scholarly journals Three Novel Virophage Genomes Discovered from Yellowstone Lake Metagenomes

2014 ◽  
Vol 89 (2) ◽  
pp. 1278-1285 ◽  
Author(s):  
Jinglie Zhou ◽  
Dawei Sun ◽  
Alyson Childers ◽  
Timothy R. McDermott ◽  
Yongjie Wang ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Evolutionary Relationship ◽  
Gc Content ◽  
Open Reading Frames ◽  
Lake Ecosystem ◽  
Photic Zone ◽  
Yellowstone Lake ◽  
Dna Viruses ◽  
Double Stranded Dna ◽  
Unique Distribution

ABSTRACTVirophages are a unique group of circular double-stranded DNA viruses that are considered parasites of giant DNA viruses, which in turn are known to infect eukaryotic hosts. In this study, the genomes of three novel Yellowstone Lake virophages (YSLVs)—YSLV5, YSLV6, and YSLV7—were identified from Yellowstone Lake through metagenomic analyses. The relative abundance of these three novel virophages and previously identified Yellowstone Lake virophages YSLV1 to -4 were determined in different locations of the lake, revealing that most of the sampled locations in the lake, including both mesophilic and thermophilic habitats, had multiple virophage genotypes. This likely reflects the diverse habitats or diversity of the eukaryotic hosts and their associated giant viruses that serve as putative hosts for these virophages. YSLV5 has a 29,767-bp genome with 32 predicted open reading frames (ORFs), YSLV6 has a 24,837-bp genome with 29 predicted ORFs, and YSLV7 has a 23,193-bp genome with 26 predicted ORFs. Based on multilocus phylogenetic analysis, YSLV6 shows a close evolutionary relationship with YSLV1 to -4, whereas YSLV5 and YSLV7 are distantly related to the others, and YSLV7 represents the fourth novel virophage lineage. In addition, the genome of YSLV5 has a G+C content of 51.1% that is much higher than all other known virophages, indicating a unique host range for YSLV5. These results suggest that virophages are abundant and have diverse genotypes that likely mirror diverse giant viral and eukaryotic hosts within the Yellowstone Lake ecosystem.IMPORTANCEThis study discovered novel virophages present within the Yellowstone Lake ecosystem using a conserved major capsid protein as a phylogenetic anchor for assembly of sequence reads from Yellowstone Lake metagenomic samples. The three novel virophage genomes (YSLV5 to -7) were completed by identifying specific environmental samples containing these respective virophages, and closing gaps by targeted PCR and sequencing. Most of the YSLV genotypes were associated primarily with photic-zone and nonhydrothermal samples; however, YSLV5 had a unique distribution with an occurrence in vent samples similar to that in photic-zone samples and with a higher GC content that suggests a distinct host and habitat compared to other YSLVs. In addition, genome content and phylogenetic analyses indicate that YSLV5 and YSLV7 are distinct from known virophages and that additional as-yet-uncharacterized virophages are likely present within the Yellowstone Lake ecosystem.

scholarly journals Exceptionally diverse morphotypes and genomes of crenarchaeal hyperthermophilic viruses

2004 ◽  
Vol 32 (2) ◽  
pp. 204-208 ◽  
Author(s):  
D. Prangishvili ◽  
R.A. Garrett
Keyword(s):  
Aquatic Ecosystems ◽  
African Swine Fever Virus ◽  
African Swine Fever ◽  
Open Reading Frames ◽  
Dna Viruses ◽  
Double Stranded Dna ◽  
Sequence Patterns ◽  
Hydrothermal Environments ◽  
Homologous Orfs ◽  
Reading Frames

The remarkable diversity of the morphologies of viruses found in terrestrial hydrothermal environments with temperatures >80°C is unprecedented for aquatic ecosystems. The best-studied viruses from these habitats have been assigned to novel viral families: Fuselloviridae, Lipothrixviridae and Rudiviridae. They all have double-stranded DNA genomes and infect hyperthermophilic crenarchaea of the orders Sulfolobales and Thermoproteales. Representatives of the different viral families share a few homologous ORFs (open reading frames). However, about 90% of all ORFs in the seven sequenced genomes show no significant matches to sequences in public databases. This suggests that these hyperthermophilic viruses have exceptional biochemical solutions for biological functions. Specific features of genome organization, as well as strategies for DNA replication, suggest that phylogenetic relationships exist between crenarchaeal rudiviruses and the large eukaryal DNA viruses: poxviruses, the African swine fever virus and Chlorella viruses. Sequence patterns at the ends of the linear genome of the lipothrixvirus AFV1 are reminiscent of the telomeric ends of linear eukaryal chromosomes and suggest that a primitive telomeric mechanism operates in this virus.

