Nucleotide Sequence Identity (nucleotide + sequence_identity)

Distribution by Scientific Domains

Selected Abstracts

Molecular Characterization of a Strain of Squash Leaf Curl China Virus from the Philippines

T. Kon
Abstract The complete nucleotide sequence of infectious cloned DNA components (A and B) of the causal agent of squash leaf curl disease in the Philippines was determined. DNA-A and DNA-B comprise 2739 and 2705 nucleotides, respectively; the common region is 174 bases in length. Five ORFs were found in DNA-A and two in DNA-B. Partial dimeric clones containing DNA-A and DNA-B, constructed in a binary vector and transformed into Agrobacterium tumefaciens, induced systemic infection in agro-inoculated pumpkin plants (Cucurbita moschata). The total DNA-A sequence was most closely related to that of Squash leaf curl China virus (SLCCNV) (88% identity), although the existence of B component of SLCCNV has not been reported. The deduced coat protein was like that of SLCCNV (98% amino acid sequence identity) and the Philippines virus has low sequence identity to Squash leaf curl virus (SLCV) and Squash mild leaf curl virus (SMLCV) (63 and 64% total nucleotide sequence identities, respectively). From these results, we propose that the Philippines virus be designated Squash leaf curl China virus -[Philippines] (SLCCNV-[PH]). [source]

Genome sequences of two novel phages infecting marine roseobacters

Yanlin Zhao
Summary Two bacteriophages, DSS3,2 and EE36,1, which infect marine roseobacters Silicibacter pomeroyi DSS-3 and Sulfitobacter sp. EE-36, respectively, were isolated from Baltimore Inner Harbor water. These two roseophages resemble bacteriophage N4, a large, short-tailed phage infecting Escherichia coli K12, in terms of their morphology and genomic structure. The full genome sequences of DSS3,2 and EE36,1 reveal that their genome sizes are 74.6 and 73.3 kb, respectively, and they both contain a highly conserved N4-like DNA replication and transcription system. Both roseophages contain a large virion-encapsidated RNA polymerase gene (> 10 kb), which was first discovered in N4. DSS3,2 and EE36,1 also possess several genes (i.e. ribonucleotide reductase and thioredoxin) that are most similar to the genes in roseobacters. Overall, the two roseophages are highly closely related, and share 80,94% nucleotide sequence identity over 85% of their ORFs. This is the first report of N4-like phages infecting marine bacteria and the second report of N4-like phage since the discovery of phage N4 40 years ago. The finding of these two N4-like roseophages will allow us to further explore the specific phage,host interaction and evolution for this unique group of bacteriophages. [source]

Isolation of a cyprinid herpesvirus 2 from goldfish, Carassius auratus (L.), in the UK

K R Jeffery
Abstract Haematopoietic necrosis virus [cyprinid herpesvirus 2 (CyHV-2)] was isolated during disease outbreaks in goldfish, Carassius auratus, at an ornamental fish retail site in southern England in 2004. Signs of disease included lethargy and inappetence and were first seen after water temperatures increased from 14,15 to 19,21 C. External gross pathology included pale patches on the gills and skin and internally the spleen was enlarged, often with distinctive white nodules. The most prominent histopathological changes observed were necrotic lesions in the spleen and kidney and focal patches of necrosis in the gill lamellae. Necrotic cells often contained nuclei with marginated chromatin and pale intranuclear inclusions. Ultrastructural examination of the spleen tissue revealed typical herpesvirus-like particles measuring 100 nm in diameter. The virus was isolated from extracts of gill tissue in KF-1 cells at 20 C and oligonucleotide primer sets were designed based on conserved gene sequences and used to amplify viral DNA by polymerase chain reaction (PCR). The PCR assays were then used to detect the virus in DNA extracted from tissues sampled during earlier disease investigations at the retail site owner's holding facility in 2002 and 2003 and stored at ,70 C since then. Polymerase gene-specific PCR amplification products obtained from tissue samples and from the virus isolated in cell culture shared 100% nucleotide sequence identity with the published sequence for CyHV-2. [source]

Molecular Characterization of two Distinct Begomoviruses from Ageratum conyzoides and Malvastrum coromandelianum in China

