scholarly journals First Report of Pepper yellow leaf curl Indonesia virus in Ageratum conyzoides in Indonesia

Plant Disease ◽  
2007 ◽  
Vol 91 (9) ◽  
pp. 1198-1198 ◽  
Author(s):  
Y. Shibuya ◽  
J. Sakata ◽  
N. Sukamto ◽  
T. Kon ◽  
P. Sharma ◽  
...  
Keyword(s):  
Nucleotide Sequence ◽  
Nucleotide Sequence Identity ◽  
Restriction Site ◽  
Full Length ◽  
Yellow Vein ◽  
Yellow Leaf ◽  
Ageratum Conyzoides ◽  
Sequence Identity ◽  
Vein Disease ◽  
Sense Primer

Ageratum conyzoides L. plants affected with yellow vein disease were collected from Magelang, Bandung, and Purwokerto locations in Indonesia during 2001. A. conyzoides is a naturally occurring weed that is found in and around fields of cultivated pepper (Capsicum annuum L.) and tomato (Lycopersicon esculentum L.). It is frequently found with symptoms of yellow vein disease and the abundance of whiteflies on the affected plants suggested the possible involvement of a geminivirus. Total nucleic acids were extracted from nine samples collected from these locations of A. conyzoides-affected plants exhibiting yellow vein disease and amplified using PCR with geminivirus DNA-A-specific designed primers (virion-sense primer 5′-GAGCTCTTAGCCGCCTGAATGTTC-3′; complementary-sense primer 5′-GAGCTCGTCAGATGTTAAGACCTAC-3′) (1). A PCR-amplified product of approximately 2.7 kbp was obtained from each sample. Five independent sequences were cloned and sequenced from each sample. Sequence analysis showed that five of nine samples were Ageratum yellow vein virus (one each from Bandung and Purwokerto and three from Magelang) and the remaining four samples (two samples each from Bandung and Purwokerto) were a strain of Pepper yellow leaf curl Indonesia virus (PepYLCIDV). Full-length DNA-A of PepYLCIDV from systemic A. coniziodes was amplified using PCR with additional primers designed at only one restriction site (BamHI) (5′-GGATCCGCTTGTTCATCCTTTTCCAG-3′/5′-GGATCCCACATCTTTGGTTAGTGGAGGGTG-3′) and cloned. Three independent clones obtained were sequenced and analyzed. The sequence of a full-length DNA-A component was determined (2,760 bases, GenBank Accession No. AB267838). PCR using degenerate primers (DNABLC1: 5′-GTVAATGGRGTDCACTTCTG-3′; DNABLC2: 5′-RGTDCACTTCTGYARGATGC-3′, DNABLV2: 5′-GAGTAGTAGTGBAKGTTGCA-3′) of begomovirus DNA-B component (2), five independent clones were obtained and sequenced. Primers designed to amplify a full-length B component were constructed around a unique restriction site (BamHI) (5′-GGATCCCCTCATTCCTTTTGCGGAG-3′/5′-GGATCCACAGAGGAAAACTCGCAAGGC-3′). A PCR product was obtained from A. conyzoides samples and three independent clones were sequenced and analyzed. A full-length sequence of a begomovirus B component was determined (2,746 bases, GenBank Accession No. AB267839). Five open reading frames (ORF) were found in DNA-A and two in DNA-B. The DNA-A and DNA-B had a common region (CR) (74% nucleotide sequence identity) that comprised approximately 160 nucleotides. The DNA-A and DNA-B had an identical 31-base stem loop region in the CR. In addition, DNA-A and DNA-B had the highest nucleotide sequence identity (93%) with those of PepYLCIDV (GenBank Accession Nos. AB267834 and AB267835), suggesting it is a strain of PepYLCIDV, which is widely prevalent in Indonesia. To our knowledge, this is the first report of PepYLCIDV isolated from A. conyzoides plants affected with yellow vein disease. References: (1) R. W. Briddon and P. G. Markham. Mol. Biotechnol. 1:202, 1994. (2) S. K. Green et al. Plant Dis. 85:1286, 2001.

scholarly journals First Report of Kudzu mosaic virus on Pueraria montana (Kudzu) in China