scholarly journals Isolation and characterization of bacteriophages from India, with lytic activity againstMycobacterium tuberculosis

2018 ◽  
Vol 64 (7) ◽  
pp. 483-491 ◽  
Author(s):  
Urmi Bajpai ◽  
Abhishek Kumar Mehta ◽  
Kandasamy Eniyan ◽  
Avni Sinha ◽  
Ankita Ray ◽  
...  
Keyword(s):  
Antimicrobial Agents ◽  
Sequence Similarity ◽  
Gc Content ◽  
Polymerase Chain Reaction Analysis ◽  
Open Reading Frames ◽  
Genome Maintenance ◽  
Isolation And Characterization ◽  
Virion Release ◽  
Double Stranded Dna ◽  
Transmission Electron

Bacteriophages are being considered as a promising natural resource for the development of alternative strategies against mycobacterial diseases, especially in the context of the wide-spread occurrence of drug resistance among the clinical isolates of Mycobacterium tuberculosis. However, there is not much information documented on mycobacteriophages from India. Here, we report the isolation of 17 mycobacteriophages using Mycobacterium smegmatis as the bacterial host, where 9 phages also lyse M. tuberculosis H37Rv. We present detailed analysis of one of these mycobacteriophages — PDRPv. Transmission electron microscopy and polymerase chain reaction analysis (of a conserved region within the TMP gene) show PDRPv to belong to the Siphoviridae family and B1 subcluster, respectively. The genome (69 110 bp) of PDRPv is circularly permuted double-stranded DNA with ∼66% GC content and has 106 open reading frames (ORFs). On the basis of sequence similarity and conserved domains, we have assigned function to 28 ORFs and have broadly categorized them into 6 groups that are related to replication and genome maintenance, DNA packaging, virion release, structural proteins, lysogeny-related genes and endolysins. The present study reports the occurrence of novel antimycobacterial phages in India and highlights their potential to contribute to our understanding of these phages and their gene products as potential antimicrobial agents.

scholarly journals Genome Analysis of a Novel Clade b Betabaculovirus Isolated from the Legume Pest Matsumuraeses phaseoli (Lepidoptera: Tortricidae)

Viruses ◽  
2020 ◽  
Vol 12 (10) ◽  
pp. 1068
Author(s):  
Ruihao Shu ◽  
Qian Meng ◽  
Lin Miao ◽  
Hongbin Liang ◽  
Jun Chen ◽  
...  
Keyword(s):  
Northeast Asia ◽  
Gc Content ◽  
Open Reading Frames ◽  
Chinese Medicinal Herb ◽  
Double Stranded Dna ◽  
Clade B ◽  
Potential Biocontrol Agent ◽  
Conserved Genes ◽  
Inhibitors Of Apoptosis Proteins ◽  
Lepidopteran Pest

Matsumuraeses phaseoli is a Lepidopteran pest that primarily feeds on numerous species of cultivated legumes, such as Glycine and Phaseolus. It is widely distributed in northeast Asia. A novel granulovirus, designated as Matsumuraeses phaseoli granulovirus (MaphGV), was isolated from pathogenic M. phaseoli larvae that dwell in rolled leaves of Astragalus membranaceus, a Chinese medicinal herb. In this study, using next-generation sequencing, we report the complete genome of MaphGV. MaphGV genome comprises a double-stranded DNA of 116,875 bp, with 37.18% GC content. It has 128 hypothetical open reading frames (ORFs). Among them, 38 are baculovirus core genes, 18 are lepidopteran baculovirus conserved genes, and 5 are unique to Baculoviridae. MaphGV has one baculovirus repeat ORF (bro) and three inhibitors of apoptosis proteins (iap), including a newfound iap-6. We found two atypical baculoviral homologous regions (hrs) and four direct repeats (drs) in the MaphGV genome. Based on phylogenetic analysis, MaphGV belongs to Clade b of Betabaculovirus and is closely related to Cydia pomonellagranulovirus (CpGV) and Cryptophlebia leucotretagranulovirus (CrleGV). This novel baculovirus discovery and sequencing are invaluable in understanding the evolution of baculovirus and MaphGV may be a potential biocontrol agent against the bean ravaging pest.

scholarly journals Characterization of Novel Erwinia amylovora Jumbo Bacteriophages from Eneladusvirus Genus

