scholarly journals Three Previously Unidentified Begomoviral Genotypes from Tomato Exhibiting Leaf Curl Disease Symptoms from Central Sudan

Plant Disease ◽  
2001 ◽  
Vol 85 (11) ◽  
pp. 1209-1209
Author(s):  
A. M. Idris ◽  
J. K. Brown
Keyword(s):  
Phylogenetic Analysis ◽  
Nucleotide Sequence ◽  
Nucleotide Sequence Identity ◽  
Degenerate Primers ◽  
Disease Symptoms ◽  
Old World ◽  
Sequence Identity ◽  
Central Sudan ◽  
Leaf Curl Disease ◽  
Leaf Curl

Field tomato plants exhibiting upward curling of leaflets, chlorosis, and stunting symptoms described for tomato leaf curl disease in Sudan (2) were collected in 1996 from Gezira (GZ) and Shambat (SH), Sudan. Disease symptoms were reproduced following experimental transmission of the causal agent(s) by the whitefly Bemisia tabaci from field tomato to virus-free tomato seedlings in a glasshouse at Gezira Research Station, Wad Medani, Sudan. Total nucleic acids were extracted from symptomatic tomato test plants. An ≈1.3-kbp fragment, diagnostic for begomovirus, was obtained from extracts by polymerase chain reaction using degenerate primers that amplify the coat protein gene (CP) and the respective flanking sequences for most begomoviuses (1). A second pair of degenerate primers was used to amplify a 2.3-kbp begomoviral fragment that overlaps both ends of the (CP) amplicon by >200 nt (1). At least 10 amplicons for each were cloned, and their sequences were determined, revealing three unique, tomato-infecting begomoviruses genotypes, two from GZ and one from SH. No B component was detected using degenerate primers that direct the amplification of a diagnostic fragment of the B component (1.4 kbp) for most bipartite begomoviruses. The organization of the three, apparently full-length viral genomes, was typical of other monopartite begomoviruses. A GenBank search revealed that the three viruses were previously undescribed. The GZ and SH tomato isolates are herein provisionally named ToLCV-GZ1 (GenBank Accession No. AY044137), ToLCV-GZ2 (GenBank Accession No. AY044138), and ToLCV-SH (GenBank Accession No. AY044139), respectively. All three tomato-infecting begomoviruses have identical stem-loop structures containing the conserved nonanucleotide motif characteristic of all members of the family Geminiviridae; however, the predicted Rep binding element located in the common region is unique for each virus. Phylogenetic analysis of the three viral sequences placed them in a large clade containing all other Old World begomoviruses. Distance comparisons among these and other well-studied begomoviruses indicated that ToLCV-GZ1 and ToLCV-SH shared an overall 90% nucleotide sequence identity, with ˜83% nucleotide sequence identity to ToLCV-GZ2. ToLCV-GZ1 and ToLCV-SH were 83% identical, with their closest relative, Tomato yellow leaf curl virus (TYLCV), while ToLCV-GZ2 shared 93% identity with TYLCV. The genomes of all three Sudan viruses contained regions of homologous nucleotide sequences, suggesting intermolecular exchange among these viruses. Exclusion of the homologous sequences (>800 nt) from the phylogenetic analysis indicated even lower shared nucleotide identities (<90%, the arbitrary cut-off for distinct species), which may warrant their classification as separate species. These three newly described begomoviruses are indigenous to central Sudan, and comprise a unique Old World lineage distinct from previously described begomoviruses associated with leaf curl disease of tomato in Africa and the Mediterranean Region. References: (1) A. M. Idris and J. K. Brown. Phytopathology 83:548, 1998. (2) A. M. Yassin. Trop. Pest Manage. 29:253, 1983.

