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.

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 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 Sequence Analysis of the Genome of the Neodiprion sertifer Nucleopolyhedrovirus

2004 ◽  
Vol 78 (13) ◽  
pp. 7036-7051 ◽  
Author(s):  
Alejandra Garcia-Maruniak ◽  
James E. Maruniak ◽  
Paolo M. A. Zanotto ◽  
Aissa E. Doumbouya ◽  
Jaw-Ching Liu ◽  
...  
Keyword(s):  
Ring Finger ◽  
Open Reading Frames ◽  
Neodiprion Sertifer ◽  
Pine Sawfly ◽  
Culex Nigripalpus ◽  
Conserved Genes ◽  
European Pine Sawfly ◽  
Conserved Core ◽  
Reading Frames ◽  
Core Genes

ABSTRACT The genome of the Neodiprion sertifer nucleopolyhedrovirus (NeseNPV), which infects the European pine sawfly, N. sertifer (Hymenoptera: Diprionidae), was sequenced and analyzed. The genome was 86,462 bp in size. The C+G content of 34% was lower than that of the majority of baculoviruses. A total of 90 methionine-initiated open reading frames (ORFs) with more than 50 amino acids and minimal overlapping were found. From those, 43 ORFs were homologous to other baculovirus ORFs, and 29 of these were from the 30 conserved core genes among all baculoviruses. A NeseNPV homolog to the ld130 gene, which is present in all other baculovirus genomes sequenced to date, could not be identified. Six NeseNPV ORFs were similar to non-baculovirus-related genes, one of which was a trypsin-like gene. Only one iap gene, containing a single BIR motif and a RING finger, was found in NeseNPV. Two NeseNPV ORFs (nese18 and nese19) were duplicates transcribed in opposite orientations from each other. NeseNPV did not have an AcMNPV ORF 2 homolog characterized as the baculovirus repeat ORF (bro). Six homologous regions (hrs) were located within the NeseNPV genome, each containing small palindromes embedded within direct repeats. A phylogenetic analysis was done to root the tree based upon the sequences of DNA polymerase genes of NeseNPV, 23 other baculoviruses, and other phyla. Baculovirus phylogeny was then constructed with 29 conserved genes from 24 baculovirus genomes. Culex nigripalpus nucleopolyhedrovirus (CuniNPV) was the most distantly related baculovirus, branching to the hymenopteran NeseNPV and the lepidopteran nucleopolyhedroviruses and granuloviruses.

scholarly journals Baculovirus: Molecular Insights on Their Diversity and Conservation

2011 ◽  
Vol 2011 ◽  
pp. 1-15 ◽  
Author(s):  
Solange Ana Belen Miele ◽  
Matías Javier Garavaglia ◽  
Mariano Nicolás Belaich ◽  
Pablo Daniel Ghiringhelli
Keyword(s):  
Phylogenetic Analyses ◽  
Core Gene ◽  
Gene Sequences ◽  
Genome Sequences ◽  
Coding Sequences ◽  
Large Group ◽  
Double Stranded Dna ◽  
Core Genes ◽  
Insect Viruses

The Baculoviridae is a large group of insect viruses containing circular double-stranded DNA genomes of 80 to 180 kbp. In this study, genome sequences from 57 baculoviruses were analyzed to reevaluate the number and identity of core genes and to understand the distribution of the remaining coding sequences. Thirty one core genes with orthologs in all genomes were identified along with other 895 genes differing in their degrees of representation among reported genomes. Many of these latter genes are common to well-defined lineages, whereas others are unique to one or a few of the viruses. Phylogenetic analyses based on core gene sequences and the gene composition of the genomes supported the current division of the Baculoviridae into 4 genera: Alphabaculovirus, Betabaculovirus, Gammabaculovirus, and Deltabaculovirus.

scholarly journals Whole genome analysis of the Epiphyas postvittana nucleopolyhedrovirus

2002 ◽  
Vol 83 (4) ◽  
pp. 957-971 ◽  
Author(s):  
Otto Hyink ◽  
Ross A. Dellow ◽  
Michael J. Olsen ◽  
Katherine M. B. Caradoc-Davies ◽  
Kylie Drake ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Open Reading Frames ◽  
Data Sets ◽  
Epiphyas Postvittana ◽  
Whole Genome ◽  
Whole Genome Analysis ◽  
Orgyia Pseudotsugata ◽  
Group I ◽  
Intergenic Regions ◽  
Reading Frames

