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PubMed2026

The first complete genome sequence of Ammi majus latent virus from the new natural host culantro.

A potyvirus (isolate AMLV-CQ) infecting culantro (Eryngium foetidum L.) imported from Vietnam was identified by RT-PCR. The complete genome sequence of AMLV-CQ was determined to be 9,549 nucleotides in length. It contains a large open reading frame encoding a 3,082-amino-acid putative polyprotein, flanked by 5´ and 3´ untranslated regions (UTRs) of 77 and 226 nt, respectively. AMLV-CQ is closely related to five other completely sequenced potyviruses, sharing 68-69% nucleotide and 69-70% amino acid sequence identity. However, the coat protein (CP) gene shares 89% nucleotide and 93% amino acid sequence identity with that of a partially sequenced potyvirus, Ammi majus latent virus (isolate AMLV-WF17). These results suggest that AMLV-CQ and AMLV-WF17 are isolates of the same species. To our knowledge, this is the first report of a complete genome sequence of an AMLV isolate, and culantro was identified as a new natural host for this virus. In addition, a one-step RT-PCR assay was developed that provides a rapid, robust, and highly sensitive approach for the detection of AMLV.

Eryngium↗
PubMed2026

Complete genome sequences of three effective nitrogen-fixing strains of Bradyrhizobium ottawaense from Canada.

We report complete genome sequences of three nitrogen-fixing Bradyrhizobium ottawaense strains isolated from soybeans in Canada. Each ~9.0 Mb genome (chromosome and plasmid) harbors predicted genes for nodulation, nitrogen fixation, N2O mitigation, phosphate solubilization, iron acquisition, phytohormone production, and stress tolerance, highlighting their potential for sustainable agriculture.

Bradyrhizobium ottawaense↗
PubMed2002

[Complete genome sequence of 84FLi, a Hantaan virus strain isolated from the liver of fetus aborted by a pregnant women with hemmorrhagic fever with renal syndrome].

OBJECTIVE: To study the complete genome sequence of the Chinese Hantaan virus vaccine strain 84FLi and learn about its molecular characters. METHODS: The virus strain 84FLi was isolated from the liver of a fetus aborted by pregnant women with hemorrhagic fever with renal syndrome. The cDNAs of L M and S segments were amplified fragment by fragment using RT-PCR. The purified PCR products were sequenced directly or cloned into pMD18-T vector and then sequenced. RESULTS: The complete genome of strain 84FLi was composed of L ( 6 533 bp) M (3 616 bp) and S (1 688 bp) coding 2151 1135 and 429 amino acids respectively. The entire sequence composition was 3830A 2050C 2510G and 3447T the GC and AT contents were 38.52% and 61.48%. Homology analysis showed that the homologies of 84 FLi S segment nucleotide sequences with strain RG9 (isolated in Guangzhou) and strain Chen4 (isolated in Anhui) were 99.6%. There were 83.7% 84.0% and 87.2% nucleotide sequences homology with the three segments of Hantaan virus foreign standard strain 76-118 while the amino acids sequences homology with those of 76-118 were 97.5% 96.0% and 97.9% respectively. CONCLUSION: The strain 84FLi is highly related to other Chinese Hantaan virus isolates and is in the same subtype with the other two Chinese isolates RG9 and Chen4.

Amino Acid Sequence↗
PubMed1995

Complete genomic sequence of the fish rhabdovirus infectious haematopoietic necrosis virus.

The complete nucleotide sequence of the genome of the fish rhabdovirus infectious haematopoietic necrosis virus (IHNV) has been determined after cDNA cloning of the viral genomic RNA. Sequence analysis showed the presence of six open reading frames encoding the nucleoprotein N, the matrix proteins M1 and M2, the glycoprotein G, a so-called non-structural protein NV, and the RNA polymerase L. The genome organization is 3'N-M1-M2-G-NV-L 5'. The extreme 5' and 3' ends of the genome were sequenced after RNA ligation or RACE. Prokaryotic expression products of the open reading frames predicted to encode the matrix proteins M1 and M2, the glycoprotein G and the NV protein reacted with rabbit anti-IHNV serum thereby confirming their identity. This is the first complete nucleotide sequence of a fish rhabdovirus. Knowledge of the complete sequence is an essential prerequisite for future manipulation of the genome and also serves to provide gene- and protein specific reagents for use in further examination of the replication of the fish rhabdoviruses.