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 MOLECULAR IDENTIFICATION OF Pepper yellow leaf curl Indonesia virus ON CHILI PEPPER IN NUSA PENIDA ISLAND

2021 ◽  
Vol 21 (2) ◽  
pp. 97-102
Author(s):  
Dewa Gede Wiryangga Selangga ◽  
Listihani Listihani
Keyword(s):  
Sequence Analysis ◽  
Molecular Identification ◽  
Disease Incidence ◽  
Analysis Data ◽  
Chili Pepper ◽  
Yellow Leaf ◽  
Degenerate Primers ◽  
Disease Symptoms ◽  
Leaf Curl Disease ◽  
Leaf Curl

Molecular identification of Pepper yellow leaf curl Indonesia virus on chili pepper in Nusa Penida Island. Pepper yellow leaf curl Indonesia virus (PYLCV) has been reported as caused yellow leaf curl disease in Bali Island since early 2012. Dominant symptoms of PYLCV infection in chili pepper were yellowing, leaf curl, yellow mosaic, and mottle. Bemisia tabaci, has been known to vector on the case yellow leaf curl disease. Observations on the Nusa Penida Island in 2020 showed symptoms such as yellow leaf curl disease, however, identification of PYLCV in Nusa Penida Island has not been studied. Molecular identification was conducted using polymerase chain reaction and sequence analysis. Data collected in this study was disease symptoms and disease incidence. The results showed that dominant disease symptoms caused by virus from Nusa Penida were yellow mosaic, yellowing, and mottle. Universal DNA fragments of 912 bp were successfully amplified from 50 leaf samples using Begomovirus degenerate primers SPG 1 (5’-CCCCKGTGCGWRAATCCAT-3’) and SPG 2 (5’ATCCVAA YWTYCAGGGAGCT-3’). Sequence analysis showed that the isolate from Nusa Penida was a Pepper yellow leaf curl Indonesia virus with a 98–100% homology with several reference isolates.

scholarly journals First Report of Squash leaf curl Philippines virus Infecting Chayote (Sechium edule) in Taiwan

Plant Disease ◽  
2011 ◽  
Vol 95 (9) ◽  
pp. 1197-1197 ◽  
Author(s):  
W. S. Tsai ◽  
C. J. Hu ◽  
D. P. Shung ◽  
L. M. Lee ◽  
J. T. Wang ◽  
...  
Keyword(s):  
Nucleotide Sequence ◽  
Mosaic Virus ◽  
Nucleotide Sequence Identity ◽  
Zucchini Yellow Mosaic Virus ◽  
Yellow Mosaic Virus ◽  
First Report ◽  
Sequence Identity ◽  
Sechium Edule ◽  
Complementary Sense ◽  
Leaf Curl

Young shoots and leaves of chayote (Sechium edule (Jacq.) Sw.) are commonly consumed as a vegetable in Taiwan. In Hualien County, the major chayote-production area of Taiwan, as much as 15% of chayote plants were not marketable between September and October 2010 because of mosaic symptoms on the leaves. Three symptomatic leaves were collected from each of three fields in Hualien. All nine samples tested positive for a begomovirus by PCR using general primer pair PAL1v1978B/PAR1c715H (3) and negative for Zucchini yellow mosaic virus, Cucumber mosaic virus, Cucumber green mottle mosaic virus, Melon yellow spot virus, Papaya ringspot virus - type W, Watermelon mosaic virus, and Watermelon silver mottle virus by ELISA (2). On the basis of the high nucleotide sequence identity (97.7 to 99.6%) of the 1.5-kb begomoviral DNA-A fragments, all nine samples were considered infected by the same begomovirus species. The 1.5-kb sequences had greatest nucleotide sequence identity (96.6 to 97.8%) with Squash leaf curl Philippines virus (SLCPHV) pumpkin isolate from Taiwan (1) (GenBank Accession No. DQ866135; SLCPHV-TW[TW:Pum:05]). One sample was selected to complete viral genomic DNA analysis. Abutting primer pairs PKA-V/C (PKA-V: 5′-AACGGATCCACTTATGCACGATTTCCCT-3′; PKA-C: 5′-TAAGGATCCCACATGTTGTGGAGCA-3′) and PKB-V/C (PKB-V: 5′-TGTCCATGGATTGATGCGTTATCGGA-3′; PKB-C: 5′-TGACCATGGCATTTCCGAGATCTCCCA-3′') were used to amplify the complete DNA-A and DNA-B, respectively. The sequences of DNA-A (GenBank Accession No. JF146795) and DNA-B (GenBank Accession No. JF146796) contain 2,734 and 2,715 nucleotides, respectively. The geminivirus conserved sequence TAATATTAC was found in both DNA-A and -B. The DNA-A has two open reading frames (ORFs) in the virus sense (V1 and V2) and four in the complementary sense (C1 to C4). The DNA-B also had one ORF each in the virus sense (BV1) and the complementary sense (BC1). When compared by BLASTn in GenBank and analyzed by MEGALIGN software (DNASTAR, Madison, WI), they were found to have greatest nucleotide identity (98.0 to 99.0% of DNA-A and 96.7% of DNA-B) with SLCPHV isolates from Taiwan. In addition, SLCPHV caused similar symptoms on leaves when transmitted to healthy chayote by viruliferous whitefly. In Taiwan, SLCPHV has been detected and sequenced from naturally infected melon (GenBank Accession No. EU479710), pumpkin (GenBank Accession No. DQ866135), and wax gourd (GenBank Accession No. EU310406). To our knowledge, this is the first report of SLCPHV infecting chayote plants in Taiwan. The prevalence of SLCPHV infection on different cucurbit crops should be taken into consideration for managing viral diseases in Taiwan. References: (1) W. S. Tsai et al. Plant Dis. 91:907, 2007. (2) W. S. Tsai et al. Plant Dis. 94:923, 2010. (3) W. S. Tsai et al. Online publication. doi: 10.1111/j.1365-3059.2011.02424.x. Plant Pathol., 2011.