The nucleotide sequence of the Epiphyas postvittana nucleopolyhedrovirus (EppoMNPV) genome has been determined and analysed. The circular dsDNA genome contains 118584 bp, making it the smallest group I NPV sequenced to date. The genome has a G+C content of 40·7% and encodes 136 predicted open reading frames (ORFs), five homologous repeat regions and one unique repeat region. Of the genome, 92·9% encodes predicted ORFs and 2·2% is in repeat regions; the remaining 4·9% of the genome comprises nonrepeat intergenic regions. EppoMNPV encodes homologues of 126 Orgyia pseudotsugata MNPV (OpMNPV) ORFs and 120 Autographa californica MNPV ORFs, with average identities of 64·7 and 53·5%, respectively. Between the four sequenced group I NPVs, 117 ORFs are conserved, whereas 86 ORFs are conserved between all fully sequenced NPVs. A total of 62 ORFs is present in all baculoviruses sequenced to date, with EppoMNPV lacking a homologue of the superoxide dismutase (sod) gene, which has been found in all other fully sequenced baculoviruses. Whole genome phylogenetic analyses of the ten fully sequenced baculoviruses using the sequences of the 62 shared genes, gene content and gene order data sets confirmed that EppoMNPV clusters tightly with OpMNPV in the group I NPVs. The main variation between EppoMNPV and OpMNPV occurs where extra clusters of genes are present in OpMNPV, with sod occurring in one such cluster. EppoMNPV encodes one truncated baculovirus repeated ORF (bro) gene. The only repeated ORFs are the four iap genes. Eight, randomly distributed, unique ORFs were identified on EppoMNPV, none of which show any significant homology to genes in GenBank.

scholarly journals Molecular Epidemiology and Whole-Genome Analysis of Bovine Foamy Virus in Japan

Viruses ◽  
2021 ◽  
Vol 13 (6) ◽  
pp. 1017
Author(s):  
Hirohisa Mekata ◽  
Tomohiro Okagawa ◽  
Satoru Konnai ◽  
Takayuki Miyazawa
Keyword(s):  
Phylogenetic Analyses ◽  
Foamy Virus ◽  
Pcr Analysis ◽  
Whole Genome ◽  
Genome Sequences ◽  
Whole Genome Analysis ◽  
Virus Family ◽  
Bovine Foamy Virus ◽  
Novel Genotype

Bovine foamy virus (BFV) is a member of the foamy virus family in cattle. Information on the epidemiology, transmission routes, and whole-genome sequences of BFV is still limited. To understand the characteristics of BFV, this study included a molecular survey in Japan and the determination of the whole-genome sequences of 30 BFV isolates. A total of 30 (3.4%, 30/884) cattle were infected with BFV according to PCR analysis. Cattle less than 48 months old were scarcely infected with this virus, and older animals had a significantly higher rate of infection. To reveal the possibility of vertical transmission, we additionally surveyed 77 pairs of dams and 3-month-old calves in a farm already confirmed to have BFV. We confirmed that one of the calves born from a dam with BFV was infected. Phylogenetic analyses revealed that a novel genotype was spread in Japan. In conclusion, the prevalence of BFV in Japan is relatively low and three genotypes, including a novel genotype, are spread in Japan.

scholarly journals Expanding the Diversity of the IS630-Tc1-mariner Superfamily: Discovery of a Unique DD37E Transposon and Reclassification of the DD37D and DD39D Transposons

Genetics ◽  
2001 ◽  
Vol 159 (3) ◽  
pp. 1103-1115 ◽  
Author(s):  
Hongguang Shao ◽  
Zhijian Tu
Keyword(s):  
Phylogenetic Analyses ◽  
Mosquito Species ◽  
Open Reading Frames ◽  
Inverted Repeats ◽  
Sequence Comparisons ◽  
Wide Range ◽  
Multiple Copies ◽  
Catalytic Motif ◽  
Open The Doors ◽  
Reading Frames

Abstract A novel transposon named ITmD37E was discovered in a wide range of mosquito species. Sequence analysis of multiple copies in three Aedes species showed similar terminal inverted repeats and common putative TA target site duplications. The ITmD37E transposases contain a conserved DD37E catalytic motif, which is unique among reported transposons of the IS630-Tc1-mariner superfamily. Sequence comparisons and phylogenetic analyses suggest that ITmD37E forms a novel family distinct from the widely distributed Tc1 (DD34E), mariner (DD34D), and pogo (DDxD) families in the IS630-Tc1-mariner superfamily. The inclusion in the phylogenetic analysis of recently reported transposons and transposons uncovered in our database survey provided revisions to previous classifications and identified two additional families, ITmD37D and ITmD39D, which contain DD37D and DD39D motifs, respectively. The above expansion and reorganization may open the doors to the discovery of related transposons in a broad range of organisms and help illustrate the evolution and structure-function relationships among these distinct transposases in the IS630-Tc1-mariner superfamily. The presence of intact open reading frames and highly similar copies in some of the newly characterized transposons suggests recent transposition. Studies of these novel families may add to the limited repertoire of transgenesis and mutagenesis tools for a wide range of organisms, including the medically important mosquitoes.

scholarly journals Redescription of Paradiplozoon hemiculteri (Monogenea, Diplozoidae) from the type host Hemiculter leucisculus, with neotype designation