Plant Disease ◽  
2013 ◽  
Vol 97 (1) ◽  
pp. 148-148 ◽  
Author(s):  
J. Zhang ◽  
Z. J. Wu
Keyword(s):  
Sequence Analysis ◽  
Nucleotide Sequence ◽  
Mosaic Virus ◽  
Nucleotide Sequence Identity ◽  
Southern China ◽  
Full Length ◽  
Yellow Vein ◽  
Mosaic Symptom ◽  
First Report ◽  
Sequence Identity

Kudzu (Pueraria montana), a weed widely distributed in southern China, is common in the Fuzhou region of Fujian Province, where many plants show yellow vein mosaic disease. In September 2008, four leaf samples from different plants exhibiting yellow vein mosaic symptom were collected in suburban district of Fuzhou (25°15′ N, 118°08′ E). Whitefly (Bemisia tabaci) infestation was also observed in this region. Total DNA was extracted from all samples using a CTAB method (4). Universal primers (PA/PB) were used to amplify part of the intergenic region and coat protein gene of DNA-A of begomoviruses (1). An amplicon of approximately 500 bp was obtained from all four samples and then sequenced. Comparison of 500-bp fragments (GenBank Accession Nos. FJ539016-18 and FJ539014) revealed the presence of the same virus (98.8 to 99.4%). A pair of back-to-back primers (Yg3FL-F: 5′-GGATCCTTTGTTGAACGCCTTTCC-3′/Yg3FL-R: 5′-GGATCCCACATGTTTAAAGTAAAGC-3′) were designed to amplify the full-length DNA-A from the Chinese isolate identified as Yg3. Sequence analysis showed that full-length DNA-A of Yg3 isolate comprised 2,729 nucleotides (GenBank Accession No. FJ539014) and shared the highest nucleotide sequence identity (91.9%) with Kudzu mosaic virus (KuMV, GenBank Accession No. DQ641690) from Vietnam. To further test the association of DNA-B fragments with the four samples from southern China, rolling circle amplification (RCA) was performed (3). When RCA products were digested with Sph I, approximately 2.7 kb was obtained from all samples. Yg3 isolate was chosen to be sequenced. Sequence analysis showed that full-length DNA-B of Yg3 isolate comprised 2,677 nucleotides (GenBank Accession No. FJ539015) and shared the highest nucleotide sequence identity (76.8%) with KuMV DNA-B (GenBank Accession No. DQ641691) from Vietnam. Based on the current convention of begomovirus species demarcation of <89% sequence identity cut-off criterion (2), Yg3 was identified as an isolate of KuMV. To our knowledge, this is the first report of association of KuMV with yellow vein mosaic symptom of kudzu in China. References: (1). D. Deng et al. Annals Appl. Biol. 125:327, 1994. (2). C. M. Fauquet et al. Arch. Virol. 148:405, 2003. (3). D. Haible et al. J. Virol. Methods 135:9, 2006. (4). Y. Xie et al. Chinese Sci. Bull. 47:197, 2002.

scholarly journals First Report of Ageratum yellow vein virus Causing Tobacco Leaf Curl Disease in Fujian Province, China

Plant Disease ◽  
2008 ◽  
Vol 92 (1) ◽  
pp. 177-177 ◽  
Author(s):  
Z. Liu ◽  
C. X. Yang ◽  
S. P. Jia ◽  
P. C. Zhang ◽  
L. Y. Xie ◽  
...  
Keyword(s):  
Nucleotide Sequence ◽  
Nucleotide Sequence Identity ◽  
Yellow Vein ◽  
Tobacco Plants ◽  
Tobacco Leaf ◽  
Leaf Curling ◽  
Sequence Identity ◽  
Ageratum Yellow Vein Virus ◽  
Leaf Curl Disease ◽  
Leaf Curl