scholarly journals High-Quality Draft Genome Sequence of Bacillus subtilis Strain WAUSV36

2016 ◽  
Vol 4 (3) ◽  
Author(s):  
Jennifer Town ◽  
Patrice Audy ◽  
Susan M. Boyetchko ◽  
Tim J. Dumonceaux
Keyword(s):  
Bacillus Subtilis ◽  
Nucleotide Sequence ◽  
Nucleotide Sequence Identity ◽  
Draft Genome ◽  
High Nucleotide Sequence Identity ◽  
Subtilis Strain ◽  
High Quality ◽  
Disease Symptoms ◽  
Sequence Identity ◽  
Very High

Bacillus subtilis strain WAUSV36 inhibits the growth of and decreases disease symptoms caused by the potato pathogen Phytophthora infestans . We determined the sequence of the 4.7-Mbp genome of this strain. WAUSV36 shared very high nucleotide sequence identity with previously sequenced strains of B. subtilis .

scholarly journals Identification of a New, Monopartite Begomovirus Associated with Leaf Curl Disease of Cotton in Gezira, Sudan

Plant Disease ◽  
2000 ◽  
Vol 84 (7) ◽  
pp. 809-809 ◽  
Author(s):  
A. M. Idris ◽  
J. K. Brown
Keyword(s):  
Cotton Leaf ◽  
Degenerate Primers ◽  
Monopartite Begomovirus ◽  
Sequence Identity ◽  
Eastern Hemisphere ◽  
Cotton Leaf Curl Virus ◽  
Leaf Curl Virus ◽  
Leaf Curl Disease ◽  
Begomoviral Species ◽  
Leaf Curl

Cotton leaf curl disease (CLCuD) was first reported in Sudan in 1931. Disease symptoms in cotton were characterized by vein thickening and leaf curling, and the suspect causal agent was shown to be transmitted by the whitefly Bemisia tabaci (Genn.) among cotton, okra, and several weed species (2). Although begomovirus etiology was suspected based on symptomatology and vector transmission, no evidence was available that confirmed or disputed this hypothesis. During 1994 to 1996, four cotton samples exhibiting typical CLCuD symptoms were collected from different fields in the Gezira region in Central Sudan and examined for presence of begomovirus DNA. Total nucleic acids were isolated from cotton plants and subjected to polymerase chain reaction (PCR) using degenerate primers (pAV 2644 and pAC 1154) to amplify begomovirus coat protein (Cp) gene and its flanking sequences (1). An amplicon of the expected size (1,300 bp) was obtained by PCR from each sample, and their nucleotide (nt) sequences were determined. Virus-specific primers designed around the Cp sequence were used to amplify an apparent full-length DNA component. Amplicons were cloned and their sequences were determined, yielding a begomoviral component of approximately 2,761 nt (AF260241). Despite exhaustive attempts to amplify a putative viral B-component using degenerate primers based on the intergenic region sequence of the putative “A-component,” or sequences that are highly conserved for other begomoviruses, no B component was detected. The four cotton isolates shared 99.9 to 100% nt sequence identity, and the number and arrangement of predicted open reading frames were similar to those known for other monopartite begomoviruses. Phylogenetic analysis of the putative CLCuV genome with other begomoviruses indicated that its closest relative was Althea rosea enation virus (AREV) from Egypt (AF014881) with which it shares 79% sequence identity, indicating that CLCuV is a unique begomovirus species with a probable origin in the Eastern Hemisphere. CLCuV shared 66% identity with its second closest relative, Cotton leaf curl virus-Pakistan (CLCuV-PK) (AJ002448). These data provide the first direct evidence for the association of a monopartite begomovirus with the leaf curl disease of cotton in Gezira, Sudan, that is distinct from all other begomoviral species described to date. Herein, we provisionally designate this unique begomoviral species as Cotton leaf curl virus from Sudan (CLCuV-SD). References: (1) A. M. Idris and J. K. Brown. Phytopathology 88:648, 1998. (2) A. M. Nour and J. J. Nour. Emp. Cott. Gr. Rev. 41:27, 1964.

