ABSTRACT
Next-generation sequencing (NGS) allowed the assembly of the complete RNA-1 and RNA-2 sequences of a grapevine isolate of artichoke Italian latent virus (AILV). RNA-1 and RNA-2 are 7,338 and 4,630 nucleotides in length excluding the 3' terminal poly(A) tail, and encode two putative polyproteins of 255.8 kDa (p1) and 149.6 kDa (p2), respectively. All conserved motifs and predicted cleavage sites, typical for nepovirus polyproteins, were found in p1 and p2. AILV p1 and p2 share high amino acid identity with their homologues in beet ringspot virus (p1, 81% and p2, 71%), tomato black ring virus (p1, 79% and p2, 63%), grapevine Anatolian ringspot virus (p1, 65% and p2, 63%), and grapevine chrome mosaic virus (p1, 60% and p2, 54%), and to a lesser extent with other grapevine nepoviruses of subgroup A and C. Phylogenetic and sequence analyses, all confirmed the strict relationship of AILV with members classified in subgroup B of genus Nepovirus.
Subject(s)
Nepovirus/genetics , Amino Acid Sequence , Cynara scolymus/virology , High-Throughput Nucleotide Sequencing , Italy , Nepovirus/classification , Nepovirus/isolation & purification , Phylogeny , Plant Diseases/virology , Polyproteins/genetics , Sequence Analysis, DNAABSTRACT
Complete genomic sequences of Artichoke latent virus (ArLV) have been obtained by classical or high-throughput sequencing for an ArLV isolate from Italy (ITBr05) and for two isolates from France (FR37 and FR50). The genome is 8,278 to 8,291 nucleotides long and has a genomic organization comparable with that of Chinese yam necrotic mosaic virus (CYNMV), the only macluravirus fully sequenced to date. The cleavage sites of the viral polyprotein have been tentatively identified by comparison with CYNMV, confirming that macluraviruses are characterized by the absence of a P1 protein, a shorter and N-terminally truncated coat protein (CP). Sequence comparisons firmly place ArLV within the genus Macluravirus, and confirm previous results suggesting that Ranunculus latent virus (RALV), a previously described Macluravirus sp., is very closely related to ArLV. Serological relationships and comparisons of the CP gene and of the partial RaLV sequence available all indicate that RaLV should not be considered as a distinct species but as a strain of ArLV. The results obtained also suggest that the spectrum of currently used ArLV-specific molecular hybridization or polymerase chain reaction detection assays should be improved to cover all isolates and strains in the ArLV species.
Subject(s)
Cynara scolymus/virology , Genome, Viral/genetics , Plant Diseases/virology , Potyviridae/genetics , Base Sequence , France , High-Throughput Nucleotide Sequencing , Italy , Molecular Sequence Data , Phylogeny , Potyviridae/classification , Potyviridae/isolation & purification , Potyviridae/ultrastructure , RNA, Viral/chemistry , RNA, Viral/genetics , Sequence Analysis, RNA , Viral Proteins/geneticsABSTRACT
Most of the 25 viruses found in globe artichoke (Cynara scolymus L.) and cardoon (Cynara cardunculus L.) were recorded from Europe and the Mediterranean basin, where they decrease both the productivity and the quality of the crop. Although, sometimes, these viruses are agents of diseases of different severity, most often their infections are symptomless. These conditions have contributed to spread virus-infected material since farmers multiply traditional artichoke types vegetatively with no effective selection of virus-free plants. This review reports the main properties of these viruses and the techniques used for their detection and identification. ELISA kits are commercially available for most of the viruses addressed in this review but have seldom been used for their detection in artichoke. Conversely, nucleic acid-based diagnostic reagents, some of which are commercially available, have successfully been employed to identify some viruses in artichoke sap. Control measures mainly use virus-free stocks for new plantations. A combined procedure of meristem-tip culture and thermotherapy proved useful for producing virus-free regenerants of the reflowering southern Italian cultivar Brindisino, which kept earliness and typical heads shape.
Subject(s)
Cynara scolymus/virology , Plant Diseases/virology , Plant Viruses/pathogenicity , Mediterranean Region , Plant Viruses/isolation & purificationABSTRACT
An elongated virus was isolated from artichoke crops in Liguria, and a 700-bp fragment was amplified by RT-PCR using oligonucleotides to detect members of the family Potyviridae. Comparison of fragment sequences showed 98% identity at the nucleotide level with the ranunculus isolate of the macluravirus Ranunculus latent virus (RaLV). RaLV was then detected by DAS-ELISA in symptomatic and asymptomatic artichoke plants from Liguria, Sardinia and Latium. The sequence of a 5.5-kb region was assembled from a cDNA library, and a 500-bp NIa fragment showed 80% identity to Artichoke latent virus.
Subject(s)
Cynara scolymus/virology , Potyviridae/classification , Potyviridae/genetics , Ranunculus/virology , Base Sequence , DNA, Complementary , Molecular Sequence Data , Potyviridae/isolation & purification , RNA, Viral/genetics , Reverse Transcriptase Polymerase Chain ReactionABSTRACT
Afilamentous virus was isolated in Japan from virus-infected Chinese artichoke showing mosaic symptoms. This virus was assigned to the genus Potyvirus, based on particle morphology and serological properties. The virus could be transmitted to several test plants but not to Perilla frutesence, the host plant of Perilla mottle virus. cDNA corresponding to the 3'-terminal 1675 nucleotides of the viral RNA, excluding the poly (A) tail, was cloned and sequenced. The amino acid sequence of the coat protein was different from those of 74 distinct potyviruses. Therefore, we propose that the new potyvirus should be designated as Chinese artichoke mosaic virus (ChAMV).