Viruses ◽  
2020 ◽  
Vol 12 (12) ◽  
pp. 1373
Author(s):  
Sang Guen Kim ◽  
Sung Bin Lee ◽  
Sib Sankar Giri ◽  
Hyoun Joong Kim ◽  
Sang Wha Kim ◽  
...  
Keyword(s):  
Genome Size ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Gc Content ◽  
Genomic Analysis ◽  
Open Reading Frames ◽  
Comparative Genomic ◽  
Limited Information ◽  
High Sequence Similarity ◽  
A Genome

Jumbo phages, which have a genome size of more than 200 kb, have recently been reported for the first time. However, limited information is available regarding their characteristics because few jumbo phages have been isolated. Therefore, in this study, we aimed to isolate and characterize other jumbo phages. We performed comparative genomic analysis of three Erwinia phages (pEa_SNUABM_12, pEa_SNUABM_47, and pEa_SNUABM_50), each of which had a genome size of approximately 360 kb (32.5% GC content). These phages were predicted to harbor 546, 540, and 540 open reading frames with 32, 34, and 35 tRNAs, respectively. Almost all of the genes in these phages could not be functionally annotated but showed high sequence similarity with genes encoded in Serratia phage BF, a member of Eneladusvirus. The detailed comparative and phylogenetic analyses presented in this study contribute to our understanding of the diversity and evolution of Erwinia phage and the genus Eneladusvirus.

scholarly journals A novel nudivirus infecting the invasive demon shrimp Dikerogammarus haemobaphes (Amphipoda)

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Thomas W. Allain ◽  
Grant D. Stentiford ◽  
David Bass ◽  
Donald C. Behringer ◽  
Jamie Bojko
Keyword(s):  
Penaeus Monodon ◽  
Penaeid Shrimp ◽  
Open Reading Frames ◽  
The Novel ◽  
Dna Viruses ◽  
Gene Synteny ◽  
Double Stranded Dna ◽  
The Family ◽  
Novel Virus ◽  
Dikerogammarus Haemobaphes

Abstract The Nudiviridae are a family of large double-stranded DNA viruses that infects the cells of the gut in invertebrates, including insects and crustaceans. The phylogenetic range of the family has recently been enhanced via the description of viruses infecting penaeid shrimp, crangonid shrimp, homarid lobsters and portunid crabs. Here we extend this by presenting the genome of another nudivirus infecting the amphipod Dikerogammarus haemobaphes. The virus, which infects cells of the host hepatopancreas, has a circular genome of 119,754 bp in length, and encodes a predicted 106 open reading frames. This novel virus encodes all the conserved nudiviral genes (sharing 57 gene homologues with other crustacean-infecting nudiviruses) but appears to lack the p6.9 gene. Phylogenetic analysis revealed that this virus branches before the other crustacean-infecting nudiviruses and shares low levels of gene/protein similarity to the Gammanudivirus genus. Comparison of gene synteny from known crustacean-infecting nudiviruses reveals conservation between Homarus gammarus nudivirus and Penaeus monodon nudivirus; however, three genomic rearrangements in this novel amphipod virus appear to break the gene synteny between this and the ones infecting lobsters and penaeid shrimp. We explore the evolutionary history and systematics of this novel virus, suggesting that it be included in the novel Epsilonnudivirus genus (Nudiviridae).

scholarly journals Genome Analysis of a Glossina pallidipes Salivary Gland Hypertrophy Virus Reveals a Novel, Large, Double-Stranded Circular DNA Virus

2008 ◽  
Vol 82 (9) ◽  
pp. 4595-4611 ◽  
Author(s):  
Adly M. M. Abd-Alla ◽  
François Cousserans ◽  
Andrew G. Parker ◽  
Johannes A. Jehle ◽  
Nicolas J. Parker ◽  
...  
Keyword(s):  
Salivary Gland ◽  
Glossina Pallidipes ◽  
Open Reading Frames ◽  
Tsetse Flies ◽  
Sequence Comparisons ◽  
Dna Viruses ◽  
Circular Dna ◽  
Double Stranded Dna ◽  
Salivary Gland Hypertrophy ◽  
Salivary Gland Hypertrophy Virus