Parasite ◽  
2018 ◽  
Vol 25 ◽  
pp. 4 ◽  
Author(s):  
Dagmar Jirsová ◽  
Xuejuan Ding ◽  
Kristína Civáňová ◽  
Eliška Jirounková ◽  
Jana Ilgová ◽  
...  
Keyword(s):  
Southern China ◽  
Phylogenetic Analyses ◽  
Posterior Part ◽  
Original Description ◽  
Molecular Data ◽  
The Body ◽  
Type Host ◽  
Hemiculter Leucisculus ◽  
Morphological And Molecular Data ◽  
Median Plate

Paradiplozoon hemiculteri (Ling, 1973), a member of the Diplozoidae, parasitizes the gills of Asian fish. Not only is the type material unavailable for this species, the original description was poor and somewhat conflicting, and adequate molecular data were not available. What is more, the available morphological and molecular data are inconsistent and fluctuate significantly. Here, we present a redescription of P. hemiculteri based on morphological and molecular data from new isolates collected from the type host, the sharpbelly Hemiculter leucisculus (Basilewsky, 1855), captured at the neotype locality (Shaoguan, Guangdong Province, southern China); a neotype for P. hemiculteri was designated from this collection. The length and width of the body, buccal suckers, pharynx, attachment clamps, sickle and the central hook handle were all measured and the shape of the anterior and posterior part of the median plate and anterior and posterior joining sclerites accurately documented. Phylogenetic analyses based on the sequences of the second rDNA internal transcribed spacer (ITS2) indicated that all new samples clustered together and differed clearly from sequences attributed to P. hemiculteri, which are deposited in GenBank. Our results confirm that P. hemiculteri is the only diplozoid that has demonstrably been found on the gills of H. leucisculus to date.

scholarly journals Reconsideration of the ‘well-known’ hypotrichous ciliate Pleurotricha curdsi (Shi et al., 2002) Gupta et al., 2003 (Ciliophora, Sporadotrichida), with notes on its morphology, morphogenesis and molecular phylogeny

2015 ◽  
Vol 65 (Pt_9) ◽  
pp. 3216-3225 ◽  
Author(s):  
Xiaoteng Lu ◽  
Chen Shao ◽  
Yuhe Yu ◽  
Alan Warren ◽  
Jie Huang
Keyword(s):  
Sequence Data ◽  
Southern China ◽  
Phylogenetic Analyses ◽  
Large Body ◽  
Small Subunit ◽  
Variable Number ◽  
Ssu Rdna ◽  
Intermediate Form ◽  
Rdna Sequence Data

The oxytrichid species Pleurotricha curdsi (Shi et al., 2002) Gupta et al., 2003, isolated from a tributary of the Yangtze River in the Mudong district of Chongqing, southern China, was reinvestigated with emphasis on its morphology, morphogenesis and small-subunit (SSU) rDNA-based phylogeny. Compared with three previously described populations, the Mudong population of P. curdsi is characterized by its large body size, 170–295 × 65–110 μm in vivo, and by having a variable number of right marginal rows, either two or three. Likewise, the number of right marginal rows anlagen (RMA) is also variable, i.e. usually two, but sometimes several small extra anlagen that give rise to the formation of the third row, are present to the left of the RMAs. We posit that the Mudong population is an intermediate form between the three previously described populations. Phylogenetic analyses based on the SSU rDNA sequence data show that all populations of P. curdsi cluster with the type species of the genus, Pleurotricha lanceolata, in a clade nested within the Oxytrichidae.

scholarly journals Evolutionary History of Cucumber Mosaic Virus Deduced by Phylogenetic Analyses

2002 ◽  
Vol 76 (7) ◽  
pp. 3382-3387 ◽  
Author(s):  
Marilyn J. Roossinck
Keyword(s):  
Cucumber Mosaic Virus ◽  
Mosaic Virus ◽  
Virus Isolate ◽  
Phylogenetic Analyses ◽  
Open Reading Frames ◽  
Broad Host Range ◽  
Nontranslated Region ◽  
History Of ◽  
Evolutionary Success ◽  
Reading Frames

ABSTRACT Cucumber mosaic virus (CMV) is an RNA plant virus with a tripartite genome and an extremely broad host range. Previous evolutionary analyses with the coat protein (CP) and 5′ nontranslated region (NTR) of RNA 3 suggested subdivision of the virus into three groups, subgroups IA, IB, and II. In this study 15 strains of CMV whose nucleotide sequences have been determined were used for a complete phylogenetic analysis of the virus. The trees estimated for open reading frames (ORFs) located on the different RNAs were not congruent and did not completely support the subgrouping indicated by the CP ORF, indicating that different RNAs had independent evolutionary histories. This is consistent with a reassortment mechanism playing an important role in the evolution of the virus. The evolutionary trees of the 1a and 3a ORFs were more compact and displayed more branching than did those of the 2a and CP ORFs. This may reflect more rigid host-interactive constraints exerted on the 1a and 3a ORFs. In addition, analysis of the 3′ NTR that is conserved among all RNAs indicated that evolutionary constraints on this region are specific to the RNA component rather than the virus isolate. This indicates that functions other than replication are encoded in the 3′ NTR. Reassortment may have led to the genetic diversity found among CMV strains and contributed to its enormous evolutionary success.

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