A leaf curling disease was observed on 7% of tobacco plants during December 2005 in research plots in the Cangshan District of Fuzhou, Fujian, China. Tobacco plants were infested with Bemisia tabaci, suggesting begomovirus etiology. To identify possible begomoviruses, total DNA was extracted from four symptomatic leaf samples (F1, F2, F3, and F4). The degenerate primers PA and PB were used to amplify part of the intergenic region and AV2 gene of DNA-A-like molecules (3). A 500-bp DNA fragment was amplified by PCR from all four samples. The PCR products were cloned and sequenced (GenBank Accession Nos. EF531601–EF531603 and EF527823). Alignment of the 500-bp sequences for the four isolates indicated that they shared 98.5 to 99.6% nt identity, suggesting that the plants were all infected by the same virus. Overlapping primers TV-Full-F (5′-GGATCCTCTTTTGAACGAGTTTCC-3′) and TV-Full-R (5′-GGATCCCACATGTTTAAAATAATAC-3′) were then designed to amplify the full-length DNA-A from sample F2. The sequence was 2,754 nucleotides long (GenBank Accession No. EF527823). A comparison with other begomoviruses indicated the F2 DNA-A had the highest nucleotide sequence identity (95.7%) with Ageratum yellow vein virus (AYVV; GenBank Accession No. X74516) from Singapore. To further test whether DNAβ was associated with the four viral isolates, a universal DNAβ primer pair (beta 01 and beta 02) was used (4). An amplicon of approximately 1.3 kb was obtained from all samples. The DNAβ molecule from F2 was then cloned and sequenced. F2 DNAβ was 1,345 nucleotides long (GenBank Accession No. EF527824), sharing the highest nucleotide sequence identity with the DNAβ of Tomato leaf curl virus (97.2%) from Taiwan (GenBank Accession No. AJ542495) and AYVV (88.8%) from Singapore (GenBank Accession No. AJ252072). The disease agent was transmitted to Nicotiana tabacum, N. glutinosa, Ageratum conyzoides, Oxalis corymbosa, and Phyllanthus urinaria plants by whiteflies (B. tabaci) when field infected virus isolate F2 was used as inoculum. In N. tabacum and N. glutinosa plants, yellow vein symptoms were initially observed in young leaves. However, these symptoms disappeared later during infection and vein swelling and downward leaf curling symptoms in N. tabacum and vein swelling and upward leaf curling in N. glutinosa were observed. In A. conyzoides, O. corymbosa, and P. urinaria plants, typical yellow vein symptoms were observed. The presence of the virus and DNAβ in symptomatic plants was verified by PCR with primer pairs TV-Full-F/TV-Full-R and beta 01/beta 02, respectively. The above sequence and whitefly transmission results confirmed that the tobacco samples were infected by AYVV. In China, Tobacco leaf curl Yunnan virus, Tobacco curly shoot virus, and Tomato yellow leaf curl China virus were reported to be associated with tobacco leaf curl disease (1,3). To our knowledge, this is the first report of AYVV infecting tobacco in China. A. conyzoides is a widely distributed weed in south China and AYVV was reported in A. conyzoides in Hainan Island, China (2). Therefore, this virus may pose a serious threat to tobacco production in south China. References: (1) Z. Li et al. Phytopathology 95:902, 2005. (2) Q. Xiong et al. Phytopathology 97:405, 2007. (3) X. Zhou et al. Arch. Virol. 146:1599, 2001. (4) X. Zhou et al. J. Gen. Virol. 84:237, 2003.

scholarly journals First Report of Tomato yellow leaf curl virus in China

Plant Disease ◽  
2006 ◽  
Vol 90 (10) ◽  
pp. 1359-1359 ◽  
Author(s):  
J. B. Wu ◽  
F. M. Dai ◽  
X. P. Zhou
Keyword(s):  
Nucleotide Sequence ◽  
Nucleotide Sequence Identity ◽  
Mosaic Disease ◽  
Tomato Yellow Leaf ◽  
Yellow Leaf ◽  
Yellow Mosaic Disease ◽  
Tomato Plants ◽  
First Report ◽  
Sequence Identity ◽  
Leaf Curl Virus