Amino Acid Sequence↗
PubMed2003

Complete genomic sequence of Pepper vein banding virus (PVBV): a distinct member of the genus Potyvirus.

The complete genomic sequence of Pepper vein banding virus (PVBV), a potyvirus infecting chilli and other solanaceous plants in south India, was determined and compared with those of other potyviruses. The viral genome contained 9711 nucleotides, excluding the poly-A tail. The length of the 5'- and 3'-untranslated regions (UTR) were 163 and 281 nucleotides respectively. As for other potyviruses, the PVBV genome has a single open reading frame (ORF) starting at nucleotide 164 and ending at nt 9430, which encodes a polyprotein of 3088 amino acid residues. There are nine putative conserved cleavage sites within the polyprotein, which can result in ten functionally distinct protein products. Phylogenetic analysis of the potyviral polyprotein sequences showed that PVBV is a distinct species of this genus.

Capsicum↗
PubMed2003

The complete genome sequence of the Arabidopsis and tomato pathogen Pseudomonas syringae pv. tomato DC3000.

We report the complete genome sequence of the model bacterial pathogen Pseudomonas syringae pathovar tomato DC3000 (DC3000), which is pathogenic on tomato and Arabidopsis thaliana. The DC3000 genome (6.5 megabases) contains a circular chromosome and two plasmids, which collectively encode 5,763 ORFs. We identified 298 established and putative virulence genes, including several clusters of genes encoding 31 confirmed and 19 predicted type III secretion system effector proteins. Many of the virulence genes were members of paralogous families and also were proximal to mobile elements, which collectively comprise 7% of the DC3000 genome. The bacterium possesses a large repertoire of transporters for the acquisition of nutrients, particularly sugars, as well as genes implicated in attachment to plant surfaces. Over 12% of the genes are dedicated to regulation, which may reflect the need for rapid adaptation to the diverse environments encountered during epiphytic growth and pathogenesis. Comparative analyses confirmed a high degree of similarity with two sequenced pseudomonads, Pseudomonas putida and Pseudomonas aeruginosa, yet revealed 1,159 genes unique to DC3000, of which 811 lack a known function.

Arabidopsis↗
PubMed2006

First complete genome sequence of two Staphylococcus epidermidis bacteriophages.

Staphylococcus epidermidis is an important opportunistic pathogen causing nosocomial infections and is often associated with infections in patients with implanted prosthetic devices. A number of virulence determinants have been identified in S. epidermidis, which are typically acquired through horizontal gene transfer. Due to the high recombination potential, bacteriophages play an important role in these transfer events. Knowledge of phage genome sequences provides insights into phage-host biology and evolution. We present the complete genome sequence and a molecular characterization of two S. epidermidis phages, phiPH15 (PH15) and phiCNPH82 (CNPH82). Both phages belonged to the Siphoviridae family and produced stable lysogens. The PH15 and CNPH82 genomes displayed high sequence homology; however, our analyses also revealed important functional differences. The PH15 genome contained two introns, and in vivo splicing of phage mRNAs was demonstrated for both introns. Secondary structures for both introns were also predicted and showed high similarity to those of Streptococcus thermophilus phage 2972 introns. An additional finding was differential superinfection inhibition between the two phages that corresponded with differences in nucleotide sequence and overall gene content within the lysogeny module. We conducted phylogenetic analyses on all known Siphoviridae, which showed PH15 and CNPH82 clustering with Staphylococcus aureus, creating a novel clade within the S. aureus group and providing a higher overall resolution of the siphophage branch of the phage proteomic tree than previous studies. Until now, no S. epidermidis phage genome sequences have been reported in the literature, and thus this study represents the first complete genomic and molecular description of two S. epidermidis phages.

