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.

Fig 1

CyHV1 genome map. The terminal direct repeat (TR) is shown in a thicker format than the unique region (U). ORFs predicted to encode functional proteins are indicated by colored arrows (see the key at the foot), with nomenclature lacking the ORF prefix given below. Introns are shown as narrow white bars. Colors of protein-coding regions indicate core ORFs that are convincingly conserved among alloherpesviruses, families of related ORFs, and other ORFs. Telomere-like repeats at the ends of TR are shown by gray-shaded blocks. Predicted poly(A) sites are indicated by vertical arrows above and below the genome for rightward- and leftward-oriented ORFs, respectively.

Fig 2

CyHV2 genome map. See the Fig. 1 legend for schematic details. Inverted repeats at approximately 36 and 75 kbp are indicated by light-gray-shaded blocks. Names of fragmented ORFs are given in square brackets, with the ORFs depicted as intact. Pale yellow ORFs downstream from ORF25B and ORF25C represent remnants of additional ORFs in the ORF25 family.

Fig 3

CyHV3 genome map. See the Fig. 1 and 2 legends for schematic details. Updated from reference .

Fig 4

Aligned sequences at the CyHV genome termini. Terminal nucleotides are highlighted in black, conserved residues are in gray, and gaps are indicated by hyphens. The corresponding unaligned AngHV1 sequences are shown below. For each sequence, the ellipsis indicates the remainder of the genome.

Fig 5

Amino acid sequence alignments of selected CyHV proteins. (a) A motif conserved among CyHV ORF47 and its counterparts in other alloherpesviruses and DNA packaging terminase subunit 2 in various human herpesviruses (HHVs), as representatives of the family Herpesviridae (herpes simplex virus type 1 [human herpesvirus 1 {HHV1}], GenBank accession number X14112; varicella-zoster virus [HHV3], GenBank accession number X04370; human herpesvirus 6A [HHV6A], GenBank accession number X83413; Epstein-Barr virus [HHV4], GenBank accession number V01555; Kaposi's sarcoma-associated herpesvirus [HHV8], GenBank accession number U75698). Residues shaded gray are conserved in at least two members of each group, which are separated by a line. (b) A motif conserved in CyHV ORF66 and its counterparts in other alloherpesviruses. Residues shaded gray are conserved among the three CyHVs and at least one other alloherpesvirus. (c) JunB-related sequences encoded by CyHV1. The ORF151B, ORF151C, and ORF151D sequences are shown aligned against the carp JunB sequence (GenBank accession number U81506), and conserved residues (shaded gray) and the DNA-binding and dimerization domains are indicated, with the residues forming the leucine zipper underlined. Initiating methionine residues are shaded in black, C termini are indicated by bull's-eyes, and N- and C-terminal regions that are not shown are denoted by arrowheads. Thus, the alignment includes the entire coding region of the ORF151D protein, the C-terminal regions of carp JunB and the ORF151C protein, and the N-terminal region of the ORF151B protein. An additional short sequence similar to part of JunB is encoded 1 bp upstream from ORF151B in an alternative reading frame and is shown in lowercase type. Residues shaded gray are conserved among at least three sequences.

Fig 6

Relative gene layout in CyHVs. The genomes are shown to scale as horizontal bars with the boundaries of the terminal direct repeat (TR) marked by vertical black lines. Omission of the region from 60 to 180 kbp in each genome is implied by the dotted lines. The positions of ORFs that differ in location or orientation between CyHV1 and CyHV3 or CyHV2 and CyHV3 are indicated by gray shading, with the ORF prefix omitted from names. The situation in the region containing ORF128 to ORF140 is complex because ORF130 and ORF139 are transposed in CyHV2, the former remaining within this region but the latter not remaining (for details, see Fig. 2 and 3).