Tomato yellow leaf curl virus (TYLCV) is a devastating pathogen of tomato that causes significant yield losses in many tropical and subtropical regions (2). In China, however, there has as yet been no report of this virus, although other begomoviruses have been reported infecting tomato (1,3). A yellow mosaic disease was observed on tomato with 90% disease incidence during March 2006 in fields of Sunqiao, Shanghai Province, China. Triple-antibody sandwich enzyme-linked immunosorbent assay (TAS-ELISA) tests indicated that tomato plants were not infected by Tomato mosaic virus or Cucumber mosaic virus. Tomato plants were found to be infested with Bemisia tabaci, suggesting a begomovirus etiology. The disease agent was transmitted to tomato by whiteflies and produced yellow mosaic and stunting symptoms that were identical to those observed in the field. Total DNA was isolated from eight collected leaf samples. Polymerase chain reaction (PCR) was performed with begomovirus degenerate primers PA and PB (3), and an amplicon of the expected size (~500 bp) was obtained in all eight samples but not from healthy leaf samples. The PCR products from two samples (SH1 and SH2) were cloned and sequenced. All residues in the sequences were confirmed by comparison of duplicate clones. Alignment of the sequences showed that they shared 97.4% nucleotide sequence identity (GenBank Accession No. AM282874–75), suggesting that they were infected by an identical virus. Overlapping primers Full/F (5′-AGCCCAATACATTGGGCC ACGA-3′) and Full/R (5′-CGTAAGTTTCCTCAACGGACTGC-3′) were then designed to amplify the full length DNA-A of SH2. The sequence was determined to be 2,781 nucleotides long (GenBank Accession No. AM282874). A comparison with other begomoviruses shows SH2 DNA-A has the highest nucleotide sequence identity (99.8%) with TYLCV isolate Tosa from Japan (GenBank Accession No. AB192966). The above results indicate that the virus associated with yellow mosaic disease of tomato in Shanghai is an isolate of TYLCV. To our knowledge, this is the first report of TYLCV in China and the first report of a begomovirus in Shanghai. References: (1) X. F. Cui et al. J. Virol. 78:13966, 2004. (2) E. Moriones and J. Navas-Castillo. Virus Res. 71:123, 2000. (3) Z. H. Li et al. Arch. Virol. 149:1721, 2004.

scholarly journals A New Begomovirus Inducing Yellow Mottle in Okra Crops in Mexico is Related to Sida yellow vein virus

Plant Disease ◽  
2006 ◽  
Vol 90 (3) ◽  
pp. 378-378 ◽  
Author(s):  
R. De La Torre-Almaraz ◽  
A. Monsalvo-Reyes ◽  
A. Romero-Rodriguez ◽  
G. R. Argüello-Astorga ◽  
S. Ambriz-Granados
Keyword(s):  
Nucleotide Sequence ◽  
Nucleotide Sequence Identity ◽  
Blot Hybridization ◽  
Pcr Amplification ◽  
Yellow Vein ◽  
Universal Primers ◽  
Degenerate Primers ◽  
Sequence Identity ◽  
Pcr Products ◽  
Yellow Mottle

Okra (Abelmoschus esculentus L. Moench), an annual vegetable of African origin, has been cultivated in Mexico for 3 decades. Since 2000, the most important okra-producing areas in the states of Guerrero and Morelos have been affected by a disease causing yellow streak and severe distortion of fruits, a bright yellow mottle, and curling and distortion of leaves. These symptoms and the presence of whiteflies (Bemisia tabaci Gennadius) suggest a viral etiology. Samples of symptomatic plants from three localities, Iguala (Guerrero), Mazatepec, and Xochitepec (Morelos) were collected in November 2004 and tested for the presence of viruses. Single whitefly transmissions, grafting experiments, and experimental inoculation of healthy plants by biolistic delivery of DNA extracts from symptomatic plants consistently induced yellow mottle in okra plants and suggest the presence of a DNA virus. Total DNA extracts from symptomatic plants from field and greenhouse conditions were analyzed by Southern blot hybridization using the coat protein gene of Pepper yellow vein huasteco virus as a probe at low stringency. More than 20 positive samples were subsequently used as templates for polymerase chain reaction (PCR) amplification with the degenerate primers pRepMot and pCPMot (1). PCR products of approximately 600 bp were obtained and directly sequenced. Eight isolates from the three localities (GenBank Accession Nos. AY624016 to AY624023) shared 97 to 100% nucleotide identity but were significantly different from other known begomoviruses. The complete genome A sequence of one isolate from Mazatepec (Ok-M3) was determined using PCR amplification of viral DNA with the degenerate primers PAL1v1978 and PAL1c1960 (3) and four new universal primers, pRepQGR (5′-TCCCTGWATGTTYGGATGGAAATG-3′), pRepQGR-rev (5′-CATTTCCATCCRAACATWCAGGGA-3′), pCp70-MAC (5′-GTC TAGACCTTRCANGGNCCTTCACA-3′), and pCp70-MAC-rev (5′-GAA GGSCCNTGYAAGGTNCAGTC-3′). Partially overlapping PCR products of 0.9, 1.3, and 1.7 kb were cloned into pGEM-T easy vector (Promega, Madison, WI) and sequenced. The 2612-bp DNA-A sequence of Ok-M3 (GenBank Accession No. DQ022611) was compared with sequences available from GenBank using the Clustal alignment method (MegAlign, DNASTAR software, London). The highest sequence identity was obtained with Sida yellow vein virus (SiYVV; Accession No. Y11099), Sida golden mosaic Honduras virus (SiGMHV; Accession No. Y11097), and Chino del tomate virus (CdTV; Accession No. AF101478) that had 85.4, 85.4, and 84.4% nucleotide sequence identity with the Ok-M3 isolate, respectively. Comparative analysis of the intergenic region of the Ok-M3 isolate and its closest relatives revealed that these viruses display different putative Rep-binding sites (iterons): Ok-M3 (GGTACACA), SiYVV (GGAGTA), and SiGMHV (GGKGTA). Current taxonomic criteria for the classification of begomoviruses establishes that less than 89% DNA-A nucleotide sequence identity with the closest relative of a virus is indicative of a separate species (2). Our results indicate that the okra-infecting virus identified in this study is a new begomovirus species, and the provisional name of Okra yellow mottle Mexico virus is proposed. References: (1) J. T. Ascencio-Ibañez et al. Plant Dis. 86:692, 2002. (2) C. Fauquet et al. Arch. Virol. 148:405, 2003. (3) M. Rojas et al. Plant Dis. 77:340, 1993.