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 Complete Genome Sequences of Tomato Leaf Curl Guam Virus, a Novel Tomato-Infecting Begomovirus from Guam, USA

2021 ◽  
Vol 10 (49) ◽  
Author(s):  
Robert L. Schlub ◽  
Rugang Li ◽  
Jesse P. Bamba ◽  
Mari Marutani ◽  
Kai-Shu Ling
Keyword(s):  
Nucleotide Sequence ◽  
Complete Genome ◽  
Nucleotide Sequence Identity ◽  
Tomato Leaf ◽  
Genome Sequences ◽  
Sequence Identity ◽  
Tomato Leaf Curl ◽  
Leaf Curl

Genome sequences of a novel begomovirus infecting tomato on Guam were obtained using primer-walking and sequencing. The complete genome sequences are 2,750 nucleotides long with a typical monopartite organization and display less than 91% nucleotide sequence identity to other begomoviruses. A provisional name, tomato leaf curl Guam virus (ToLCGuV), is proposed.

scholarly journals A New Begomovirus Species Causing Leaf Curl Disease of Radish in India

Plant Disease ◽  
2007 ◽  
Vol 91 (8) ◽  
pp. 1053-1053 ◽  
Author(s):  
A. K. Singh ◽  
B. Chattopadhyay ◽  
P. K. Pandey ◽  
A. K. Singh ◽  
S. Chakraborty
Keyword(s):  
Sequence Analysis ◽  
Electron Microscopic Observation ◽  
Begomovirus Species ◽  
Infected Leaf ◽  
Electron Microscopic ◽  
Degenerate Primers ◽  
Sequence Identity ◽  
Leaf Curl Virus ◽  
Leaf Curl Disease ◽  
Leaf Curl

