Identification, molecular detection and phylogenetic analysis of four viruses infecting Allium cepa in Ankara Province, Turkey

Santosa, Adyatma Irawan; Ertunç, Filiz

doi:10.1007/s41348-020-00347-5

Cited by 8 publications

(11 citation statements)

References 25 publications

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“…Molecular variation studies on the GarCLV, thus far, have mostly been limited to the construction of phylogenetic trees based on the CP gene sequences which divide the isolates into two or three phylogroups (Parrano et al 2012;Pramesh & Baranwal 2013;Torrico et al 2015;Santosa & Ertunc 2020). Moreover, variations in the TGB genes have never been reported before.…”

Section: Discussionmentioning

confidence: 99%

“…Earlier phylogenetic analyses on the complete nucleotide (nt) sequence of the CP region showed that most GarCLV isolates were divided into two major groups only, which had relatively low diversities between them (Parrano et al 2012;Pramesh & Baranwal 2013;Torrico et al 2015). However, the presence of a third phylogroup that was predicted by Parrano et al (2012) has been proven recently by Santosa and Ertunc (2020). Isolates belong to the third group seem to be much less common in the nature and have higher genetic variability than the isolates in the two other groups, indicating that they were products of a recent evolution of isolates from the two other groups.…”

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confidence: 95%

“…The Garlic common latent virus (GarCLV, Carlavirus) is found globally in garlic (Allium sativum Linnaeus), its main host (Shahraeen et al 2008;Parrano et al 2012). The virus was also reported to infect onions (Allium cepa Linnaeus) and leeks (Allium ampeloprasum Linnaeus) (Shahraeen et al 2008;Santosa & Ertunc 2020).…”

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confidence: 98%

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Phylogenetic and diversity analyses of Garlic common latent virus based on the TGB and CP gene sequence

Santosa¹,

Ertunç²

2021

Plant Prot. Sci.

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Garlic common latent virus (GarCLV, Carlavirus), in co-infection, often worsens the severity of other Allium viruses on the garlic (Allium sativum Linnaeus). The nucleotide (nt) and amino acid (aa) sequences of the TGB and CP genes were analysed to get the first deep insight into the genomic variations and population structure of GarCLV. Global recombinant-free isolates were clustered into three clades in both the nt-based phylogenetic trees of TGB and CP. The clade 3 isolates shared low similarity percentages among themselves, as well as to the clade 1 and 2 isolates. Most major aa changes in the CP were observed on its 5' and 3' ends. Clade 2 obtained the lowest S, η, k, and π values for both the TGB and CP, which indicated low variations among its isolates. Both TGB and CP have undergone a negative selection, with CP being under stronger negative pressure than TGB. Neutrality tests estimated the non-significant negative values to all clades for TGB and CP, except Tajima's D for clade 2 of the TGB. The results of the Ks*, Kst*, Z*, and Snn tests suggested that all three phylogroups were divergent to each other for both TGB and CP. The high Fst on all the clade comparisons for both TGB and CP showed a large gene flow among three clades.

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Section: Discussionmentioning

confidence: 99%

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confidence: 95%

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Phylogenetic and diversity analyses of Garlic common latent virus based on the TGB and CP gene sequence

Santosa¹,

Ertunç²

2021

Plant Prot. Sci.

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“…Among viruses affecting Allium spp. cultivation, leek yellow stripe virus (LYSV, Potyvirus) is of particular interest since it has been identi ed worldwide as an important virus on leek (Allium ampeloprasum L.), garlic (Allium sativum L.), and onion (Allium cepa L.) [1][2][3][4]. The virus genome sequence is ca.…”

Section: Main Textmentioning

confidence: 99%

“…Studies on LYSV genetic variation mainly were limited on construction of phylogenetic trees [4,10,17,19]. Moreover, hosts difference and large genetic variances were observed among its phylogroups [2,8].…”

Section: Main Textmentioning

confidence: 99%

Phylogenetic and diversity analyses revealed that leek yellow stripe virus population consists of two types: S and N

Santosa

Ertunç

2021

Preprint

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Leek yellow stripe virus (LYSV, Potyvirus), a pathogen affecting Allium spp. worldwide, has been suspected to consist of two types: S and N, based on genetic and host species differences. In this study, phylogenetic and evolutionary analyses were performed to P1 and CP regions of genome of global LYSV isolates to clarify the variation among members of S-type and N-type. Constructed phylogenetic trees clearly divided isolates into S-type and N-type, with N-type was further split into L and N groups, according to hosts. Significant nucleotide (nt) and amino acids (aa) sequence variation were observed on full ORF, P1, HC-Pro, P3, VPg coding regions. The dN/dS values of P1 and CP confirmed that both genes are under strong negative selection pressure. Neutrality tests on Eastern Asian isolates argued that ancestor of current LYSV isolates may had evolved with garlic while they were in Asia before spread to other world regions through garlic propagative materials. The genetic differentiation and gene flow analysis showed that there was very frequent gene flow from S-type to L and N groups and these phylogroups differentiated from each other over time. Host differences, substantial nt and aa variation, inconsistent serological test results, and phylogenetic and diversity analyses results highly suggested that LYSV can be separated into two types: S and N.

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Phylogenetic and diversity analyses revealed that leek yellow stripe virus population consists of three types: S, L, and N

et al. 2022

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Leek yellow stripe virus (LYSV, Potyvirus), a pathogen affecting Allium spp. worldwide, has been suspected to consist of two types: S and N, based on genetic and host species differences. In this study, phylogenetic and evolutionary analyses were performed to P1 and CP regions of genome of global LYSV isolates to clarify the variation among members of S-type and N-type. Constructed phylogenetic trees clearly divided isolates into S-type and N-type, with N-type was further split into L and N groups, according to hosts. Signi cant nucleotide (nt) and amino acids (aa) sequence variation were observed on full ORF, P1, HC-Pro, P3, VPg coding regions. The dN/dS values of P1 and CP con rmed that both genes are under strong negative selection pressure. Neutrality tests on Eastern Asian isolates argued that ancestor of current LYSV isolates may had evolved with garlic while they were in Asia before spread to other world regions through garlic propagative materials. The genetic differentiation and gene ow analysis showed that there was very frequent gene ow from S-type to L and N groups and these phylogroups differentiated from each other over time. Host differences, substantial nt and aa variation, inconsistent serological test results, and phylogenetic and diversity analyses results highly suggested that LYSV can be separated into two types: S and N.

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Identification, molecular detection and phylogenetic analysis of four viruses infecting Allium cepa in Ankara Province, Turkey

Cited by 8 publications

References 25 publications

Phylogenetic and diversity analyses of Garlic common latent virus based on the TGB and CP gene sequence

Phylogenetic and diversity analyses of Garlic common latent virus based on the TGB and CP gene sequence

Phylogenetic and diversity analyses revealed that leek yellow stripe virus population consists of two types: S and N

Phylogenetic and diversity analyses revealed that leek yellow stripe virus population consists of three types: S, L, and N

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