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Figure 2

From: A novel nudivirus infecting the invasive demon shrimp Dikerogammarus haemobaphes (Amphipoda)

Figure 2

(a) Gene synteny among the Epsilonnudivirus, Gammandivirus and Deltanuvirus reveals a gene order among decapod-infecting nudiviruses, which is missing from peracarid-infecting nudiviruses. The genomes are annotated with positive strand (gold) and negative strand (silver) coding regions. In Fig. 2a, Dikerogammarus haemobaphes nudivirus gene synteny (white) is compared to Tipula oleracea nudivirus gene synteny (pink). Ribbons connecting the two genomes link up the homologous gene and its location on the viral genome. Scale ticks = 2 kb. The comparative plots were developed in Circa (www.omgenomics.com/circa/). (b) Dikerogammarus haemobaphes nudivirus gene synteny (white) is compared to Penaeus monodon nudivirus gene synteny (blue). Ribbons connecting the two genomes link up the homologous gene and its location on the viral genome. Scale ticks = 2 kb. The comparative plots were developed in Circa (www.omgenomics.com/circa/). (c) Dikerogammarus haemobaphes nudivirus gene synteny (white) is compared to Hommarus gammarus nudivirus gene synteny (green). Ribbons connecting the two genomes link up the homologous gene and its location on the viral genome. Scale ticks = 2 kb. The comparative plots were developed in Circa (www.omgenomics.com/circa/). (d) All four virus are compared together, indicating regions of novelty in the Dikerogammarus haemoabphes nudivirus genome. The white triangles on the DhNV genome highlight the areas of novel sequence information that do not correspond to genes on the other nudivirus genomes. Scale ticks = 10 kb. The comparative plots were developed in Circa (www.omgenomics.com/circa/). (e) The crustacean nuidviruses contain 24 nudivirus core genes (VLF-1, ODV-E66 and Helicase 2 are duplicated) (p6.9 is missing from Dikerogammarus haemobaphes nudivirus) (orange) and 11 other gene homologs conserved across the crustacean-infecting nudiviruses (yellow). These conserved homologues are based on similarity, synteny and functional identity. Comparison with DhNV (peracarid-infecting nudivirus) highlights three main areas of gene reorganization. ‘X’ corresponds to a rearrangement of the DhNV_032, DhNV_34 and pif-1 genes, ‘Y’ corresponds to a rearrangement of the vlf-1 and p74 genes and finally, ‘Z’ corresponds to a rearrangement of six genes (vlf-1, ac68, DhNV_080, ac81 and both helicase 2 homologues). The Gammanudivirus members that infect decapods share the same gene synteny across these conserved motifs.

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