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Identification of garlic-infecting leek yellow stripe virus through deep-sequencing analyses from Iran.

ABSTRACT: In the study presented here, the first complete genome sequence of Leek yellow stripe virus (LYSV) designated as isolate LYSV-AE65 from Southwest of Iran, was reported. The small RNA deep sequencing analysis showed that, the Iranian isolate has a full RNA genome of 10,142 nucleotide in length (Except for poly (A) tail) and it was shared 77.91-92.16% nucleotide (nt) and 83.62-96.35% amino acid (aa) sequences identities with other known LYSV isolates. The coat protein (CP) region showed 80.21-95.24% nucleotide identity to those of other isolates, while high degrees of nucleotide sequence identity with G77-LYSV isolate (MN059504) from China. Phylogenetic analysis based on full genome sequence of LYSV-AE65, showed the closest relationship with LYSV isolates from China, Australia, Spain and Mexico. Also, phylogenetic analysis of the 5´-untranslated region (UTR)-P1 gene sequences of 44 isolates, confirmed the formation of two main groups, N-type and S-type, in agreement with the previous studies. Isolate LYSV-AE65 was similar to the members of clade S and has two large deletions in P1 gene. Recombination analysis demonstrated that LYSV-AE65 was a recombinant with most part of its genome was derived from already reported LYSV isolates infecting allium species. To the best of our knowledge, this is the first report of complete genome sequencing of LYSV isolate infecting garlic through small RNA deep sequencing method in Iran.

Supplementary information

The online version contains supplementary material available at (10.1007/s13337-021-00733-z).

SUBMITTER: Entezari A

PROVIDER: S-EPMC8473468 | biostudies-literature | 2021 Sep

REPOSITORIES: biostudies-literature

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Identification of garlic-infecting leek yellow stripe virus through deep-sequencing analyses from Iran.

Entezari Azadeh A Mehrvar Mohsen M Zakiaghl Mohammad M

Virusdisease 20210810 3

In the study presented here, the first complete genome sequence of <i>Leek yellow stripe virus</i> (LYSV) designated as isolate LYSV-AE65 from Southwest of Iran, was reported. The small RNA deep sequencing analysis showed that, the Iranian isolate has a full RNA genome of 10,142 nucleotide in length (Except for poly (A) tail) and it was shared 77.91-92.16% nucleotide (nt) and 83.62-96.35% amino acid (aa) sequences identities with other known LYSV isolates. The coat protein (CP) region showed 80. ...[more]

PMID: 34631984

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Project description:Host adaptation plays a crucial role in virus evolution and is a consequence of long-term interactions between virus and host in a complex arms race between host RNA silencing and viral RNA silencing suppressor (RSS) as counterdefense. Leek yellow stripe virus (LYSV), a potyvirus causing yield loss of garlic, infects several species of Allium plants. The unexpected discovery of an interspecific hybrid of garlic, leek, and great-headed (GH) garlic motivated us to explore the host-adaptive evolution of LYSV. Here, using Bayesian phylogenetic comparative methods and a functional assay of viral RSS activity, we show that the evolutionary context of LYSV has been shaped by the host adaptation of the virus during its coevolution with Allium plants. Our phylogenetic analysis revealed that LYSV isolates from leek and their taxonomic relatives (Allium ampeloprasum complex; AAC) formed a distinct monophyletic clade separate from garlic isolates and are likely to be uniquely adapted to AAC. Our comparative studies on viral accumulation indicated that LYSV accumulated at a low level in leek, whereas LYSVs were abundant in other Allium species such as garlic and its relatives. When RSS activity of the viral P1 and HC-Pro of leek LYSV isolate was analyzed, significant synergism in RSS activity between the two proteins was observed in leek but not in other species, suggesting that viral RSS activity may be important for the viral host-specific adaptation. We thus consider that LYSV may have undergone host-specific evolution at least in leek, which must be driven by speciation of its Allium hosts. IMPORTANCE Potyviruses are the most abundant plant RNA viruses and are extremely diversified in terms of their wide host range. Due to frequent host switching during their evolution, host-specific adaptation of potyviruses may have been shaped by numerous host factors. However, any critical determinants for viral host range remain largely unknown, possibly because of the repeated gain and loss of virus infectivity of plants. Leek yellow stripe virus (LYSV) is a species of the genus Potyvirus, which has a relatively narrow host range, generally limited to hosts in the genus Allium. Our investigations on leek and leek relatives (Allium ampeloprasum complex), which must have been generated through interspecies hybridization, revealed that LYSV accumulation remained low in leek as a result of viral host adaptation in competition with host resistance such as RNA silencing. This study presents LYSV as an ideal model to study the process of host-adaptive evolution and virus-host coevolution.

Project description:A new rice viral disease exhibiting distinct symptoms-yellow stripes, mosaic and twisted tips on leaves-was found in China. Electron microscopy of infected leaf cells revealed the presence of bacilliform virions and electron-translucent granular-fibrillar viroplasm in the cytoplasm. The enveloped viral particles were 300 to 375 nm long and 45 to 55 nm wide. The leafhopper Recilia dorsalis was able to transmit the virus to rice seedlings, which subsequently exhibited symptoms similar to those observed in fields. The complete genome of the virus was obtained by small-RNA deep sequencing and reverse transcription-PCR product sequencing. The anti-genome contains seven open reading frames (ORFs). The deduced amino acids of ORF1, ORF5, and ORF7 are, respectively, homologous to the nucleocapsid protein (N), glycoprotein (G), and large polymerase protein (L) of known rhabdoviruses. The predicted product of ORF2 is identified as a phosphoprotein (P) based on its multiple potential phosphorylation sites and 12.6 to 21.0% amino acid (aa) identities with the P proteins of plant rhabdoviruses. The product of ORF4 is presumed to be the viral matrix (M) protein for it shares 10.3 to 14.3% aa identities with those of other rhabdoviruses. The above five products were confirmed as the viral structural proteins by SDS-PAGE and aa sequencing analyses of purified virus preparation. ORF3 and ORF6 are considered to encode two nonstructural proteins with unknown functions. Phylogenetic analysis based on protein N, G, and L amino acid sequences indicated that the isolated virus, which we have tentatively named Rice stripe mosaic virus (RSMV), is a new species in the genus Cytorhabdovirus. To our knowledge, RSMV is the only cytorhabdovirus naturally infecting rice and the first reported leafhopper-transmitted cytorhabdovirus. Our surveys of rice fields indicate that RSMV occurs frequently in Guangdong Province, China. Although the disease incidence is low at present, it might become serious with the vector insect population increasing.

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Identification of garlic-infecting leek yellow stripe virus through deep-sequencing analyses from Iran.

Supplementary information

Publications

Identification of garlic-infecting leek yellow stripe virus through deep-sequencing analyses from Iran.

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