Cucumis melo endornavirus: Genome organization, host range and co-divergence with the host

Abstract

A high molecular weight dsRNA was isolated from a Cucumis melo L. plant (referred to as 'CL01') of an unknown cultivar and completely sequenced. Sequence analyses showed that dsRNA is associated with an endornavirus for which a name Cucumis melo endornavirus (CmEV) is proposed. The genome of CmEV-CL01 consists of 15,078 nt, contains a single, 4939 codons-long ORF and terminates with a stretch of 10 cytosine residues. Comparisons of the putative CmEV-encoded polyprotein with available references in protein databases revealed a unique genome organization characterized by the presence of the following domains: viral helicase Superfamily 1 (Hel-1), three glucosyltransferases (doublet of putative capsular polysaccharide synthesis proteins and a putative C_28_Glycosyltransferase), and an RNA-dependent RNA polymerase (RdRp). The presence of three glycome-related domains of different origin makes the genome organization of CmEV unique among endornaviruses. Phylogenetic analyses of viral RdRp domains showed that CmEV belongs to a specific lineage within the family Endornaviridae made exclusively of plant-infecting endornaviruses. An RT-PCR based survey demonstrated high incidence of CmEV among melon germplasm accession (>87% of tested samples). Analyses of partial genome sequences of CmEV isolates from 26 different melon genotypes suggest fine-tuned virus adaptation and co-divergence with the host. Finally, results of the present study revealed that CmEV is present in plants belonging to three different genera in the family Cucurbitaceae. Such diverse host range is unreported for known endornaviruses and suggests a long history of CmEV association with cucurbits predating their speciation.

Extracción y purificación de dsRNAs largos de plantas infectadas con virus y hongos; aplicación en la detección e identificación de virus

“…En la literatura existen numerosos ejemplos del uso de dsRNA viral para detectar, identificar y estudiar los virus, los satélites y los DIs que infectan plantas (Aboughanem- Sabanadzovic et al, 2016 by electrophoretic analysis of their dsRNAs (Chu et al, 2004;Herrero et al, 2012;Kousik et al, 1994). Another advantage of this technique is that in some cases, strains of the same virus can be differentiated by the mobility or the number of dsRNA fragments after gel electrophoresis.…”

“…Viral dsRNAs have been used to clone and sequence plant and fungal RNA viruses (Aboughanem- Sabanadzovic et al, 2016;Antoniw et al, 1986;Bar-Joseph et al, 1983;Enebak et al, 1994;Herrero et al, 2009;Khalifa and Pearson, 2014;Kim et al, 2005;Okada et al 2011;Rott and Jelkmann, 2001;Jelkmann et al, 1989;Valverde and Sabanadzovic, 2009;Zhang and Rowhani, 2000). Virus specific primers have been developed for RT-PCR detection of most plant and fungal viruses reported to date.…”

“…Zhang and Rowhani (2000) developed a rapid cDNA cloning method from dsRNA templates to partially characterized grape viruses. Random cDNA clones from CTV nem- Sabanadzovic et al, 2016;Antoniw et al, 1986;Bar-Joseph et al, 1983;Enebak et al, 1994;Herrero et al, 2009;Khalifa y Pearson, 2014;Kim et al, 2005;Okada et al 2011;Rott y Jelkmann, 2001;Jelkmann et al, 1989;Valverde y Sabanadzovic, 2009;Valverde y Sabanadzovic;Zhang y Rowhani, 2000). Se han creado iniciadores según el tipo de virus para detectar mediante RT-PCR la mayoría de los fitovirus y los micovirus reportados a la fecha.…”

“…No existe evidencia de que estos virus causen enfermedades en las plantas. La caracterización molecular de muchos de los virus persistentes en plantas se ha realizado a partir de material genómico o purificando RF dsRNA (Fukuhara, 1999;Pfeiffer, 1998;Okada, et al, 2011;Sabanadzovic y Valverde, 2011;Sabanadzovic et al, 2016;Sabanadzovic et al, 2010;Sabanadzovic et al, 2009). Utilizando una combinación de análisis electroforéticos de dsRNA viral y RT-PCR, Khankhum et al (2015) se demostró que dos endornavirus tenían patrones diferenciales de infección entre los dos centros de domesticación del frijol común (Phaseolus vulgaris).…”

Complete sequence of a double-stranded RNA from the phytopathogenic fungus Erysiphe cichoracearum that might represent a novel endornavirus

“…Endornavirus genomes contain a single long open reading frame (ORF) coding for a large polyprotein precursor, which invariably contains a RNA-dependent RNA polymerase (RdRp) domain at the C-terminus and, in most cases, has a RNA helicase domain at the N-terminus [14]. One or a few other conserved motifs that may differ in their arrangement are found in some, but not all, endornaviruses [14,16]. Unlike most other viruses, endornaviruses are not encapsidated to form virions [15].…”