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

2013 ◽  
Vol 161 (11-12) ◽  
pp. 774-783 ◽  
Author(s):  
Abdelaleim Ismail ElSayed ◽  
Ewald Komor
Keyword(s):  
Transcript Level ◽  
Suppressor Gene ◽  
Virus Genome ◽  
Open Reading Frames ◽  
Yellow Leaf ◽  
Rt Pcr ◽  
Sugarcane Yellow Leaf Virus ◽  
High Transcript Level ◽  
Leaf Virus ◽  
Reading Frames

Diagnosis of Sugarcane yellow leaf virus in asymptomatic sugarcane by RT-PCR

Sugar Tech ◽  
2009 ◽  
Vol 11 (4) ◽  
pp. 368-372 ◽  
Author(s):  
R. Viswanathan ◽  
R. Karuppaiah ◽  
P. Malathi ◽  
V. Ganesh Kumar ◽  
C. Chinnaraja
Keyword(s):  
Yellow Leaf ◽  
Rt Pcr ◽  
Sugarcane Yellow Leaf Virus ◽  
Leaf Virus

scholarly journals Presencia del sugarcane yellow leaf virus (SCYLV) en caña de azúcar (Saccharum spp.) aislado de Colima

2018 ◽  
Vol 9 (8) ◽  
pp. 1751-1762
Author(s):  
Maria Ines Barbosa Villa ◽  
José Luis Cruz Jaramillo ◽  
Hilda Victoria Silva Rojas ◽  
Karina De la Paz García Mariscal ◽  
José Concepción García Preciado ◽  
...  
Keyword(s):  
Yellow Leaf ◽  
Rt Pcr ◽  
Sugarcane Yellow Leaf Virus ◽  
Saccharum Spp ◽  
Para Determinar ◽  
Leaf Virus

  La caña de azúcar es uno de los cultivos industriales importantes a nivel mundial y es afectado por diversas enfermedades virales, incluido el sugarcane yellow leaf virus (SCYLV). En México este virus se ha detectado basado en sintomatología y °Brix; sin embargo, el diagnóstico basado en estos parámetros no es concluyente. El objetivo del estudio fue detectar la presencia y distribución del SCYLV en zonas cañeras del Occidente de México (Colima, Jalisco y Nayarit) y determinar el origen filogenético de un aislado de Colima. El trabajo se desarrolló en el Campo Experimental Tecomán durante 2013-2014. Se aisló el RNA total a partir de hojas colectadas y se realizaron las RT-PCR con oligonucleótidos específicos para SCYLV. Se analizaron 233 muestras y la incidencia de plantas portadoras del SCYLV fue 14.6%, afectando a los híbridos CP 72-2086, Mex 69-290 y Atemex 96-40. El análisis BLAST mostró que la secuencia parcial CP de Colmex-317 (512 pb) es homóloga con secuencias de Brasil, China, India, Kenia y USA, además comparte porcentajes de identidad superior a 99% con otras secuencias provenientes de varios países. El análisis filogenético de Colmex-317 con secuencias parciales y genomas completos del SCYLV aislados de diversas partes del mundo reveló que el aislado mexicano pertenece al genotipo de Brasil (BRA) y se agrupó con secuencias de Brasil, China, Kenia y Sudáfrica. Sin embargo, es necesario evaluar un mayor número de aislados y secuencias de mayor longitud para determinar si el genotipo BRA es el único presente en México.

scholarly journals Detection of Sugarcane yellow leaf virus in Quarantine and Production of Virus-free Sugarcane by Apical Meristem Culture

Plant Disease ◽  
2001 ◽  
Vol 85 (11) ◽  
pp. 1177-1180 ◽  
Author(s):  
M. Chatenet ◽  
C. Delage ◽  
M. Ripolles ◽  
M. Irey ◽  
B. E. L. Lockhart ◽  
...  
Keyword(s):  
Apical Meristem ◽  
False Negative ◽  
Hot Water ◽  
Meristem Culture ◽  
Vascular Bundles ◽  
Yellow Leaf ◽  
Rt Pcr ◽  
Sugarcane Yellow Leaf Virus ◽  
Leaf Virus