scholarly journals Sequence identity in an early chorion multigene family is the result of localized gene conversion.

Genetics ◽  
1991 ◽  
Vol 128 (3) ◽  
pp. 595-606
Author(s):  
B L Hibner ◽  
W D Burke ◽  
T H Eickbush
Keyword(s):  
Nucleotide Sequence ◽  
Gene Conversion ◽  
Nucleotide Sequence Identity ◽  
Early Period ◽  
Gene Families ◽  
Multigene Families ◽  
Coding Regions ◽  
Sequence Identity ◽  
Isolation And Characterization ◽  
Sequence Exchange

Abstract The multigene families that encode the chorion (eggshell) of the silk moth, Bombyx mori, are closely linked on one chromosome. We report here the isolation and characterization of two segments, totaling 102 kb of genomic DNA, containing the genes expressed during the early period of choriogenesis. Most of these early genes can be divided into two multigene families, ErA and ErB, organized into five divergently transcribed ErA/ErB gene pairs. Nucleotide sequence identity in the major coding regions of the ErA genes was 96%, while nucleotide sequence identity for the ErB major coding regions was only 63%. Selection pressure on the encoded proteins cannot explain this difference in the level of sequence conservation between the ErA and ErB gene families, since when only fourfold redundant codon positions are considered, the divergence within the ErA genes is 8%, while the divergence within the ErB genes (corrected for multiple substitutions at the same site) is 110%. The high sequence identity of the ErA major exons can be explained by sequence exchange events similar to gene conversion localized to the major exon of the ErA genes. These gene conversions are correlated with the presence of clustered copies of the nucleotide sequence GGXGGX, encoding paired glycine residues. This sequence has previously been correlated with gradients of gene conversion that extend throughout the coding and noncoding regions of the High-cysteine (Hc) chorion genes of B. mori. We suggest that the difference in the extent of the conversion tracts in these gene families reflects a tendency for these recombination events to become localized over time to the protein encoding regions of the major exons.

scholarly journals First Report of Cucurbit aphid-borne yellows virus in Spain

Plant Disease ◽  
2004 ◽  
Vol 88 (8) ◽  
pp. 907-907 ◽  
Author(s):  
M. Juarez ◽  
V. Truniger ◽  
M. A. Aranda
Keyword(s):  
Nucleotide Sequence ◽  
Nucleotide Sequence Identity ◽  
Rt Pcr ◽  
Sequence Comparisons ◽  
E Coli ◽  
Sequence Identity ◽  
Tissue Print ◽  
Sigma Chemical ◽  
Beet Pseudo Yellows Virus ◽  
Cucumis Melo L