Base Sequence↗
PubMed2005

Complete genomic sequence of human coronavirus OC43: molecular clock analysis suggests a relatively recent zoonotic coronavirus transmission event.

Coronaviruses are enveloped, positive-stranded RNA viruses with a genome of approximately 30 kb. Based on genetic similarities, coronaviruses are classified into three groups. Two group 2 coronaviruses, human coronavirus OC43 (HCoV-OC43) and bovine coronavirus (BCoV), show remarkable antigenic and genetic similarities. In this study, we report the first complete genome sequence (30,738 nucleotides) of the prototype HCoV-OC43 strain (ATCC VR759). Complete genome and open reading frame (ORF) analyses were performed in comparison to the BCoV genome. In the region between the spike and membrane protein genes, a 290-nucleotide deletion is present, corresponding to the absence of BCoV ORFs ns4.9 and ns4.8. Nucleotide and amino acid similarity percentages were determined for the major HCoV-OC43 ORFs and for those of other group 2 coronaviruses. The highest degree of similarity is demonstrated between HCoV-OC43 and BCoV in all ORFs with the exception of the E gene. Molecular clock analysis of the spike gene sequences of BCoV and HCoV-OC43 suggests a relatively recent zoonotic transmission event and dates their most recent common ancestor to around 1890. An evolutionary rate in the order of 4 x 10(-4) nucleotide changes per site per year was estimated. This is the first animal-human zoonotic pair of coronaviruses that can be analyzed in order to gain insights into the processes of adaptation of a nonhuman coronavirus to a human host, which is important for understanding the interspecies transmission events that led to the origin of the severe acute respiratory syndrome outbreak.

Animals↗
PubMed1999

Divergence of the hyperthermophilic archaea Pyrococcus furiosus and P. horikoshii inferred from complete genomic sequences.

Divergence of the hyperthermophilic Archaea, Pyrococcus furiosus and Pyrococcus horikoshii, was assessed by analysis of complete genomic sequences of both species. The average nucleotide identity between the genomic sequences is 70-75% within ORFs. The P. furiosus genome (1.908 mbp) is 170 kbp larger than the P. horikoshii genome (1.738 mbp) and the latter displays significant deletions in coding regions, including the trp, his, aro, leu-ile-val, arg, pro, cys, thr, and mal operons. P. horikoshii is auxotrophic for tryptophan and histidine and is unable to utilize maltose, unlike P. furiosus. In addition, the genomes differ considerably in gene order, displaying displacements and inversions. Six allelic intein sites are common to both Pyrococcus genomes, and two intein insertions occur in each species and not the other. The bacteria-like methylated chemotaxis proteins form a functional group in P. horikoshii, but are absent in P. furiosus. Two paralogous families of ferredoxin oxidoreductases provide evidence of gene duplication preceding the divergence of the Pyrococcus species.

Archaeal Proteins↗
PubMed2026

Complete genome sequences of three co-occurring Pseudomonas isolates from California Botanic Garden topsoil.

We report the complete genome sequences of three Pseudomonas isolates recovered from topsoil at the California Botanic Garden. Two isolates share ~99.4% average nucleotide identity, enabling investigation of intraspecies microvariation; the third represents a co-occurring distinct species, together capturing species- and strain-level genomic diversity within a natural soil community.

Pseudomonas↗
PubMed2003

Complete genome sequence of the oral pathogenic Bacterium porphyromonas gingivalis strain W83.