Leaf curl disease of radish (RLCD) was observed for the first time in India in commercial fields and kitchen gardens of the Varanasi District and adjoining areas of eastern Uttar Pradesh during November 2003. Infected plants exhibited typical upward and downward leaf curling, leaf distortion, reduction of leaf area, and conspicuous enations on the underside of the leaves. Incidence of RLCD was estimated to be between 10 and 40% depending on the cultivars used. Electron microscopic observation revealed typical geminate particles in infected leaf samples. The causal virus could be transmitted to radish cv. Minu Early by whiteflies (Bemisia tabaci) and grafting. Inoculated plants developed symptoms similar to those observed in naturally infected radish plants. Viral DNA was isolated from artificially inoculated symptomatic radish plants (4) followed by concentration of super-coiled DNA by alkaline denaturation (1). The presence of a geminivirus was confirmed by PCR using DNA-A degenerate primers (3), and a 1.5-kb amplified product was obtained from six artificially and three naturally infected plants. Amplification of the full-length DNA-A was achieved using a primer combination derived from sequences obtained from a 1.5-kb amplicon. Amplification of 1.3-kb DNA-β sequences was achieved using specific primers (2) in three infected plants. Sequence analysis revealed that DNA-A (GenBank Accession No. EF 175733) contained 2,756 nt and DNA-β contained 1,358 nt (GenBank Accession No. EF 175734). DNA-A of the causal virus shares 87.7% identity with Tomato leaf curl Bangladesh virus (GenBank Accession No. AF 188481) and 62% identity with Mungbean yellow mosaic India virus (GenBank Accession No. AF126406). The begomovirus DNA-A sequence associated with RLCD contained seven open reading frames (AV1, AV2, AC1, AC2, AC3, AC4, and AC5). The DNA-β associated with RLCD shared the highest nucleotide sequence identity (84.9%) with DNA-β of Tobacco leaf curl virus isolate NIB 12-1 (GenBank Accession No. AJ316033) reported from Pakistan. Despite exhaustive attempts to amplify a putative viral B-component using degenerate primers based on the intergenic region sequence of the DNA-A or sequences that are highly conserved for other begomoviruses, no DNA-B component was detected. On the basis of DNA-A sequence analysis, the ICTV species demarcation criteria of 89% sequence identity, and genome organization, the virus causing RLCD should be considered a new Begomovirus species, for which the name Radish leaf curl virus (RLCV) is proposed. To our knowledge, this is the first report of the association of a Begomovirus with a disease of radishes in India. References: (1) H. C. Birnboim and J. Doly. Nucleic Acids Res. 7:1513, 1979. (2) R. W. Briddon et al. Mol. Biotechnol. 20:315, 2002. (3) M. R. Rojas et al. Plant Dis. 77:340, 1993. (4) K. M. Srivastava et al. J. Virol. Methods 51:297, 1995.

scholarly journals Emergence of a New Cucurbit-Infecting Begomovirus Species Capable of Forming Viable Reassortants with Related Viruses in the Squash leaf curl virus Cluster

2002 ◽  
Vol 92 (7) ◽  
pp. 734-742 ◽  
Author(s):  
J. K. Brown ◽  
A. M. Idris ◽  
C. Alteri ◽  
Drake C. Stenger
Keyword(s):  
Nucleotide Sequence ◽  
Host Range ◽  
Nucleotide Sequence Identity ◽  
Begomovirus Species ◽  
Progeny Virus ◽  
Bipartite Begomovirus ◽  
Sequence Identity ◽  
Squash Leaf Curl Virus ◽  
Leaf Curl Virus ◽  
Leaf Curl

Cucurbit leaf curl virus (CuLCV), a whitefly-transmitted geminivirus previously partially characterized from the southwestern United States and northern Mexico, was identified as a distinct bipartite begomovirus species. This virus has near sequence identity with the previously partially characterized Cucurbit leaf crumple virus from California. Experimental and natural host range studies indicated that CuLCV has a relatively broad host range within the family Cucurbitaceae and also infects bean and tobacco. The genome of an Arizona isolate, designated CuLCV-AZ, was cloned and completely sequenced. Cloned CuLCV-AZ DNA A and B components were infectious by biolistic inoculation to pumpkin and progeny virus was transmissible by the whitefly vector, Bemisia tabaci, thereby completing Koch's postulates. CuLCV-AZ DNA A shared highest nucleotide sequence identity with Squash leaf curl virus-R (SLCV-R), SLCV-E, and Bean calico mosaic virus (BCaMV) at 84, 83, and 80%, respectively. The CuLCV DNA B component shared highest nucleotide sequence identity with BCaMV, SLCV-R, and SLCV-E at 71, 70, and 68%, respectively. The cis-acting begomovirus replication specificity element, GGTGTCCTGGTG, in the CuLCV-AZ origin of replication is identical to that of SLCV-R, SLCV-E, and BCaMV, suggesting that reassortants among components of CuLCV-AZ and these begomoviruses may be possible. Reassortment experiments in pumpkin demonstrated that both reassortants of CuLCV-AZ and SLCV-E A and B components were viable. However, for CuLCV-AZ and SLCV-R, only one reassortant (SLCV-R DNA A/CuLCV-AZ DNA B) was viable on pumpkin, even though the cognate component pairs of both viruses infect pumpkin. These results demonstrate that reassortment among sympatric begomovirus species infecting cucurbits are possible, and that, if generated in nature, could result in begomoviruses bearing distinct biological properties.

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.

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