In late spring 2003, field-grown melon plants (Cucumis melo L.) showing bright yellowing of older leaves were observed near Valladolises in Campo de Cartagena, Murcia, Spain. Symptoms resembled those caused by viruses of the genus Crinivirus (family Closteroviridae), but absence or very low populations of whiteflies were observed. However, diseased foci showed clear indications of heavy aphid infestations. Later, during the fall of 2003, squash plants (Cucurbita pepo L.) grown in open fields in the same area showed similar symptoms. Tissue print hybridizations to detect Cucurbit yellow stunting disorder virus (CYSDV) and Beet pseudo yellows virus (BPYV) in symptomatic samples were negative. CYSDV and BPYV are two yellowing-inducing criniviruses previously described in Spain. In contrast, standard double-antibody sandwich enzyme-linked immunosorbent assays (DAS-ELISA) with antiserum against Cucurbit aphid-borne yellows virus (CABYV; genus Polerovirus, family Luteoviridae) that was kindly provided by H. Lecoq (INRA-Montfavet Cedex, France) were consistently positive. Definitive confirmation of CABYV associated with symptomatic samples was obtained by performing reverse-transcription polymerase chain reaction (RT-PCR) analyses for the CABYV coat protein gene. Total RNA extracts (TRI reagent; Sigma Chemical, St. Louis, MO) were obtained from symptomatic and asymptomatic leaf samples and RT-PCR reactions were carried out using the primers 5′-GAATACGGTCGCGGCTAGAAATC-3′ (CE9) and 5′-CTATTTCGGGTTCTGGACCTGGC-3′ (CE10) based on the CABYV sequence published by Guilley et al. (2). A single DNA product of approximately 600 bp was obtained only from symptomatic samples. Amplified DNA fragments from two independent samples (samples 36-2 and 37-5) were cloned in E. coli and sequenced (GenBank Accession Nos. AY529653 and AY529654). Sequence comparisons showed a 95% nucleotide sequence identity between the two sequences. A 97% and 94% nucleotide sequence identity was found among 36-2 and 37-5, respectively and the CABYV sequence published by Guilley et al. (2). CABYV seems to be widespread throughout the Mediterranean Basin (1,3) but to our knowledge, it has not previously been described in Spain. Additionally, our data suggest that significant genetic variability might be present in the Spanish CABYV populations. References: (1) Y. Abou-Jawdah et al. Crop Prot. 19:217, 2000. (2) H. Guilley et al. Virology 202:1012, 1994. (3) H. Lecoq et al. Plant Pathol. 41:749, 1992.

scholarly journals Human Herpesvirus 6B Genome Sequence: Coding Content and Comparison with Human Herpesvirus 6A

1999 ◽  
Vol 73 (10) ◽  
pp. 8040-8052 ◽  
Author(s):  
Geraldina Dominguez ◽  
Timothy R. Dambaugh ◽  
Felicia R. Stamey ◽  
Stephen Dewhurst ◽  
Naoki Inoue ◽  
...  
Keyword(s):  
Nucleotide Sequence ◽  
Genome Sequence ◽  
Nucleotide Sequence Identity ◽  
Genomic Sequence ◽  
Human Herpesvirus ◽  
Amino Acid Sequences ◽  
Open Reading Frames ◽  
Sequence Identity ◽  
T Cell Lines ◽  
The Right

