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Comparative genomics of carp herpesviruses

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Comparative genomics of carp herpesviruses. / Davison, Andrew J.; Kurobe, Tomofumi; Gatherer, Derek et al.

In: Journal of Virology, Vol. 87, No. 5, 03.2013, p. 2908-2922.

Research output: Contribution to Journal/MagazineJournal articlepeer-review

Harvard

Davison, AJ, Kurobe, T, Gatherer, D, Cunningham, C, Korf, I, Fukuda, H, Hedrick, RP & Waltzek, TB 2013, 'Comparative genomics of carp herpesviruses', Journal of Virology, vol. 87, no. 5, pp. 2908-2922. https://doi.org/10.1128/JVI.03206-12

APA

Davison, A. J., Kurobe, T., Gatherer, D., Cunningham, C., Korf, I., Fukuda, H., Hedrick, R. P., & Waltzek, T. B. (2013). Comparative genomics of carp herpesviruses. Journal of Virology, 87(5), 2908-2922. https://doi.org/10.1128/JVI.03206-12

Vancouver

Davison AJ, Kurobe T, Gatherer D, Cunningham C, Korf I, Fukuda H et al. Comparative genomics of carp herpesviruses. Journal of Virology. 2013 Mar;87(5):2908-2922. doi: 10.1128/JVI.03206-12

Author

Davison, Andrew J. ; Kurobe, Tomofumi ; Gatherer, Derek et al. / Comparative genomics of carp herpesviruses. In: Journal of Virology. 2013 ; Vol. 87, No. 5. pp. 2908-2922.

Bibtex

@article{1d3e931217aa454dbdc0b5df20025827,
title = "Comparative genomics of carp herpesviruses",
abstract = "Three alloherpesviruses are known to cause disease in cyprinid fish: cyprinid herpesviruses 1 and 3 (CyHV1 and CyHV3) in common carp and koi and cyprinid herpesvirus 2 (CyHV2) in goldfish. We have determined the genome sequences of CyHV1 and CyHV2 and compared them with the published CyHV3 sequence. The CyHV1 and CyHV2 genomes are 291,144 and 290,304 bp, respectively, in size, and thus the CyHV3 genome, at 295,146 bp, remains the largest recorded among the herpesviruses. Each of the three genomes consists of a unique region flanked at each terminus by a sizeable direct repeat. The CyHV1, CyHV2, and CyHV3 genomes are predicted to contain 137, 150, and 155 unique, functional protein-coding genes, respectively, of which six, four, and eight, respectively, are duplicated in the terminal repeat. The three viruses share 120 orthologous genes in a largely colinear arrangement, of which up to 55 are also conserved in the other member of the genus Cyprinivirus, anguillid herpesvirus 1. Twelve genes are conserved convincingly in all sequenced alloherpesviruses, and two others are conserved marginally. The reference CyHV3 strain has been reported to contain five fragmented genes that are presumably nonfunctional. The CyHV2 strain has two fragmented genes, and the CyHV1 strain has none. CyHV1, CyHV2, and CyHV3 have five, six, and five families of paralogous genes, respectively. One family unique to CyHV1 is related to cellular JUNB, which encodes a transcription factor involved in oncogenesis. To our knowledge, this is the first time that JUNB-related sequences have been reported in a herpesvirus.",
keywords = "Amino Acid Sequence, Animals, Base Sequence, Carps, DNA, Viral, Fish Diseases, Genome, Viral, Genomics, Herpesviridae, Herpesviridae Infections, Molecular Sequence Data, Open Reading Frames, Sequence Alignment, Sequence Analysis, DNA, Viral Proteins",
author = "Davison, {Andrew J.} and Tomofumi Kurobe and Derek Gatherer and Charles Cunningham and Ian Korf and Hideo Fukuda and Hedrick, {Ronald P} and Waltzek, {Thomas B}",
year = "2013",
month = mar,
doi = "10.1128/JVI.03206-12",
language = "English",
volume = "87",
pages = "2908--2922",
journal = "Journal of Virology",
issn = "0022-538X",
publisher = "American Society for Microbiology",
number = "5",

}

RIS

TY - JOUR

T1 - Comparative genomics of carp herpesviruses

AU - Davison, Andrew J.