The complete 2,343,479-bp genome sequence of the gram-negative, pathogenic oral bacterium Porphyromonas gingivalis strain W83, a major contributor to periodontal disease, was determined. Whole-genome comparative analysis with other available complete genome sequences confirms the close relationship between the Cytophaga-Flavobacteria-Bacteroides (CFB) phylum and the green-sulfur bacteria. Within the CFB phyla, the genomes most similar to that of P. gingivalis are those of Bacteroides thetaiotaomicron and B. fragilis. Outside of the CFB phyla the most similar genome to P. gingivalis is that of Chlorobium tepidum, supporting the previous phylogenetic studies that indicated that the Chlorobia and CFB phyla are related, albeit distantly. Genome analysis of strain W83 reveals a range of pathways and virulence determinants that relate to the novel biology of this oral pathogen. Among these determinants are at least six putative hemagglutinin-like genes and 36 previously unidentified peptidases. Genome analysis also reveals that P. gingivalis can metabolize a range of amino acids and generate a number of metabolic end products that are toxic to the human host or human gingival tissue and contribute to the development of periodontal disease.

Bacterial Proteins↗
PubMed2026

Complete genome sequence of Streptomyces californicus ADR1, an anti-infective, anti-biofilm and anti-oxidant producing endophyte isolated from the medicinal plant Datura metel.

OBJECTIVE: Streptomyces californicus strain ADR1 is an endophytic actinobacterium isolated from Datura metel that produces secondary metabolites with potent antibacterial and anti-biofilm activities against WHO-listed high-priority Gram-positive pathogens. While anti-bacterial and antioxidant potential of the strain ADR1 has been extensively characterized, its complete genome sequence remains to be investigated for further insights into its biosynthetic potential. This study presents the complete genome sequence analysis of the strain ADR1 to provide a robust genomic foundation for understanding its metabolic versatility and biosynthesis of compounds with therapeutic significance. DATA DESCRIPTION: The ADR1 genome was sequenced using Illumina HiSeq. The assembly comprised 262 scaffolds with a total genome size of 8.4 Mb and G + C content of 72.5%, containing 7427 protein-coding genes. AntiSMASH and IIT-Hyderabad novelBGC analysis revealed 39 biosynthetic gene clusters, including non-ribosomal peptide synthetases, type I polyketide synthases, terpene and melanin clusters, correlating with the diverse therapeutic compounds previously identified through GC-MS analysis. This high-quality genome provides crucial insights into the biosynthetic potential underlying potent antimicrobial and antioxidant activities of the strain ADR1.

Streptomyces↗
PubMed2002

Complete genomic sequence of bacteriophage ul36: demonstration of phage heterogeneity within the P335 quasi-species of lactococcal phages.

The complete genomic sequence of the Lactococcus lactis virulent phage ul36 belonging to P335 lactococcal phage species was determined and analyzed. The genomic sequence of this lactococcal phage contained 36,798 bp with an overall G+C content of 35.8 mol %. Fifty-nine open reading frames (ORFs) of more than 40 codons were found. N-terminal sequencing of phage structural proteins as well as bioinformatic analysis led to the attribution of a function to 24 ORFs (41%). A lysogeny module was found within the genome of this virulent phage. The putative integrase gene seems to be the product of a horizontal transfer because it is more closely related to Streptococcus pyogenes phages than it is to L. lactis phages. Comparative genome analysis with six complete genomes of temperate P335-like phages confirmed the heterogeneity among phages of P335 species. A dUTPase gene is the only conserved gene among all P335 phages analyzed as well as the phage BK5-T. A genetic relationship between P335 phages and the phage-type of the BK5-T species was established. Thus, we proposed that phage BK5-T be included within the P335 species and thereby reducing the number of lactococcal phage species to 11.

Bacteriophages↗
PubMed2006

Complete genomic sequences for hepatitis C virus subtypes 6e and 6g isolated from Chinese patients with injection drug use and HIV-1 co-infection.

