Nudivirus Remnants in the Genomes of Arthropods

Abstract

Endogenous viral elements (EVEs), derived from all major types of viruses, have been discovered in many eukaryotic genomes, representing "fossil records" of past viral infections. The endogenization of nudiviruses has been reported in several insects, leading to the question of whether genomic integration is a common phenomenon for these viruses. In this study, genomic assemblies of insects and other arthropods were analyzed to identify endogenous sequences related to Nudiviridae. A total of 359 nudivirus-like genes were identified in 43 species belonging to different groups; however, none of these genes were detected in the known hosts of nudiviruses. A large proportion of the putative EVEs identified in this study encode intact open reading frames or are transcribed as mRNAs, suggesting that they result from recent endogenization of nudiviruses. Phylogenetic analyses of the identified EVEs and inspections of their flanking regions indicated that integration of nudiviruses has occurred recurrently during the evolution of arthropods. This is the first report of a comprehensive screening for nudivirus-derived EVEs in arthropod genomes. The results of this study demonstrated that a large variety of arthropods, especially hemipteran and hymenopteran insects, have previously been or are still infected by nudiviruses. These findings have greatly extended the host range of Nudiviridae and provide new insights into viral diversity, evolution, and host-virus interactions.

Keywords: Nudiviridae; arthropods; endogenous viral elements; genomic data; host range.

Fig. 1.

—Nudivirus-like genes identified in arthropod genomes. Copy numbers for each nudivirus homolog are indicated. Core genes conserved between baculoviruses and nudiviruses are shown in dark gray, and nudivirus-specific core genes are shown in light gray. Sequences with or without flanking host sequences were colored in green and yellow, respectively. Ap, Acyrthosiphon pisum; Pv, Pachypsylla venusta; Gb, Gerris buenoi; Dn, Diuraphis noxia; Ms, Melanaphis sacchari; Hv, Homalodisca vitripennis; Mh, Maconellicoccus hirsutus; Sg, Schizaphis graminum; Sf, Sipha flava; Fv, Ferrisia virgate; Pm, Paracoccus marginatus; Tp, Trionymus perrisii; Tm, Trabutina mannipara; Mp, Myzus persicae; Bt, Bemisia tabaci; Ps, Philaenus spumarius; Cc, Cephus cinctus; Cf, Camponotus floridanus; Hs, Harpegnathos saltator; Dq, Dinoponera quadriceps; Fa, Fopius arisanus; Hl, Habropoda laboriosa; Lh, Linepithema humile; Cv, Cotesia vestalis; Ln, Lasius niger; Sj, Synergus japonicas; Op, Ormyrus pomaceus; Pg, Pseudomyrmex gracilis; Pd, Polistes dominula; Ed, Euglossa dilemma; Bd, Bactrocera dorsalis; Pp, Phlebotomus papatasi; Cp, Condylostylus patibulatus; Sb, Sphyracephala brevicornis; Ph, Phortica variegate; Md, Mayetiola destructor; Dp, Danaus plexippus; Pa, Papilio glaucus; Tc, Triops cancriformis; Is, Ixodes scapularis; Lr, Loxosceles reclusa; Sm, Stegodyphus mimosarum; and Tu, Tetranychus urticae. *EST data available; ^#TSA data available. Boxes surrounding the numbers indicate that gene expression was detected. Sequences with intact ORFs were indicated by boldface.

Fig. 2.

—Conserved gene clusters identified in A. pisum and Di. noxia genomes. ORFs are indicated by boxed arrows, and conserved gene clusters are colored in blue; double slashes indicate the omitted genomic ranges. GbNV: Gryllus bimaculatus nudivirus.

Fig. 3.

—Schematic representation of nudivirus-like genes with flanking regions. Predicted viral ORFs and their transcriptional directions are indicated as white boxes with arrows, and predicted host genes are shown as gray boxes with arrows. Double slashes indicate the omitted genomic ranges. The vertical lines indicate the predicted frameshift sites, and the dash lines indicate premature stop codons. The red lines below represent matched regions of a trace record.

Fig. 4.

—Phylogenetic analysis of nudivirus-like genes in arthropod genomes. The tree is based on the amino acid sequences of P74 proteins and was constructed by MrBayes, using mixed models of amino acid substitutions. The BI posterior probabilities are presented at the nodes as percent values. Associated host groups are indicated by tip colors. The following viruses were included in this analysis, with abbreviated names: Autographa californica nucleopolyhedrovirus (AcMNPV), Helicoverpa armigera nucleopolyhedrovirus (HearSNPV), Pieris rapae granulosis virus (PrGV), Culex nigripalpus NPV (CuniNPV), Neodiprion lecontei NPV (NeleNPV), Cotesia congregata bracovirus (CcBV), Chelonus inanitus bracovirus (CiBV), Musca domestica salivary gland hypertrophy virus (MdSGHV), Glossina pallidipes salivary gland hypertrophy virus (GpSGHV), White spot syndrome virus (WSSV), Gryllus bimaculatus nudivirus (GbNV), Oryctes rhinoceros nudivirus (OrNV), Heliothis zea nudivirus 1 (HzNV-1), Drosophila innubila nudivirus (DiNV), Tipula oleracea nudivirus (ToNV), Penaeus monodon nudivirus (PmNV), and Nilaparvata lugens endogenous nudivirus (NlENV). WSSV was used to root the tree. GenBank accession number is given for each sequence.

Fig. 5.

—Phylogenetic diversity of nudivirus hosts. (a) Distribution of exogenous and endogenous nudiviruses in arthropods. A cladogram for the arthropods screened in this study was downloaded from the NCBI Taxonomy database. Red triangles indicate species in which nudivirus-like genes were identified, and gray circles indicate the known hosts of circulating nudiviruses. (b) Number of species from different arthropod groups screened in this study and number of genomes containing putative EVEs derived from nudiviruses.