Faculty Opinions recommendation of Evaluation of annotation strategies using an entire genome sequence.

ABSTRACT Bovine herpesvirus 4 (BoHV-4) is a gammaherpesvirus of cattle. The complete long unique coding region (LUR) of BoHV-4 strain 66-p-347 was determined by a shotgun approach. Together with the previously published noncoding terminal repeats, the entire genome sequence of BoHV-4 is now available. The LUR consists of 108,873 bp with an overall G+C content of 41.4%. At least 79 open reading frames (ORFs) are present in this coding region, 17 of them unique to BoHV-4. In contrast to herpesvirus saimiri and human herpesvirus 8, BoHV-4 has a reduced set of ORFs homologous to cellular genes. Gene arrangement as well as phylogenetic analysis confirmed that BoHV-4 is a member of the genusRhadinovirus. In addition, an origin of replication (ori) in the genome of BoHV-4 was identified byDpnI assays. A minimum of 1.69 kbp located between ORFs 69 and 71 was sufficient to act as a cis signal for replication.

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Genome Sequence of a Spodoptera frugiperda Multiple Nucleopolyhedrovirus Isolated from Fall Armyworm (Spodoptera frugiperda) in Nigeria, West Africa

Microbiology Resource Announcements ◽

10.1128/mra.00565-21 ◽

2021 ◽

Vol 10 (34) ◽

Author(s):

Jörg T. Wennmann ◽

Ghislain T. Tepa-Yotto ◽

Johannes A. Jehle ◽

Georg Goergen

Keyword(s):

West Africa ◽

Genome Sequence ◽

Spodoptera Frugiperda ◽

Gc Content ◽

Fall Armyworm ◽

Open Reading Frames ◽

Entire Genome ◽

Content Type ◽

Entire Genome Sequence ◽

Multiple Nucleopolyhedrovirus

We report the entire genome sequence of an isolate of Spodoptera frugiperda multiple nucleopolyhedrovirus from Nigeria, West Africa. The genome is 132,710 bp long and contains 144 open reading frames. The GC content is 40.3% and, based on baculovirus species demarcation criteria, the isolate belongs to the species Spodoptera frugiperda multiple nucleopolyhedrovirus .

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Evaluation of annotation strategies using an entire genome sequence

Bioinformatics ◽

10.1093/bioinformatics/btg077 ◽

2003 ◽

Vol 19 (6) ◽

pp. 717-726 ◽

Cited By ~ 43

Author(s):

I. Iliopoulos ◽

S. Tsoka ◽

M. A. Andrade ◽

A. J. Enright ◽

M. Carroll ◽

...

Keyword(s):

Genome Sequence ◽

Entire Genome ◽

Entire Genome Sequence

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Nucleotide sequences of the trailer, nucleocapsid protein gene and intergenic regions of Newcastle disease virus strain Beaudette C and completion of the entire genome sequence.

Journal of General Virology ◽

10.1099/0022-1317-79-10-2419 ◽

1998 ◽

Vol 79 (10) ◽

pp. 2419-2424 ◽

Cited By ~ 107

Author(s):

S Krishnamurthy ◽

S K Samal

Keyword(s):

Newcastle Disease Virus ◽

Disease Virus ◽

Virus Strain ◽

Newcastle Disease ◽

Nucleocapsid Protein ◽

Protein Gene ◽

Entire Genome ◽

Entire Genome Sequence ◽

Intergenic Regions ◽

Nucleocapsid Protein Gene

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De novo whole-genome assembly in interspecific hybrid table grape, ‘Shine Muscat’

10.1101/730762 ◽

2019 ◽

Cited By ~ 2

Author(s):

Kenta Shirasawa ◽

Akifumi Azuma ◽

Fumiya Taniguchi ◽

Toshiya Yamamoto ◽

Akihiko Sato ◽

...