ABSTRACT Several species of tsetse flies can be infected by the Glossina pallidipes salivary gland hypertrophy virus (GpSGHV). Infection causes salivary gland hypertrophy and also significantly reduces the fecundity of the infected flies. To better understand the molecular basis underlying the pathogenesis of this unusual virus, we sequenced and analyzed its genome. The GpSGHV genome is a double-stranded circular DNA molecule of 190,032 bp containing 160 nonoverlapping open reading frames (ORFs), which are distributed equally on both strands with a gene density of one per 1.2 kb. It has a high A+T content of 72%. About 3% of the GpSGHV genome is composed of 15 sequence repeats, distributed throughout the genome. Although sharing the same morphological features (enveloped rod-shaped nucleocapsid) as baculoviruses, nudiviruses, and nimaviruses, analysis of its genome revealed that GpSGHV differs significantly from these viruses at the level of its genes. Sequence comparisons indicated that only 23% of GpSGHV genes displayed moderate homologies to genes from other invertebrate viruses, principally baculoviruses and entomopoxviruses. Most strikingly, the GpSGHV genome encodes homologues to the four baculoviral per os infectivity factors (p74 [pif-0], pif-1, pif-2, and pif-3). The DNA polymerase encoded by GpSGHV is of type B and appears to be phylogenetically distant from all DNA polymerases encoded by large double-stranded DNA viruses. The majority of the remaining ORFs could not be assigned by sequence comparison. Furthermore, no homologues to DNA-dependent RNA polymerase subunits were detected. Taken together, these data indicate that GpSGHV is the prototype member of a novel group of insect viruses.

scholarly journals Characterization of Lactococcus lactis Phage 949 and Comparison with Other Lactococcal Phages

2010 ◽  
Vol 76 (20) ◽  
pp. 6843-6852 ◽  
Author(s):  
Julie E. Samson ◽  
Sylvain Moineau
Keyword(s):  
Lactococcus Lactis ◽  
Defense Mechanisms ◽  
Gc Content ◽  
Tail Length ◽  
Open Reading Frames ◽  
Phage Group ◽  
Double Stranded Dna ◽  
Group I ◽  
Sds Page ◽  
Genetic Clusters

ABSTRACT The virulent Lactococcus lactis phage 949 was isolated in 1975 from cheese whey in New Zealand. This phage is a member of the Siphoviridae family and of a rare lactococcal phage group that bears its name (949 group). It has an icosahedral capsid (79-nm diameter) and a very long noncontractile tail (length, 500 nm; width, 12 nm). It infected 7 of 59 tested L. lactis strains, a somewhat expanded host range for a rare lactococcal phage. The abortive phage infection defense mechanisms AbiQ and AbiT strongly inhibited the multiplication of phage 949, but AbiK and AbiV did not. Its double-stranded DNA (dsDNA) genome of 114,768 bp is, to date, the largest among lactococcal phages. Its GC content was calculated at 32.7%, which is the lowest reported for a lactococcal phage. Its 154 open reading frames (ORFs) share limited identity with database sequences. In addition, terminal redundancy was observed as well as the presence of six tRNAs, one group I intron, and putative recombinases. SDS-PAGE coupled with mass spectrometry identified 13 structural proteins. The genomes of the members of the 10 currently known L. lactis phage groups were used to construct a proteomic tree. Each L. lactis phage group separated into distinct genetic clusters, validating the current classification scheme. Of note, members of the polythetic P335 groups were clearly separated into subgroups.

scholarly journals Genomic Sequence of Spodoptera frugiperda Ascovirus 1a, an Enveloped, Double-Stranded DNA Insect Virus That Manipulates Apoptosis for Viral Reproduction

2006 ◽  
Vol 80 (23) ◽  
pp. 11791-11805 ◽  
Author(s):  
Dennis K. Bideshi ◽  
Marie-Véronique Demattei ◽  
Florence Rouleux-Bonnin ◽  
Karine Stasiak ◽  
Yeping Tan ◽  
...  
Keyword(s):  
Spodoptera Frugiperda ◽  
Genomic Sequence ◽  
Open Reading Frames ◽  
The Novel ◽  
Fatty Acid Elongase ◽  
Dna Viruses ◽  
Origin And Evolution ◽  
Iridescent Virus ◽  
Double Stranded Dna ◽  
New Hosts

