Dynamic integration and evolutionary trajectory of endogenous IHHNV elements in crustacean genomes

Abstract

Endogenous viral elements (EVEs) serve as molecular fossils that record the ancient co-evolutionary arms race between viruses and their hosts. In this study, by analyzing 105 host crustacean genomes, we identified 252 infectious hypodermal and haematopoietic necrosis virus-derived EVEs (IHHNV-EVEs), which include 183 ancient and 6 recently inserted EVEs. These IHHNV-EVEs are widely distributed among Decapoda, Thoracica, and Isopoda, with some of them exhibiting a syntenic distribution relative to neighboring host sequences, suggesting that the IHHNV or its ancestor are potential pathogens of these species with a long-time dynamic interaction during the evolutionary history. An expansion of IHHNV-EVEs was observed in decapoda genomes, reflecting a reinforced arm race between decapoda and IHHNV. Notably, we found that nearly all recent IHHNV-EVEs were laboratory contaminants, except for a single authentic integration in Penaeus monodon that persists intact across 16 samples from the 2 populations. These temporal dynamics-ancient genomic stabilization versus modern colonization activity-highlight that EVEs serve as dual archives: historical records of past conflicts and active participants in current evolutionary battles. Our findings redefine viral genomic colonization as a continuum, where ancient EVE fixation coexists with persistent integration processes, providing new insights into host-virus co-evolutionary trajectories.

Keywords: IHHNV-EVE; crustacean; genome; shrimp; virus–host interaction.

Fig. 1.

Characteristics and insertion structures of IHHNV-EVEs. a) Length distribution of IHHNV-EVE; b) Identity to the encoded IHHNV proteins; c) The insertion structure of IHHNV-EVEs (13 representative species were selected).

Fig. 2.

Integration of IHHNV in the crustacean genome. a) The phylogenetic tree showing the hosts in which IHHNV integration occurs, and the classes of hosts with integration are marked with pentagram shapes. The red font indicates the identification of an IHHNV-EVE in the Copepoda. The red circle represents IHHNV-EVEs with collinearity relationships in the Penaeidae family of the order Decapoda. The green circle denotes IHHNV-EVEs with collinearity relationships in the order Isopoda. The orange circle signifies IHHNV-EVEs with collinearity relationships in the genus Panulirus of the order Decapoda; b) IHHNV-EVEs that have collinear relationships in Isopoda; c) IHHNV-EVEs that have collinear relationships in Panulirus. d) IHHNV-EVEs that have collinear relationships in Penaeidae.

Fig. 3.

Stable integration of ancient IHHNV-EVE in L. vannamei. a) The primer design positions of the stably inserted EVE in L. vannamei with respect to the final genome as the reference genome; b) Amplification of stably inserted IHHNV-EVE in different germplasms of L. vannamei. N: PCR reaction mixture with no DNA. M: Maker. C: Cultured. W: Wild; c) The amplification of IHHNV-EVE in different germplasms.

Fig. 4.

New insertion of IHHNV-EVE in L. vannamei and P. monodon. a) Primer design and detection of recently inserted Lva-IHHNV-EVE4 and Lva-IHHNV-EVE5 in different populations of L. vannamei; b) Primer design and detection of recently inserted Pmo-IHHNV-EVE4 in different populations of P. monodon.

Fig. 5.

The structure and expression patterns of IHHNV-EVEs in L. vannamei. a) The genomic structure of 10-kb upstream and downstream of the stably ancient inserted IHHNV-EVE in the genome of L. vannamei; b) The qRT-PCR quantification of IHHNV-EVE in different tissues of L. vannamei. Br: Brain, Epi: Epidermis, Gi: Gill, Hc: Haemocyte, Hp: Hepatopancreas, In: Intestines, Ms: Muscle, Oka: lymphoid organ Oka, Ov: Ovary, Te: Testis, Es: Eyestalk, St: Stomach.

Fig. 6.

Dynamic integration model of IHHNV-EVEs in Crustaceans. The integration of EVEs is a continuous process. The ancestral IHHNV integrated during the evolutionary period of crustacean ancestors, with integration events occurring in Decapoda, Copepoda, Isopoda, and Thoracica—species susceptible to IHHNV infection. Subsequent integrations primarily occurred in Decapoda, including both the Penaeidae family and the genus Panulirus. Notably, integration in P. monodon is dynamic, as recently integrated IHHNV-EVEs can still be detected in its genome to date.