Complete genome characterization of Sugarcane yellow leaf virus from India: Evidence for RNA recombination

Chinnaraja, C.; Viswanathan, R.; Karuppaiah, R.; Bagyalakshmi, K.; Malathi, P.; Parameswari, B.

doi:10.1007/s10658-012-0090-6

Cited by 40 publications

(24 citation statements)

References 31 publications

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“…Los resultados del análisis filogenético realizado con el fragmento ColMex-317 y otras secuencias del SCYLV (Cuadro 2) con las que comparte 96.29-100% de identidad se muestran en la Figura 3. Se observa la formación de cinco grupos y se distinguen siete de los diez genotipos reportados para SCYLV: HAW, PER, BRA, REU, COL, CHN1 y CHN2 (Moonan y Mirkov, 2002;Abu Ahmad et al, 2006;ElSayed et al, 2011;Gao et al, 2012;Wang et al, 2012;Chinnaraja et al, 2013;Lin et al, 2015). No se consideraron secuencias de Cuba, India y CHN3.…”

Section: Resultados Y Discusiónunclassified

“…Con respecto al origen filogenético del SCYLV, a la fecha se han determinado 10 grupos genéticos diferentes: BRA (Brasil), CHN1, CHN2, CHN3 (China), COL (Colombia), CUB (Cuba), HAW (Hawái), IND (India), PER (Perú) y REU (reunión) basados en el análisis de la diversidad genética de su genoma utilizando secuencias parciales y genomas completos (Moonan y Mirkov, 2002;Abu Ahmad et al, 2006;ElSayed et al, 2011;Gao et al, 2012;Wang et al, 2012;Chinnaraja et al, 2013;Lin et al, 2015). La diversidad genética de las poblaciones del SCYLV sugieren la existencia de grandes variaciones entre los aislados del virus, las cuales pueden afectar el grado de virulencia, transmisión y gravedad de los síntomas asociados con SCYLV.…”

Section: Introductionunclassified

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

Villa

Jaramillo

Rojas

et al. 2018

Remexca

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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.

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Section: Resultados Y Discusiónunclassified

Section: Introductionunclassified

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

Villa

Jaramillo

Rojas

et al. 2018

Remexca

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“…Several recombinant genomes have been reported from luteovirids e.g. Cucurbit aphid-borne yellows virus [genus: Polerovirus] is a derived recombinant genome of polero-like and enamo-like parental viruses Gibbs and Cooper, 1995); Sugarcane yellow leaf virus [genus: Polerovirus] is derived from polero-, luteo-and enamo-like viruses (Chinnaraja et al, 2013;Smith et al, 2000); Soybean dwarf virus [genus: Luteovirus] is a probable recombinant of luteo-like and polero-like parental viruses (Rathjen et al, 1994;Terauchi et al, 2001) and Bean leaf roll virus [genus: Luteovirus] is the product two independent recombinant events between luteolike and polero-like virus ancestors (Domier et al, 2002). Recently, it has been known that exchange of hereditary material may also have occurred between two different BYDV serotypes (Boulila, 2011).…”

Section: Introductionmentioning

confidence: 99%

Phylogenetic and Genome-Wide Pairwise Distance Analysis of the Genus Luteovirus

Ali¹

2017

PAKJAS

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Luteovirus is a phytopathogenic monopartite virus of global importance. Re-assortment and recombination by exchanging genome segments play vital role in the virus evolution. Differences in the breadth and specificity of host range, serology and divergence of >10 % amino acids in any gene product (ORF) are the basis of Luteovirus species distinction. To confirm taxonomic status, single ORF that may not accommodate / represent occurrence of genetic recombination (may be of polythetic nature), therefore, may not be sufficient. Instead inference from the whole genome is required. We analyzed distribution of a total of 94 available whole genome Luteovirus sequences in a consistent classification based on pairwise sequence comparison. The adjustment of the two outlier sequences, being recognized, is also discussed.

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“…Among these ORFs, ORF0 encodes the P0 protein, which is an RNA-silencing suppressor and plays roles in viral pathogenicity and the expression of disease symptoms after infection (Mangwende et al 2009). So far, at least 10 SCYLV genotypes have been reported based on phylogenetic analysis at full genome or individual gene levels and geographic origins: BRA (from Brazil), PER (from Peru), CUB (from Cuba), REU (from Réunion Island), HAW (from Hawaii), COL (from Colombia), IND (from India), CHN1, CHN2, and CHN3 (from China) (Abu Ahmad et al 2006a, b;ElSayed et al 2011;Moonan and Mirkov 2002;Gao et al 2012;Chinnaraja et al 2013;Wang and Zhou 2010;Wang et al 2012;Lin et al 2014). SCYLV genotypes from different geographical locations may have highly heterogeneous sequences at genome level (Lin et al 2014) and distinguishing virulence characteristics by aphid transmission assays (Abu Ahmad et al 2007).…”

Section: Introductionmentioning

confidence: 99%

Molecular detection, genetic diversity and distribution of Sugarcane yellow leaf virus genotypes in China

Lin

Liu

et al. 2015

Trop. plant pathol.

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A total of 332 sugarcane leaf samples were collected from seven provinces in China during 2010 to 2013. RT-PCR was performed using the YLS111/YLS462 primers to detect the causal pathogen Sugarcane yellow leaf virus (SCYLV) causing yellow leaf disease in sugarcane. The incidence of SCYLV infection ranged from 24 to 38 % depending on geographic areas. A new primer pair (P0-R3/P0-F2) was designed to prime the amplification of a 968-nucleotide (nt) fragment from SCYLV-positive samples. The fragment contained a partial 5′ untranslated region, the complete ORF0 encoding P0, and a partial ORF1. A phylogenetic analysis of 141 P0 fragment sequences (937 nt) worldwide showed that all SCYLV isolates were clustered into eight genotypes. The 107 SCYLV isolates collected in this study were classified into three genotypes (BRA, HAW, and CHN3), of which the BRA genotype (102/107) was the most prevalent and was detected in all evaluated locations. One isolate (1/107) of genotype HAW was found in Hainan province. Four isolates (4/107) of the genotype CHN3 were observed in Guangxi, Guizhou and Hainan provinces. These findings help understand the genotypic diversity and distribution of SCYLV isolates in China.

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Complete genome characterization of Sugarcane yellow leaf virus from India: Evidence for RNA recombination

Cited by 40 publications

References 31 publications

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

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

Phylogenetic and Genome-Wide Pairwise Distance Analysis of the Genus Luteovirus

Molecular detection, genetic diversity and distribution of Sugarcane yellow leaf virus genotypes in China

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