Keyword(s):

Genome Sequence ◽

Genome Assembly ◽

De Novo ◽

Sequence Data ◽

Genome Structure ◽

Table Grape ◽

Sequencing Analysis ◽

Entire Genome ◽

Table Grapes ◽

Eukaryotic Genes

AbstractThis study presents the first genome sequence of an interspecific grape hybrid, ‘Shine Muscat’ (Vitis labruscana × V. vinifera), an elite table grape cultivar bred in Japan. The complexity of the genome structure, arising from the interspecific hybridization, necessitated the use of a sophisticated genome assembly pipeline with short-read genome sequence data. The resultant genome assemblies consisted of two types of sequences: a haplotype-phased sequence of the highly heterozygous genomes and an unphased sequence representing a “haploid” genome. The unphased sequences spanned 490.1 Mb in length, 99.4% of the estimated genome size, with 8,696 scaffold sequences with an N50 length of 13.2 Mb. The phased sequences had 15,650 scaffolds spanning 1.0 Gb with N50 of 4.2 Mb. The two sequences comprised 94.7% and 96.3% of the core eukaryotic genes, indicating that the entire genome of ‘Shine Muscat’ was represented. Examination of genome structures revealed possible genome rearrangements between the genomes of ‘Shine Muscat’ and a V. vinifera line. Furthermore, full-length transcriptome sequencing analysis revealed 13,947 gene loci on the ‘Shine Muscat’ genome, from which 26,199 transcript isoforms were transcribed. These genome resources provide new insights that could help cultivation and breeding strategies produce more high-quality table grapes such as ‘Shine Muscat’.

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Characterization of a Novel Alphaherpesvirus Isolated from the Fruit Bat Pteropus lylei in Vietnam

Journal of Virology ◽

10.1128/jvi.00673-20 ◽

2020 ◽

Vol 94 (18) ◽

Author(s):

Takuya Inagaki ◽

Souichi Yamada ◽

Hikaru Fujii ◽

Tomoki Yoshikawa ◽

Miho Shibamura ◽

...

Keyword(s):

Genome Sequence ◽

Lung Fibroblasts ◽

Whole Genome Sequence ◽

Replication Capacity ◽

Human Embryonic Lung ◽

Host Animal ◽

Entire Genome ◽

Fruit Bat ◽

Hsv 1

ABSTRACT Herpesviruses exist in nature within each host animal. Ten herpesviruses have been isolated from bats and their biological properties reported. A novel bat alphaherpesvirus, which we propose to name “Pteropus lylei-associated alphaherpesvirus (PLAHV),” was isolated from urine of the fruit bat Pteropus lylei in Vietnam and characterized. The entire genome sequence was determined to be 144,008 bp in length and predicted to include 72 genes. PLAHV was assigned to genus Simplexvirus with other bat alphaherpesviruses isolated from pteropodid bats in Southeast Asia and Africa. The replication capacity of PLAHV in several cells was evaluated in comparison with that of herpes simplex virus 1 (HSV-1). PLAHV replicated better in the bat-originated cell line and less in human embryonic lung fibroblasts than HSV-1 did. PLAHV was serologically related to another bat alphaherpesvirus, Pteropodid alphaherpesvirus 1 (PtAHV1), isolated from a Pteropus hypomelanus-related bat captured in Indonesia, but not with HSV-1. PLAHV caused lethal infection in mice. PLAHV was as susceptible to acyclovir as HSV-1 was. Characterization of this new member of bat alphaherpesviruses, PLAHV, expands the knowledge on bat-associated alphaherpesvirology. IMPORTANCE A novel bat alphaherpesvirus, Pteropus lylei-associated alphaherpesvirus (PLAHV), was isolated from urine of the fruit bat Pteropus lylei in Vietnam. The whole-genome sequence was determined and was predicted to include 72 open reading frames in the 144,008-bp genome. PLAHV is circulating in a species of fruit bats, Pteropus lylei, in Asia. This study expands the knowledge on bat-associated alphaherpesvirology.

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Characterization of a Novel Simian Sapelovirus Isolated from a Cynomolgus Monkey using PLC/PRF/5 Cells

Scientific Reports ◽

10.1038/s41598-019-56725-z ◽

2019 ◽

Vol 9 (1) ◽

Cited By ~ 2

Author(s):

Wenjing Zhang ◽

Michiyo Kataoka ◽

Hai Yen Doan ◽

Yasushi Ami ◽

Yuriko Suzaki ◽

...