ABSTRACT Human herpesvirus 6 variants A and B (HHV-6A and HHV-6B) are closely related viruses that can be readily distinguished by comparison of restriction endonuclease profiles and nucleotide sequences. The viruses are similar with respect to genomic and genetic organization, and their genomes cross-hybridize extensively, but they differ in biological and epidemiologic features. Differences include infectivity of T-cell lines, patterns of reactivity with monoclonal antibodies, and disease associations. Here we report the complete genome sequence of HHV-6B strain Z29 [HHV-6B(Z29)], describe its genetic content, and present an analysis of the relationships between HHV-6A and HHV-6B. As sequenced, the HHV-6B(Z29) genome is 162,114 bp long and is composed of a 144,528-bp unique segment (U) bracketed by 8,793-bp direct repeats (DR). The genomic sequence allows prediction of a total of 119 unique open reading frames (ORFs), 9 of which are present only in HHV-6B. Splicing is predicted in 11 genes, resulting in the 119 ORFs composing 97 unique genes. The overall nucleotide sequence identity between HHV-6A and HHV-6B is 90%. The most divergent regions are DR and the right end of U, spanning ORFs U86 to U100. These regions have 85 and 72% nucleotide sequence identity, respectively. The amino acid sequences of 13 of the 17 ORFs at the right end of U differ by more than 10%, with the notable exception of U94, the adeno-associated virus type 2 rep homolog, which differs by only 2.4%. This region also includes putative cis-acting sequences that are likely to be involved in transcriptional regulation of the major immediate-early locus. The catalog of variant-specific genetic differences resulting from our comparison of the genome sequences adds support to previous data indicating that HHV-6A and HHV-6B are distinct herpesvirus species.

scholarly journals Report of Tomato yellow spot virus Infecting Leonurus sibiricus in Paraguay and Within Tomato Fields in Brazil

Plant Disease ◽  
2014 ◽  
Vol 98 (10) ◽  
pp. 1445-1445 ◽  
Author(s):  
N. A. N. Fernandes-Acioli ◽  
L. S. Boiteux ◽  
M. E. N. Fonseca ◽  
L. R. G. Segnana ◽  
E. W. Kitajima
Keyword(s):  
Nucleotide Sequence ◽  
Nucleotide Sequence Identity ◽  
Rolling Circle Amplification ◽  
Yellow Spot ◽  
High Nucleotide Sequence Identity ◽  
Species Discrimination ◽  
Spot Virus ◽  
Sequence Identity ◽  
A Genome ◽  
Leonurus Sibiricus

Leonurus sibiricus L. (Lamiaceae) is a subtropical weed frequently found with golden mosaic symptoms. Leonurus mosaic virus (LeMV) was the first begomovirus reported on L. sibiricus in Brazil (3). Later, a new bipartite species (Tomato yellow spot virus, ToYSV) was reported affecting tomatoes, beans, and also L. sibiricus (1,2). A survey of begomovirus isolates was conducted within tomato fields also displaying high incidence of plants with begomovirus-induced symptoms. Thirty L. sibiricus and 33 tomato samples were collected (2007 to 2012) in nine districts in Paraná State, Brazil. Two L. sibiricus isolates were also obtained within citrus orchards in Major Otaño, Itapúa, Paraguay. Total DNA was extracted from all 65 isolates and PCR assays were conducted with primers for conserved DNA-A (PAL1v1978/PAR1c496) and DNA-B (PBL1v2040/PCRc1) regions (3). Nucleotide sequence identity of the 1,193-bp DNA-A amplicons of our L. sibiricus isolates ranged from 93.4 to 98.2% with LeMV (GenBank Accession No. U925321) and from 92.4 to 94.8% with ToYSV isolates from tomato (DQ336350.1) and bean (FJ538207). None of the 33 tomato samples was found to be infected by ToYSV, with all having high nucleotide sequence identity (92 to 99%) only with Tomato severe rugose virus (GU358449). Complete DNA-A genome sequence was obtained via a rolling circle amplification-based strategy for one Brazilian L. sibiricus isolate (PR-088) and one isolate from Paraguay (PAR-07). The entire DNA-A genome of PR-088 (JQ429791) had 96.8% nucleotide sequence identity with PAR-07 (KC683374) and ranged from 95.6 to 96.3% with ToYSV isolates from bean, tomato, and L. sibiricus (JX513952). The nucleotide sequence identity of the 487-bp DNA-B amplicon ranged from 87 to 92% among PR-088 (KC 683374); PAR-07 (KC740619) and ToYSV isolates from tomato (DQ336351.1) and L. sibiricus (JX513953.1). Leonurus cuttings infected with the ToYSV (PR-088) were caged together with healthy L. sibiricus and tomato ‘Alambra’ seedlings. Hybridization assays with ToYSV-specific probes (2) and sequencing of PCR amplicons indicated that Bemisia tabaci biotype B adults were able to transmit ToYSV to both hosts as reported (1). Our results suggest that L. sibiricus is the main ToYSV reservoir under natural conditions and tomato seems to be an occasional alternative host. In fact, ToYSV has not often detected in tomatoes as observed in a number of extensive surveys (4). So far, the complete LeMV genome is not available for comparison (3). However, our analyses with a DNA-A segment indicated that LeMV and ToYSV isolates might represent strains of single virus at the current threshold of 89% nucleotide sequence identity for Begomovirus species discrimination (4). Thus, a reappraisal of the taxonomic status of ToYSV is necessary to clarify its genetic relationship with LeMV. This is the first report of ToYSV on L. sibiricus in Paraguay. References: (1) J. C. Barbosa et al. Plant Dis. 97:289, 2013. (2) R. F. Calegario et al. Pesq. Agrop. Bras. 42:1335, 2007. (3) J. C. Faria and D. P. Maxwell, Phytopathology 89:262, 1999. (4) F. R. Fernandes et al. Virus Genes 36:251, 2008.

