reveals a novel recombinant genotype

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