Partial nucleotide sequence analysis of Turkish isolates of <i>Beet necrotic yellow vein virus</i> (BNYVV) RNA‐3

Yilmaz, Nazlı Dide Kutluk; Meunier, Alexandre; Schmit, Jean-François; Stas, A.; Bragard, Claude

doi:10.1111/j.1365-3059.2006.01493.x

Cited by 17 publications

(6 citation statements)

References 25 publications

(40 reference statements)

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“…the A, B and P types, have highly conserved genomes. Nucleotides 199-210 of the P25-coding region, however, show considerable sequence variation, especially in A type BNYVV (Tamada et al, 2003;Meunier et al, 2003;Schirmer et al, 2005;Ward et al, 2007;Kutluk Yilmaz et al, 2007;Li et al, 2008;Koenig et al, 2008). This stretch of nucleotides codes for the P25 aa 67-70, which in the following will be referred to as the 'tetrad'.…”

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confidence: 99%

A single U/C nucleotide substitution changing alanine to valine in the beet necrotic yellow vein virus P25 protein promotes increased virus accumulation in roots of mechanically inoculated, partially resistant sugar beet seedlings

Koenig

Loss

Specht

et al. 2009

Journal of General Virology

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Beet necrotic yellow vein virus (BNYVV) A type isolates E12 and S8, originating from areas where resistance-breaking had or had not been observed, respectively, served as starting material for studying the influence of sequence variations in BNYVV RNA 3 on virus accumulation in partially resistant sugar beet varieties. Sub-isolates containing only RNAs 1 and 2 were obtained by serial local lesion passages; biologically active cDNA clones were prepared for RNAs 3 which differed in their coding sequences for P25 aa 67, 68 and 129. Sugar beet seedlings were mechanically inoculated with RNA 1+2/RNA 3 pseudorecombinants. The origin of RNAs 1+2 had little influence on virus accumulation in rootlets. E12 RNA 3 coding for V 67 C 68 Y 129 P25, however, enabled a much higher virus accumulation than S8 RNA 3 coding for A 67 H 68 H 129 P25. Mutants revealed that this was due only to the V 67 'GUU' codon as opposed to the A 67 'GCU' codon.The Polymyxa betae-transmitted beet necrotic yellow vein virus (BNYVV) is the causal agent of the devastating rhizomania disease. Its genome consists of four, and in some geographical areas five, different RNA species. RNA 1 and 2 contain the genetic information necessary to enable replication, encapsidation, cell-to-cell movement and suppression of RNA silencing in local lesion hosts (Koenig, 2008; Dunoyer et al., 2002). The additional presence of RNA 3, which codes for a 25 kDa protein (P25), is necessary for virus movement in infected sugar beet roots and production of typical rhizomania symptoms. RNA 4 enables efficient vector transmission and suppression of gene silencing in Nicotiana benthamiana roots (Rahim et al., 2007). The severity of symptoms in sugar beet may be enhanced by the additional presence of RNA 5. The three major strain groups of BNYVV, i.e. the A, B and P types, have highly conserved genomes. Nucleotides 199-210 of the P25-coding region, however, show considerable sequence variation, especially in A type BNYVV (Tamada et al., 2003;Meunier et al., 2003;Schirmer et al., 2005;Ward et al., 2007;Kutluk Yilmaz et al., 2007;Li et al., 2008;Koenig et al., 2008). This stretch of nucleotides codes for the P25 aa 67-70, which in the following will be referred to as the 'tetrad'. Also for the sake of brevity we will refer to the variability of the tetrad rather than its coding sequence, although we do not know whether the effects described below are due to changes at the protein or the nucleic acid level. More than 15 variants of the tetrad have been identified so far, raising the question whether these variations influence the pathogenicity of the virus and may be involved in resistance-breaking phenomena. Klein et al. (2007) studied the influence of P25 sequence variation on its oligomerization and pathogenicity for Tetragonia expansa leaves. Chiba et al. (2008) investigated the influence of mutations in the P25 aa 68, 69 and 70 on the local lesion response in mechanically inoculated leaves of lines of Beta maritima and of the sugar beet varieties Rizor and Monomidori. Acosta- ...

