Phylogenetic and recombination analysis of sorghum isolates of <i>Sugarcane yellow leaf virus</i>

ElSayed, Abdelaleim Ismail; Boulila, Moncef; Odero, Dennis C.; Komor, Ewald

doi:10.1111/ppa.12708

Cited by 15 publications

(16 citation statements)

References 37 publications

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“…Such an interference of Indian strains as major and minor parents for Pakistan-originated recombinant strain highlight its potential to cross international borders 48 . Similar finding has previously been observed for another RNA virus (Yellow leaf virus) from Pakistan and India 49 . Potnetial reason for such a sharing of genetic material could be spectulative and may be attributed to an increased disease incidence rate and frequent disease outbreaks near borderline of these countries 50,51 .…”

Section: Discussionsupporting

confidence: 90%

A comprehensive global perspective on phylogenomics and evolutionary dynamics of Small ruminant morbillivirus

Shabbir

Rahman

Munir

2020

Sci Rep

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A string of complete genome sequences of Small ruminant morbillivirus (SRMV) have been reported from different parts of the globe including Asia, Africa and the Middle East. Despite individual genome sequence-based analysis, there is a paucity of comparative genomic and evolutionary analysis to provide overarching and comprehensive evolutionary insights. Therefore, we first enriched the existing database of complete genome sequences of SRMVs with Pakistan-originated strains and then explored overall nucleotide diversity, genomic and residue characteristics, and deduced an evolutionary relationship among strains representing a diverse geographical region worldwide. The average number of pairwise nucleotide differences among the whole genomes was found to be 788.690 with a diversity in nucleotide sequences (0.04889 ± S.D. 0.00468) and haplotype variance (0.00001). The RNAdependent-RnA polymerase (L) gene revealed phylogenetic relationship among SRMVs in a pattern similar to those of complete genome and the nucleoprotein (N) gene. Therefore, we propose another useful molecular marker that may be employed for future epidemiological investigations. Based on evolutionary analysis, the mean evolution rate for the complete genome, N, P, M, F, H and L genes of SRMV was estimated to be 9.953 × 10-4 , 1.1 × 10-3 , 1.23 × 10-3 , 2.56 × 10-3 , 2.01 × 10-3 , 1.47 × 10-3 and 9.75 × 10-4 substitutions per site per year, respectively. A recombinant event was observed in a Pakistan-originated strain (KY967608) revealing Indian strains as major (98.1%, KR140086) and minor parents (99.8%, KT860064). Taken together, outcomes of the study augment our knowledge and current understanding towards ongoing phylogenomic and evolutionary dynamics for better comprehensions of SRMVs and effective disease control interventions.

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Section: Discussionsupporting

confidence: 90%

A comprehensive global perspective on phylogenomics and evolutionary dynamics of Small ruminant morbillivirus

Shabbir

Rahman

Munir

2020

Sci Rep

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“…Varios autores han reportado un grupo exclusivo para cepas de Reunión (genotipo REU) (Wang et al, 2012;Chinnaraja et al, 2013;Amata et al, 2016;ElSayed et al, 2018). En este estudio secuencias de Reunión y Mauricio fueron agrupadas en un clúster, en el cual los dos aislamientos REU que resultaron homólogos entre sí compartieron 99.41 y 99.61% de identidad con dos secuencias de Mauricio: AJ491264.1 y AJ491263.1, respectivamente.…”

Section: Resultados Y Discusiónunclassified

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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“…WLYaV had the closest relationship with ScYLV (64.9% for full length nucleotide and 86.2% for deduced amino acid sequences of ORF3). When the full-length genome and ORF3 deduced amino acid sequences of 10 representative ScYLV isolates (Elsayed et al, 2017 ) were compared with WLYaV (Table S4 ), the identities were 63.7~65.3% and 85.7~86.2%, respectively, below the species demarcation thresholds (90%) in the family Luteoviridae (Domier, 2012 ; Simmonds et al, 2017 ).…”

Section: Resultsmentioning

confidence: 99%

“…ScYLV, a member of the genus Polerovirus , family Luteoviridae , causes severe leaf symptoms in sugarcane and exhibits significant genetic diversity with two phylogroups (Elsayed et al, 2017 ). Sequences comparison and phylogenetic analyses of WLYaV with 10 representative isolates of ScYLV (Table S4 , Figure S3 ) indicated that WLYaV and ScYLV are distinct.…”

Section: Discussionmentioning

confidence: 99%

Identification, Characterization and Full-Length Sequence Analysis of a Novel Polerovirus Associated with Wheat Leaf Yellowing Disease

Zhang

Liu

et al. 2017

Front. Microbiol.

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To identify the pathogens responsible for leaf yellowing symptoms on wheat samples collected from Jinan, China, we tested for the presence of three known barley/wheat yellow dwarf viruses (BYDV-GAV, -PAV, WYDV-GPV) (most likely pathogens) using RT-PCR. A sample that tested negative for the three viruses was selected for small RNA sequencing. Twenty-five million sequences were generated, among which 5% were of viral origin. A novel polerovirus was discovered and temporarily named wheat leaf yellowing-associated virus (WLYaV). The full genome of WLYaV corresponds to 5,772 nucleotides (nt), with six AUG-initiated open reading frames, one non-AUG-initiated open reading frame, and three untranslated regions, showing typical features of the family Luteoviridae. Sequence comparison and phylogenetic analyses suggested that WLYaV had the closest relationship with sugarcane yellow leaf virus (ScYLV), but the identities of full genomic nucleotides and deduced amino acid sequence of coat protein (CP) were 64.9 and 86.2%, respectively, below the species demarcation thresholds (90%) in the family Luteoviridae. Furthermore, agroinoculation of Nicotiana benthamiana leaves with a cDNA clone of WLYaV caused yellowing symptoms on the plant. Our study adds a new polerovirus that is associated with wheat leaf yellowing disease, which would help to identify and control pathogens of wheat.

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Phylogenetic and recombination analysis of sorghum isolates of Sugarcane yellow leaf virus

Cited by 15 publications

References 37 publications

A comprehensive global perspective on phylogenomics and evolutionary dynamics of Small ruminant morbillivirus

A comprehensive global perspective on phylogenomics and evolutionary dynamics of Small ruminant morbillivirus

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

Identification, Characterization and Full-Length Sequence Analysis of a Novel Polerovirus Associated with Wheat Leaf Yellowing Disease

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