Genomic Sequence of the Threespine Stickleback Iridovirus (TSIV) from Wild Gasterosteus aculeatus in Stormy Lake, Alaska

Abstract

The threespine stickleback iridovirus (TSIV), a double-stranded DNA virus, was the first megalocytivirus detected in wild North American fishes. We report a second occurrence of TSIV in threespine stickleback (Gasterosteus aculeatus) from Stormy Lake, Alaska, and assemble a nearly complete genome of TSIV. The 115-kilobase TSIV genome contains 94 open reading frames (ORFs), with 91 that share homology with other known iridoviruses. We identify three ORFs that likely originate from recent lateral gene transfers from a eukaryotic host and one ORF with homology to B22 poxvirus proteins that likely originated from a lateral gene transfer between viruses. Phylogenetic analysis of 24 iridovirus core genes and pairwise sequence identity analysis support TSIV as a divergent sister taxon to other megalocytiviruses and a candidate for a novel species designation. Screening of stickleback collected from Stormy Lake before and after a 2012 rotenone treatment to eliminate invasive fish shows 100% positivity for TSIV in the two years before treatment (95% confidence interval: 89-100% prevalence) and 0% positivity for TSIV in 2024 after treatment (95% confidence interval: 0 to 3.7% prevalence), suggesting that the rotenone treatment and subsequent crash and reestablishment of the stickleback population is associated with loss of TSIV.

Keywords: B22; Gasterosteus; iridovirus; megalocytivirus; threespine stickleback.

Figure 1

Map of the TSIV genome. The two outer circles represent predicted ORFs colored based on shared homology with proteins from other iridoviruses, poxviruses, or eukaryotic organisms. The next circle represents the breakpoints of the two contigs comprising the assembly. The two inner circles depict GC content and GC skew.

Figure 2

Phylogenetic tree of 71 iridoviruses based on the concatenated amino acid sequences of 24 core proteins. Bootstrap values ≥85 are labeled above each node. Branch lengths are based on the number of inferred substitutions, indicated by the scale bar. See Table S1 for additional information about each viral sequence.

Figure 3

Comparison of collinearity between megalocytivirus genomes. Colors refer to the core genes as numbered by Eaton et al. [3]. Lines are drawn between homologous core genes and the B22 genes in each genome. Dashed lines within genome tracks indicate positions where assemblies were rearranged and reconnected so that the transmembrane amino acid transporter gene is the first gene shown and is in the reverse orientation. See Table S1 for accessions used for each genome.

Figure 4

Phylogenetic tree based on the B22 amino acid sequences from iridoviruses, herpesviruses, and chordopoxviruses. ORFs from each viral sequence are indicated in parentheses. Bootstrap values ≥85 are labeled above each node. Branch lengths are based on the number of inferred substitutions, indicated by the scale bar. See Table S2 for additional information for each viral sequence.

Figure 5

TSIV detections in stickleback from Stormy and Wik Lake. (a) Map depicting locations of Stormy and Wik Lakes in Alaska and 2007 TSIV outbreak described by Waltzek et al. [18]. (b) Location, year, and number of stickleback screened from Stormy and Wik Lakes and TSIV positive percentage by PCR. (c) Representative samples from PCR screen for TSIV presence. Each well represents an individual fish, including (*) the STMY_2011_X_03 individual detected by the kmer screen of the Roberts Kingman et al. dataset [33], and (†) the STMY_2012_42 individual used for TSIV genome assembly. The (-) lane shows the absence of amplified products from a water negative control.