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confidence: 99%

A single U/C nucleotide substitution changing alanine to valine in the beet necrotic yellow vein virus P25 protein promotes increased virus accumulation in roots of mechanically inoculated, partially resistant sugar beet seedlings

Koenig

Loss

Specht

et al. 2009

Journal of General Virology

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“…Previous nucleotide analyses of RNA-3 and RNA-5 of Turkish isolates assigned these species as A-type and East Asian J-type 39,43 respectively. RFLP-based analyses of the isolates from the northern and central parts of Turkey designated RNA-2 and RNA-3 as A-type species 42,43 nevertheless, RFLP results of some isolates did not match the expected band profile which was the www.nature.com/scientificreports www.nature.com/scientificreports/ inspiration for the current study to examine the presence of polymorphism among Turkish isolates. RNA-1-5 analyses of BNYVV isolated from different regions of Thrace and Anatolia (modern-day Turkey) revealed a unique polymorphism which could be the probable causes of the failure of RFLP analysis in the previous study 42 .…”

Section: Discussionmentioning

confidence: 99%

“…Since the first record of BNYVV infection in Turkey 40 several research works have diagnosed the disease in sugar beet fields of the country; however, only a few studies have partially characterized the virus 39,41-43 . Partial sequence analyses of RNA-3 isolated from Tokat province in the mid Black Sea region of Anatolia described www.nature.com/scientificreports www.nature.com/scientificreports/ some differences in the amino acid sequence of the Turkish isolates 43 . Previous nucleotide analyses of RNA-3 and RNA-5 of Turkish isolates assigned these species as A-type and East Asian J-type 39,43 respectively.…”

Section: Discussionmentioning

confidence: 99%

“…Partial sequence analyses of RNA-3 isolated from Tokat province in the mid Black Sea region of Anatolia described www.nature.com/scientificreports www.nature.com/scientificreports/ some differences in the amino acid sequence of the Turkish isolates 43 . Previous nucleotide analyses of RNA-3 and RNA-5 of Turkish isolates assigned these species as A-type and East Asian J-type 39,43 respectively. RFLP-based analyses of the isolates from the northern and central parts of Turkey designated RNA-2 and RNA-3 as A-type species 42,43 nevertheless, RFLP results of some isolates did not match the expected band profile which was the www.nature.com/scientificreports www.nature.com/scientificreports/ inspiration for the current study to examine the presence of polymorphism among Turkish isolates.…”

Section: Discussionmentioning

confidence: 99%

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Genome composition analysis of multipartite BNYVV reveals the occurrence of genetic re-assortment in the isolates of Asia Minor and Thrace