AU - Kurobe, Tomofumi

AU - Gatherer, Derek

AU - Cunningham, Charles

AU - Korf, Ian

AU - Fukuda, Hideo

AU - Hedrick, Ronald P

AU - Waltzek, Thomas B

PY - 2013/3

Y1 - 2013/3

N2 - Three alloherpesviruses are known to cause disease in cyprinid fish: cyprinid herpesviruses 1 and 3 (CyHV1 and CyHV3) in common carp and koi and cyprinid herpesvirus 2 (CyHV2) in goldfish. We have determined the genome sequences of CyHV1 and CyHV2 and compared them with the published CyHV3 sequence. The CyHV1 and CyHV2 genomes are 291,144 and 290,304 bp, respectively, in size, and thus the CyHV3 genome, at 295,146 bp, remains the largest recorded among the herpesviruses. Each of the three genomes consists of a unique region flanked at each terminus by a sizeable direct repeat. The CyHV1, CyHV2, and CyHV3 genomes are predicted to contain 137, 150, and 155 unique, functional protein-coding genes, respectively, of which six, four, and eight, respectively, are duplicated in the terminal repeat. The three viruses share 120 orthologous genes in a largely colinear arrangement, of which up to 55 are also conserved in the other member of the genus Cyprinivirus, anguillid herpesvirus 1. Twelve genes are conserved convincingly in all sequenced alloherpesviruses, and two others are conserved marginally. The reference CyHV3 strain has been reported to contain five fragmented genes that are presumably nonfunctional. The CyHV2 strain has two fragmented genes, and the CyHV1 strain has none. CyHV1, CyHV2, and CyHV3 have five, six, and five families of paralogous genes, respectively. One family unique to CyHV1 is related to cellular JUNB, which encodes a transcription factor involved in oncogenesis. To our knowledge, this is the first time that JUNB-related sequences have been reported in a herpesvirus.

AB - Three alloherpesviruses are known to cause disease in cyprinid fish: cyprinid herpesviruses 1 and 3 (CyHV1 and CyHV3) in common carp and koi and cyprinid herpesvirus 2 (CyHV2) in goldfish. We have determined the genome sequences of CyHV1 and CyHV2 and compared them with the published CyHV3 sequence. The CyHV1 and CyHV2 genomes are 291,144 and 290,304 bp, respectively, in size, and thus the CyHV3 genome, at 295,146 bp, remains the largest recorded among the herpesviruses. Each of the three genomes consists of a unique region flanked at each terminus by a sizeable direct repeat. The CyHV1, CyHV2, and CyHV3 genomes are predicted to contain 137, 150, and 155 unique, functional protein-coding genes, respectively, of which six, four, and eight, respectively, are duplicated in the terminal repeat. The three viruses share 120 orthologous genes in a largely colinear arrangement, of which up to 55 are also conserved in the other member of the genus Cyprinivirus, anguillid herpesvirus 1. Twelve genes are conserved convincingly in all sequenced alloherpesviruses, and two others are conserved marginally. The reference CyHV3 strain has been reported to contain five fragmented genes that are presumably nonfunctional. The CyHV2 strain has two fragmented genes, and the CyHV1 strain has none. CyHV1, CyHV2, and CyHV3 have five, six, and five families of paralogous genes, respectively. One family unique to CyHV1 is related to cellular JUNB, which encodes a transcription factor involved in oncogenesis. To our knowledge, this is the first time that JUNB-related sequences have been reported in a herpesvirus.

KW - Amino Acid Sequence

KW - Animals

KW - Base Sequence

KW - Carps

KW - DNA, Viral

KW - Fish Diseases

KW - Genome, Viral

KW - Genomics

KW - Herpesviridae

KW - Herpesviridae Infections

KW - Molecular Sequence Data

KW - Open Reading Frames

KW - Sequence Alignment

KW - Sequence Analysis, DNA

KW - Viral Proteins

U2 - 10.1128/JVI.03206-12

DO - 10.1128/JVI.03206-12

M3 - Journal article

C2 - 23269803

VL - 87

SP - 2908

EP - 2922

JO - Journal of Virology

JF - Journal of Virology

SN - 0022-538X

IS - 5

ER -