ABSTRACT Ascoviruses (family Ascoviridae) are double-stranded DNA viruses with circular genomes that attack lepidopterans, where they produce large, enveloped virions, 150 by 400 nm, and cause a chronic, fatal disease with a cytopathology resembling that of apoptosis. After infection, host cell DNA is degraded, the nucleus fragments, and the cell then cleaves into large virion-containing vesicles. These vesicles and virions circulate in the hemolymph, where they are acquired by parasitic wasps during oviposition and subsequently transmitted to new hosts. To develop a better understanding of ascovirus biology, we sequenced the genome of the type species Spodoptera frugiperda ascovirus 1a (SfAV-1a). The genome consisted of 156,922 bp, with a G+C ratio of 49.2%, and contained 123 putative open reading frames coding for a variety of enzymes and virion structural proteins, of which tentative functions were assigned to 44. Among the most interesting enzymes, due to their potential role in apoptosis and viral vesicle formation, were a caspase, a cathepsin B, several kinases, E3 ubiquitin ligases, and especially several enzymes involved in lipid metabolism, including a fatty acid elongase, a sphingomyelinase, a phosphate acyltransferase, and a patatin-like phospholipase. Comparison of SfAV-1a proteins with those of other viruses showed that 10% were orthologs of Chilo iridescent virus proteins, the highest correspondence with any virus, providing further evidence that ascoviruses evolved from a lepidopteran iridovirus. The SfAV-1a genome sequence will facilitate the determination of how ascoviruses manipulate apoptosis to generate the novel virion-containing vesicles characteristic of these viruses and enable study of their origin and evolution.

scholarly journals Complete Genome Analysis of a Novel Alcaligenes Faecalis Phage vB_Af_QDWS595

2021 ◽  
Author(s):  
Yujie Jing ◽  
Hong Lin ◽  
Houqi Ning ◽  
Jingxue Wang
Keyword(s):  
Genome Analysis ◽  
Gc Content ◽  
Alcaligenes Faecalis ◽  
Open Reading Frames ◽  
Lytic Phage ◽  
Double Stranded Dna ◽  
Phylogeny Analysis ◽  
The Family ◽  
Complete Genome Analysis ◽  
Reading Frames

Abstract A novel lytic phage named vB_Af_QDWS595 against Alcaligenes faecalis was isolated and characterized in this study. The genome of phage vB_Af_QDWS595 was sequenced and analyzed, and the result revealed that the phage contained a 88,795 bp of circular double-stranded DNA with 41.12% of GC content. There were 74 putative open reading frames (ORFs) and 11 tRNAs predicted in genome of phage vB_Af_QDWS595. Phenotype and phylogeny analysis indicated that this phage might be a new member within the family Schitoviridae. Phage vB_Af_QDWS595 is the first sequenced phage against Alcaligenes faecalis to the best of our knowledge.

scholarly journals Genome Analysis of a Novel Clade II.b Alphabaculovirus Obtained from Artaxa digramma

Viruses ◽  
2019 ◽  
Vol 11 (10) ◽  
pp. 925 ◽  
Author(s):  
Jiang Li ◽  
Xiaoyan Duan ◽  
Qianran Wang ◽  
Lei Zhang ◽  
Fei Deng ◽  
...  
Keyword(s):  
Southern China ◽  
Phylogenetic Analyses ◽  
Open Reading Frames ◽  
Whole Genome ◽  
Viral Pathogen ◽  
Double Stranded Dna ◽  
Apoptosis Protein ◽  
Conserved Genes ◽  
Lepidopteran Pest ◽  
Core Genes

Artaxa digramma is a lepidopteran pest distributed throughout southern China, Myanmar, Indonesia, and India. Artaxa digramma nucleopolyhedrovirus (ArdiNPV) is a specific viral pathogen of A. digramma and deemed as a promising biocontrol agent against the pest. In this study, the complete genome sequence of ArdiNPV was determined by deep sequencing. The genome of ArdiNPV contains a double-stranded DNA (dsDNA) of 161,734 bp in length and 39.1% G+C content. Further, 149 hypothetical open reading frames (ORFs) were predicted to encode proteins >50 amino acids in length, covering 83% of the whole genome. Among these ORFs, 38 were baculovirus core genes, 22 were lepidopteran baculovirus conserved genes, and seven were unique to ArdiNPV, respectively. No typical baculoviral homologous regions (hrs) were identified in the genome. ArdiNPV had five multi-copy genes including baculovirus repeated ORFs (bros), calcium/sodium antiporter B (chaB), DNA binding protein (dbp), inhibitor of apoptosis protein (iap), and p26. Interestingly, phylogenetic analyses showed that ArdiNPV belonged to Clade II.b of Group II Alphabaculoviruses, which all contain a second copy of dbp. The genome of ArdiNPV was the closest to Euproctis pseudoconspersa nucleopolyhedrovirus, with 57.4% whole-genome similarity. Therefore, these results suggest that ArdiNPV is a novel baculovirus belonging to a newly identified cluster of Clade II.b Alphabaculoviruses.

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