Keyword(s):

Cynomolgus Monkey ◽

Untranslated Region ◽

Monkey Kidney ◽

Kidney Cells ◽

Serum Samples ◽

Entire Genome ◽

Reading Frame ◽

Entire Genome Sequence ◽

Virus Particles ◽

New Genotype

AbstractWe isolated a novel simian sapelovirus (SSV), Cam13, from fecal specimen of a cynomolgus monkey by using PLC/PRF/5 cells. The SSV infection of the cells induced an extensive cytopathic effect. Two types of virus particles with identical diameter (~32 nm) but different densities (1.348 g/cm3 and 1.295 g/cm3) were observed in the cell culture supernatants. The RNA genome of Cam13 possesses 8,155 nucleotides and a poly(A) tail, and it has a typical sapelovirus genome organization consisting of a 5’ terminal untranslated region, a large open reading frame (ORF), and a 3’ terminal untranslated region. The ORF encodes a single polyprotein that is subsequently processed into a leader protein (L), four structural proteins (VP1, VP2, VP3, and VP4) and seven functional proteins (2A, 2B, 2C, 3A, 3B, 3C, and 3D). We confirmed that 293 T, HepG2/C3A, Hep2C, Huh7 and primary cynomolgus monkey kidney cells were susceptible to SSV infection. In contrast, PK-15, Vero, Vero E6, RD-A, A549, and primary green monkey kidney cells were not susceptible to SSV infection. We established an ELISA for the detection of IgG antibodies against SSV by using the virus particles as the antigen. A total of 327 serum samples from cynomolgus monkeys and 61 serum samples from Japanese monkeys were examined, and the positive rates were 88.4% and 18%, respectively. These results demonstrated that SSV infection occurred frequently in the monkeys. Since Cam13 shared 76.54%–79.52% nucleotide sequence identities with other known SSVs, and constellated in a separate lineage in the phylogeny based on the entire genome sequence, we propose that Cam13 is a new genotype of the simian sapelovirus species.

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Hepatitis E virus infection in 6-month-old pigs in Taiwan

Scientific Reports ◽

10.1038/s41598-020-74034-8 ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Ming-Hui Liao ◽

Fang-Tzy Wu ◽

Huimin Bai ◽

Yen Hai Doan ◽

Jyh-Yuan Yang ◽

...

Keyword(s):

Hepatitis E Virus ◽

Phylogenetic Analyses ◽

Hepatitis E ◽

Limited Information ◽

Genotype 3 ◽

Entire Genome ◽

Entire Genome Sequence ◽

Detection Frequency ◽

Pig Farms ◽

Acute Hepatitis E

Abstract Hepatitis E virus (HEV) is the causative agent of acute hepatitis E. Genotype 3 (G3) and 4 (G4) HEV have recently been identified in and isolated from swine as the main HEV genotypes worldwide. However, there is limited information on HEV infection status among pigs in Taiwan, especially pigs in the stage before transportation to the slaughterhouse. To determine the frequency of HEV infection among pigs in Taiwan, we detected and quantified HEV RNA contained in 295 fecal specimens collected from 6-month-old pigs bred in 30 pig farms located in 8 counties. We found that 25.1% (74/295) of the fecal specimens were positive for HEV RNA by a quantitative real-time reverse transcription-polymerase chain reaction, and the copy number ranged from 2.3 × 103 to 2.08 × 107 copies/g. Amplification of a 338 bp sequence in ORF2 was achieved in 16 of 74 HEV RNA-positive samples, and their nucleotide sequences were determined. Two HEV sequences appeared to belong to subtype 3a of G3 and the remaining 14 HEV sequences belonged to subtype 4b of G4 (G4b). The entire genome sequence of two G4b HEVs was obtained by next-generation sequence analyses, and the phylogenetic analyses indicated that unique G4b HEVs were circulating in pig farms in Taiwan. In the present study, we found that both G3 and G4 HEVs were circulating in Taiwanese pig farms and G4b was the predominant subtype. In addition, the relatively high detection frequency of HEV RNA in the 6-month-old pigs indicated that Taiwanese pigs just before transportation to the slaughterhouse are at risk of carrying HEVs, and thus thorough cooking or heating of pork meat or organs is needed before consumption in Taiwan and possibly in other countries as well.

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