Özmen

Khabbazi

et al. 2020

Sci Rep

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Beet necrotic yellow vein virus (BnYVV) is the cause of rhizomania, an important disease of sugar beetaround the world. The multipartite genome of the BNYVV contains four or five single-stranded RNA that has been used to characterize the virus. Understanding genome composition of the virus not only determines the degree of pathogenicity but also is required to development of resistant varieties of sugar beet. Resistance to rhizomania has been conferred to sugar beet varieties by conventional breeding methods or modern genome engineering tools. However, over time, viruses undergo genetic alterations and develop new variants to break crop resistance. Here, we report the occurrence of genetic reassortment and emergence of new variants of BnYVV among the isolates of thrace and Asia Minor (modern-day Turkey). Our findings indicate that the isolates harbor European A-type RNA-2 and RNA-3, nevertheless, RNA-5 is closely related to East Asian J-type. Furthermore, RNA-1 and RNA-4 are either derived from A, B, and P-types or a mixture of them. The RNA-5 factor which enhance the pathogenicity, is rarely found in the isolates studied (20%). The creation of new variants of the virus emphasizes the necessity to develop new generation of resistant crops. We anticipate that these findings will be useful for future genetic characterization and evolutionary studies of BNYVV, as well as for developing sustainable strategies for the control of this destructive disease.Rhizomania is one of the most destructive soil-borne diseases of sugar beet (Beta vulgaris L.) worldwide. Since the first report of rhizomania 1 numerous studies have reported the worldwide infection of sugar beet fields with this disease. Tamada and Baba 2 first identified Beet necrotic yellow vein virus (BNYVV) as the cause of rhizomania when they isolated the virus from infected plants of sugar beet fields in Japan. This disease reduces sugar content by 8%, root yield up to 90%, and sugar yield up to 80% 3,4 . The BNYVV genome is multipartite and composed of four single-stranded RNA species designated as RNA-1, RNA-2, RNA-3, and RNA-4, coating with a 21-kDa protein 5 . In addition, a fifth RNA species (RNA-5) has been identified in some of the European and Asian BNYVV isolates 6-12 . RNA-1 and RNA-2, which contain 6746 and 4612 nt-long RNA species, respectively, encode viral "housekeeping" genes involved in virus replication, assembly, cell-to-cell movement and suppression of post transcriptional gene silencing 13,14 . Therefore, when the virus vector Polymyxa betae Keskin 15 is not present, RNA-1 and RNA-2 are required for the maintenance of BNYVV in the environment 8,14,16 . RNA-3 consisting of a 1775 nt-long RNA species, is involved in viral pathogenicity 7,10,11,17,18 . RNA-4 (1431 nt) plays a key role in transmission of the virus by P. betae 7,11,13,19 . RNA-5 (1342-1347 nt in length) is associated with rhizomania severity, but is not required for virus survival 20,21 . Comparative studies revealed that the RNA-1, RNA-4, and RNA-5 contribute to the development ...

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“…Our BNYVV isolates were not digested by these restriction enzymes, suggesting that the isolate from R. raphanistrum belongs to the A type strain (Figure 3). The A type, the most widespread strain (Schirmer et al, 2005), has been previously detected in Turkey (Kruse et al, 1994;Kutluk Yilmaz et al, 2007); the B type strain is more restricted and mainly found in Germany, France (Kruse et al, 1994;Koenig et al, 2008), Japan (Miyanishi et al, 1999), and China (Li et al, 2008).…”

Section: Detection Of Bnyvvmentioning

confidence: 99%

New natural weed host Raphanus raphanistrum L. (Brassicaceae) for Beet necrotic yellow vein virus and its vector Polymyxa betae Keskin

Yilmaz¹,

Altop²,

Phillippo³

et al. 2016

Turk J Agric For

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IntroductionBeet necrotic yellow vein virus (BNYVV), which is the agent of rhizomania disease, is transmitted by Polymyxa betae Keskin and causes significant losses in sugar beet fields all over the world. The disease is characterized in sugar beet plants by extensive rootlet proliferation from the main taproot and leaf chlorosis. BNYVV is the type species of the genus Benyvirus and it contains four or five ssRNAs (Koenig et al., 1986). Molecular analyses (restriction fragment length polymorphism, singlestrand conformation polymorphism, and sequencing) of BNYVV isolates have revealed the existence of three strain groups (A, B, and P type) in Europe (

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Partial nucleotide sequence analysis of Turkish isolates of Beet necrotic yellow vein virus (BNYVV) RNA‐3

Cited by 17 publications

References 25 publications

A single U/C nucleotide substitution changing alanine to valine in the beet necrotic yellow vein virus P25 protein promotes increased virus accumulation in roots of mechanically inoculated, partially resistant sugar beet seedlings

A single U/C nucleotide substitution changing alanine to valine in the beet necrotic yellow vein virus P25 protein promotes increased virus accumulation in roots of mechanically inoculated, partially resistant sugar beet seedlings

Genome composition analysis of multipartite BNYVV reveals the occurrence of genetic re-assortment in the isolates of Asia Minor and Thrace

New natural weed host Raphanus raphanistrum L. (Brassicaceae) for Beet necrotic yellow vein virus and its vector Polymyxa betae Keskin

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