scholarly journals First Report of Blueberry red ringspot virus Infecting Highbush Blueberry in Korea

Plant Disease ◽  
2012 ◽  
Vol 96 (7) ◽  
pp. 1074-1074 ◽  
Author(s):  
I. S. Cho ◽  
B. N. Chung ◽  
J. D. Cho ◽  
G. S. Choi ◽  
H. S. Lim
Keyword(s):  
Electron Microscopy ◽  
Nucleotide Sequence ◽  
Coat Protein ◽  
Reverse Transcriptase ◽  
Nucleotide Sequence Identity ◽  
Ringspot Virus ◽  
Highbush Blueberry ◽  
First Report ◽  
Sequence Identity ◽  
Symptomatic Plant

Blueberry red ringspot virus (BRRSV) of the Soymovirus genus in the family Caulimovididae causes red ringspot diseases in highbush blueberry (Vaccinium corymbosum L.) on leaves, stems, and fruits. The virus has been identified in the United States, Japan, Czech Republic, Slovenia, and Poland (1). In July 2010, highbush blueberry with red ringspots on leaves and circular blotches on ripening fruits was found in one plant of cv. Duke in Pyeongtaek, Korea. The symptoms were similar to red ringspot disease caused by BRRSV (3), although stems did not show any characteristic symptoms. Red ringspots on the upper surface of leaves were the most visible symptom and became more prominent as leaves matured in August through October. Leaves of the symptomatic plant were collected and tested for BRRSV infection by PCR, and were also embedded for electron microscopy. DNA was extracted from leaves using DNeasy Plant Mini Kit (Qiagen, Valencia, CA) according to the manufacturer's instructions. Primer pairs BR1512F/BR2377R (5′-ACAGGACGATTAGAAGATGG-3′/5′-CCTTTAGGGCAATATTTCTG-3′, amplifying a fragment of the coat protein region with an expected size of 865 bp) and BR2961F/BR3726R (5′-ACCGATACATCACAGTTCAC-3′/5′-TGGTTGTGATAAGATGATTCC-3′, amplifying a fragment of the reverse transcriptase region with an expected size of 766 bp) were used to amplify the indicated region of BRRV in PCR. Primers were designed on the basis of the BRRSV isolate from New Jersey (GenBank Accession No. AF404509). DNA fragments of the expected sizes were obtained from the symptomatic plant, while no amplification products were obtained from highbush blueberry without symptoms. The PCR products were cloned into pGEM-T easy vector (Promega, Madison, WI) and sequenced. BLAST analyses of obtained fragments revealed 91 to 98% nucleotide sequence identity with the coat protein gene (GenBank Accession No. JQ706341) and 96 to 98% nucleotide sequence identity with the reverse transcriptase gene (GenBank Accession No. JQ706340) of known BRRV isolates. Electron microscopy of thin sections revealed particles approximately 50 nm diameter within electron-dense inclusion bodies, characteristic of BRRSV (2) To our knowledge, this is the first report of BRRSV infection of highbush blueberry in Korea. Highbush blueberries are usually propagated by cutting, so BRRSV suspicious plants should be tested with PCR before they are propagated. References: (1) E. Kalinowska et al. Virus Genes. DOI 10.1007/s11262-011-0679-4, 2011. (2) K. S. Kim et al. Phytopathology 71:673, 1981. (3) M. Isogai et al. J. Gen. Plant Pathol. 75:140, 2009.

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