J. F. Huang
Abstract Two weed samples, G52 from Ageratum conyzoides and G87 from Malvastrum coromandelianum, showing leaf curling and vein thickening symptoms were collected in Nanning, Guangxi Province, China. The complete nucleotide sequences of DNA-A-like molecules of G52 and G87 were determined to be 2735 and 2745 nucleotides respectively. Both DNA-A molecules have a genomic organization typical of begomoviruses and share 73.4% sequence identity with each other. Sequence comparisons showed that the DNA-A of G52 and G87 were most closely related to those of Ageratum yellow vein virus (AYVV; 85% sequence identity) and Tobacco leaf curl Yunnanvirus (75.7% sequence identity) respectively. Further sequence comparisons showed that G52 has arisen by recombination among viruses related to AYVV, Papaya leaf curl China virus and an unidentified Begomovirus species. The molecular data suggest that G52 and G87 are two distinct begomoviruses, for which the names Ageratum leaf curl virus for G52 and Malvastrum leaf curl virus for G87 are proposed. The satellite DNA, molecule was only found to be associated with G87. G87 DNA, consists of 1354 nucleotides, and shares the highest nucleotide sequence identity (68.9%) with that associated with Sida yellow vein China virus. A defective DNA, molecule was also found to be associated with G87. [source]

Molecular Characterization of a Distinct Begomovirus and its Associated Satellite DNA Molecule Infecting Sida acuta in China,

Q. Xiong
Abstract Three viral isolates Hn8, Hn40 and Hn41 were obtained from Sida acuta showing yellow mosaic symptom in the Hainan province, China. Comparison of partial DNA-A sequences amplified with degenerate primers confirmed the existence of single type of Begomovirus. The complete nucleotide sequence of the DNA-A-like molecule of Hn8 was determined to be 2749 nucleotides, having a typical genetic organization of a Begomovirus. Hn8 DNA-A had the highest sequence identity (78%) with that of Ageratum yellow vein China virus-[G13] (AJ558120), and had less sequence identity with other begomoviruses. Based on the above molecular data, Hn8 was thus considered as a new Begomovirus species, for which the name Sida yellow mosaic China virus (SiYMCNV) is proposed. Satellite DNA- , molecules (Hn8- ,, Hn40- , and Hn41- ,) were found to be associated with Hn8, Hn40 and Hn41 and their complete nucleotide sequences were determined. Sequence analysis showed that Hn8- ,, Hn40- , and Hn41- , shared more than 84% nucleotide sequence identity, and they were different from other characterized DNA- ,, sharing the highest nucleotide sequence identity (47.8%) with DNA- , of Ageratum yellow vein virus. [source]

Characterization of Passionfruit severe leaf distortion virus, a novel begomovirus infecting passionfruit in Brazil, reveals a close relationship with tomato-infecting begomoviruses

S. S. Ferreira
Molecular and biological characterization of the begomovirus isolate BR:LNS2:Pas:01, obtained from yellow passionfruit plants in Livramento de Nossa Senhora, Bahia state, Brazil, was carried out. Sequence analysis demonstrated that the BR:LNS2:Pas:01 DNA-A had highest nucleotide sequence identity with Tomato chlorotic mottle virus (77%) and had five ORFs corresponding to the genes cp, rep, trap, ren and ac4. The DNA-B had highest nucleotide sequence identity with Tomato yellow spot virus (74%) and two ORFs corresponding to the genes mp and nsp. These identity values indicate that this isolate represents a new begomovirus species, for which the name Passionfruit severe leaf distortion virus (PSLDV), is proposed. Phylogenetic analysis clustered the PSLDV DNA-A and -B in a monophyletic branch with Brazilian tomato-infecting begomoviruses. The isolate's host range was restricted to species from the Passifloraceae and Solanaceae. PSLDV-[BR:LNS2:Pas:01] was capable of forming pseudorecombinants with tomato-infecting begomoviruses, reinforcing its close relationship with these viruses and suggesting a possible common origin. However, the virus was not capable of infecting tomato. [source]

Salinity stress adaptation competence in the extremophile Thellungiella halophila in comparison with its relative Arabidopsis thaliana

Qingqiu Gong
Summary In stark contrast to Arabidopsis, a related species, Thellungiella halophila (Thellungiella salsuginea; salt cress), displays extreme tolerance to high salinity, low humidity and freezing. High nucleotide sequence identity permits the use of tools developed for Arabidopsis for Thellungiella transcript profiling, for which a microarray platform with >25 000 DNA elements (70-mer oligonucleotides) was used. Microarray transcript profiling and intensity analysis, quantitative RT-PCR, and metabolite profiles define genes and pathways that showed shared and divergent responses to salinity stress in the two species. Shared responses are exemplified by 40% of the regulated genes functioning in confining ribosomal functions, photosynthesis and cell growth, as well as activating osmolyte production, transport activities and abscisic acid-dependent pathways. An additional 60% of regulated genes distinguished Thellungiella from Arabidopsis. Analysis of the differences showed that Arabidopsis exhibited a global defense strategy that required bulk protein synthesis, while Thellungiella induced genes functioning in protein folding, post-translational modification and protein redistribution. At 150 mm NaCl, Thellungiella maintained unimpeded growth. Transcript intensity analyses and metabolite profiles supported the microarray results, pointing towards a stress-anticipatory preparedness in Thellungiella. [source]