In one of our recent studies, two HCV genotype 6 variants were identified in patients from Hong Kong and Guangxi in southern China, with injection drug use and HIV-1 co-infection. We report the complete genomic sequences for these two variants: GX004 and HK6554. Their entire genome lengths were 9,468 and 9,462 nt; the 5' UTRs were 338 nt followed by single ORFs of 9,069 nt; the 3' UTRs were 61 and 55 nt including 29 and 23 nt poly(U) tracks. Phylogenetic analysis using a maximum likelihood method showed that HK6554 was classified into subtype 6g and GX004 represented the first complete genome sequence for subtype 6e. Further analysis with reference sequences in three different genomic regions revealed that GX004 closely clustered with a group of subtype 6e variants, which were previously exclusively found in Vietnam and recently increasingly identified in injection drug users from the Guangxi province in southern China that borders Vietnam. This suggests that subtype 6e could become epidemic in southern China by network transmission among injection drug users.

China↗
PubMed2004

Evidence for frequent recombination within species human enterovirus B based on complete genomic sequences of all thirty-seven serotypes.

The species Human enterovirus B (HEV-B) in the family Picornaviridae consists of coxsackievirus A9; coxsackieviruses B1 to B6; echoviruses 1 to 7, 9, 11 to 21, 24 to 27, and 29 to 33; and enteroviruses 69 and 73. We have determined complete genome sequences for the remaining 22 HEV-B serotypes whose sequences were not represented in public databases and analyzed these in conjunction with previously available complete sequences in GenBank. Members of HEV-B were monophyletic relative to all other human enterovirus species in all regions of the genome except in the 5'-nontranslated region (NTR), where they are known to cluster with members of HEV-A. Within HEV-B, phylogenies constructed from the structural (P1) and nonstructural regions of the genome (P2 and P3) are incongruent, suggesting that recombination had occurred. Similarity plots and bootscanning analysis across the complete genome identified multiple sites at which the phylogeny of a given strain's sequence shifted, indicating potential recombination points. These points are distributed in the 5'-NTR and throughout P2 and P3, but no sites with >80% bootstrap support were identified within the capsid. Individual sequence comparisons and phylogenetic analyses suggest that members of HEV-B have recombined with one another on multiple occasions, resulting in a complex mosaic of sequences derived from multiple parental viruses in the nonstructural regions of the genome. We conclude that RNA recombination is a common mechanism for enterovirus evolution and that recombination within the nonstructural regions of the genome (P2 and P3) has been observed only among members of the same species.

Enterovirus B, Human↗
PubMed2004

Complete genome sequences of all members of the species Human enterovirus A.

The species Human enterovirus A (HEV-A) in the family Picornaviridae consists of coxsackieviruses (CV) A2-A8, A10, A12, A14 and A16 and enterovirus 71. Complete genome sequences for the prototype strains of the 10 serotypes whose sequences were not represented in public databases have been determined and analysed in conjunction with previously available complete sequences in GenBank. Members of HEV-A are monophyletic relative to all other human enterovirus species in all regions of the genome except in the 5' non-translated region (NTR), where they are known to cluster with members of HEV-B. The HEV-A prototype strains were about 66 to 86 % identical to one another in deduced capsid amino acid sequence. Antigenic cross-reactivity has been reported between CVA3-Olson and CVA8-Donovan, between CVA5-Swartz and CVA12-Texas-12 and between CVA16-G-10 and EV71-BrCr. Similarity plots, individual sequence comparisons and phylogenetic analyses demonstrate a high degree of capsid sequence similarity within each of these three pairs of prototype strains, providing a molecular basis for the observed antigenic relationships. In several cases, phylogenies constructed from the structural (P1) and non-structural regions of the genome (P2 and P3) are incongruent. The incongruent phylogenies and the similarity plot analyses imply that recombination has played a role in the evolution of the HEV-A prototype strains. CVA6-Gdula clearly contains sequences that are also present in CVA10-Kowalik and CVA12-Texas-12, suggesting that these three strains have a shared evolutionary history despite their lack of similarity in the capsid region.

3' Untranslated Regions↗