Sugarcane yellow leaf virus (SCYLV) was detected for the first time in 1996 in the Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD) sugarcane quarantine at Montpellier by reverse transcription-polymerase chain reaction (RT-PCR) in varieties from Brazil, Florida, Mauritius, and Réunion. Between 1997 and 2000, the virus was found by RT-PCR and/or tissue-blot immunoassay (TBIA) in additional varieties from Barbados, Cuba, Guadeloupe, Indonesia, Malaysia, Philippines, Puerto Rico, and Taiwan, suggesting a worldwide distribution of the pathogen. An excellent correlation was observed between results obtained for the two diagnostic techniques. However, even though only a few false negative results were obtained by either technique, both are now used to detect SCYLV in CIRAD's sugarcane quarantine in Montpellier. The pathogen was detected by TBIA or RT-PCR in all leaves of sugarcane foliage, but the highest percentage of infected vascular bundles was found in the top leaves. The long hot water treatment (soaking of cuttings in water at 25°C for 2 days and then at 50°C for 3 h) was ineffective in eliminating SCYLV from infected plants. Sugarcane varieties from various origins were grown in vitro by apical bud culture and apical meristem culture, and the latter proved to be the most effective method for producing SCYLV-free plants.

Prevalence of Sugarcane yellow leaf virus in Sugarcane-Producing Regions in Kenya Revealed by Reverse-Transcription Loop-Mediated Isothermal Amplification Method

Plant Disease ◽  
2016 ◽  
Vol 100 (2) ◽  
pp. 260-268 ◽  
Author(s):  
Ruth L. Amata ◽  
Emmanuel Fernandez ◽  
Denis Filloux ◽  
Darren P. Martin ◽  
Philippe Rott ◽  
...  
Keyword(s):  
Reverse Transcription ◽  
Lamp Assay ◽  
Isothermal Amplification ◽  
Yellow Leaf ◽  
Rt Pcr ◽  
Pairwise Identity ◽  
Sugarcane Yellow Leaf Virus ◽  
Actual Distribution ◽  
Loop Mediated Isothermal Amplification ◽  
Leaf Virus

Yellow leaf (YL) is a disease of sugarcane that is currently widespread throughout most American and Asian sugarcane-producing countries. However, its actual distribution in Africa remains largely unknown. A reverse-transcription loop-mediated isothermal amplification (RT-LAMP) assay was developed to facilitate and improve the detection of Sugarcane yellow leaf virus (SCYLV), the causal agent of YL. The RT-LAMP assay was found to be comparable with or superior to conventional RT-polymerase chain reaction (PCR) for the detection of SCYLV genotypes CUB and BRA in infected sugarcane ‘C132-81’ and ‘SP71-6163’, respectively. Additionally, 68 sugarcane samples that tested negative by RT-PCR were found positive by RT-LAMP, whereas the RT-LAMP assay failed to detect SCYLV in only 5 samples that tested positive by RT-PCR. Combining RT-PCR and RT-LAMP data enabled the detection of SCYLV in 86 of 183 Kenyan sugarcane plants, indicating high SCYLV prevalence throughout the country (ranging from 36 to 64% in individual counties). Seminested PCR assays were developed that enabled the amplification of a fragment encompassing the capsid protein coding region gene and its flanking 5′ and 3′ genomic regions. Sequences of this fragment for four Kenyan SCYLV isolates indicated that they shared 99.2 to 99.6% pairwise identity with one another and clearly clustered phylogenetically with SCYLV-BRA genotype isolates. To our knowledge, this is the first report of SCYLV in Kenya.

scholarly journals Geographical Distribution of Four Sugarcane yellow leaf virus Genotypes

Plant Disease ◽  
2006 ◽  
Vol 90 (9) ◽  
pp. 1156-1160 ◽  
Author(s):  
Youssef Abu Ahmad ◽  
Monique Royer ◽  
Jean-Henrich Daugrois ◽  
Laurent Costet ◽  
Jean-Michel Lett ◽  
...  
Keyword(s):  
Pcr Primers ◽  
Yellow Leaf ◽  
Rt Pcr ◽  
Sugarcane Yellow Leaf Virus ◽  
On This Island ◽  
Virus Genotypes ◽  
Polymerase Chain ◽  
Leaf Virus ◽  
Geographical Locations ◽  
Local Transmission

Specific primer pairs were designed to distinguish four genotypes (BRA for Brazil, CUB for Cuba, PER for Peru, and REU for Réunion Island) of Sugarcane yellow leaf virus (SCYLV) by reverse transcription-polymerase chain reaction (RT-PCR). A unique genome fragment was amplified from each genotype, with the exception of genotypes BRA and PER that are phylogenetically relatively close and were designated genotype BRA-PER. These RT-PCR primers were then used to identify the SCYLV genotype(s) present in 18 different sugarcane growing locations in the world, and 245 leaf samples infected by the virus were analyzed. Most samples were infected by only one of the three genotypes, but mixed infections occurred. Genotype BRA-PER was found in all sugarcane growing locations, whereas genotypes CUB and REU were each found in four geographical locations only. Genotypes BRA-PER, CUB, and REU were all three detected in locally bred sugarcane cultivars in Guadeloupe, indicating local transmission of these genotypes. In contrast, only genotypes BRA-PER and CUB were found in locally bred cultivars in Brazil, whereas genotype REU was detected in this country in cultivar R570 imported from Réunion. Similarly, genotypes BRA-PER and REU are both present in Réunion, but genotype BRA-PER has not, as of yet, spread on this island. Presence of several SCYLV genotypes in Brazil, Colombia, Guadeloupe, Mauritius, and Réunion suggests different virus introductions and/or different evolution histories of the virus after its introduction into a new environment.

scholarly journals Pan-cancer analysis of transcripts encoding novel open-reading frames (nORFs) and their potential biological functions

2021 ◽  
Vol 6 (1) ◽  
Author(s):  
Chaitanya Erady ◽  
Adam Boxall ◽  
Shraddha Puntambekar ◽  
N. Suhas Jagannathan ◽  
Ruchi Chauhan ◽  
...  
Keyword(s):  
Transcript Level ◽  
Open Reading Frames ◽  
The Cancer Genome Atlas ◽  
Small Subset ◽  
Cancer Tissue ◽  
Post Translational Modifications ◽  
Cancer Genome Atlas ◽  
Systematic Identification ◽  
Reading Frames

AbstractUncharacterized and unannotated open-reading frames, which we refer to as novel open reading frames (nORFs), may sometimes encode peptides that remain unexplored for novel therapeutic opportunities. To our knowledge, no systematic identification and characterization of transcripts encoding nORFs or their translation products in cancer, or in any other physiological process has been performed. We use our curated nORFs database (nORFs.org), together with RNA-Seq data from The Cancer Genome Atlas (TCGA) and Genotype-Expression (GTEx) consortiums, to identify transcripts containing nORFs that are expressed frequently in cancer or matched normal tissue across 22 cancer types. We show nORFs are subject to extensive dysregulation at the transcript level in cancer tissue and that a small subset of nORFs are associated with overall patient survival, suggesting that nORFs may have prognostic value. We also show that nORF products can form protein-like structures with post-translational modifications. Finally, we perform in silico screening for inhibitors against nORF-encoded proteins that are disrupted in stomach and esophageal cancer, showing that they can potentially be targeted by inhibitors. We hope this work will guide and motivate future studies that perform in-depth characterization of nORF functions in cancer and other diseases.

scholarly journals Characterization of Cestrum yellow leaf curling virus: a new member of the family Caulimoviridae

2003 ◽  
Vol 84 (12) ◽  
pp. 3459-3464 ◽  
Author(s):  
Livia Stavolone ◽  
Antonio Ragozzino ◽  
Thomas Hohn
Keyword(s):  
Genomic Sequence ◽  
Infected Plant ◽  
Virus Genome ◽  
Mosaic Disease ◽  
Open Reading Frames ◽  
Primer Binding Site ◽  
Yellow Leaf ◽  
Leaf Curling ◽  
Chlorotic Mottle Virus ◽  
Chlorotic Mottle

Cestrum yellow leaf curling virus (CmYLCV) has been characterized as the aetiological agent of the Cestrum parqui mosaic disease. The virus genome was cloned and the clone was proven to be infectious to C. parqui. The presence of typical viroplasms in virus-infected plant tissue and the information obtained from the complete genomic sequence confirmed CmYLCV as a member of the Caulimoviridae family. All characteristic domains conserved in plant pararetroviruses were found in CmYLCV. Its genome is 8253 bp long and contains seven open reading frames (ORFs). Phylogenetic analysis of the relationships with other members of the Caulimoviridae revealed that CmYLCV is closely related to the Soybean chlorotic mottle virus (SbCMV)-like genus and particularly to SbCMV. However, in contrast to the other members of this genus, the primer-binding site is located in the intercistronic region following ORF Ib rather than within this ORF, and an ORF corresponding to ORF VII is missing.

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