Five whole genome shotgun (WGS) databases are available in GenBank for the Pacific whiteleg shrimp Penaeus vannamei (WGS_VDB://DAWKWD01, WGS_VDB://JANIEY01, WGS_VDB://JBFNAF01, WGS_VDB://QCYY01, WGS_VDB://QWLK01). In addition, a pilot sequence (470-Mb) of the first specific pathogen-free (SPF) P. vannamei produced by the breeding program of the United States Marine Shrimp Farming Program (USMSFP) generated 441 repetitive elements. Present in these WGS assemblies are DNA transposons [transposable elements and simple sequence repeats (SSRs)] homologous to endogenous viruses like nimavirus Nimav-1_LVa (279,905-bp) and white spot syndrome virus (WSSV)-like [DNAV-1_LVa (279,384-bp)]. Some SSRs show similarity to P. vannamei microsatellites including the telomeric pentanucleotide (TAACC)n microsatellite, the site of insertion of Nimav-1_LVa.
Other virus sequences are integrated in P. vannamei including portions of infectious hypodermal and hematopoietic necrosis virus (IHHNV; renamed Decapod penstylhamaparvovirus 1; AF218266.2, 3,909-bp) and P. vannamei solinvivirus (PvSV) (OP265432, 10,447-bp) identified in diseased Brazilian shrimp. BLASTN searches revealed 93% identity of OP265432 to Wenzhou shrimp virus 8 (KX883984, 10,445-bp) and 91% identity to P. vannamei picornavirus (OK662577, 10,550-bp). WGS searches identified portions of the 3’-end of OP265432 (92-93% identical) to three sequences [QWLK01003484, QWLK01003486, QWLK01003485] in the contig-level genome assembly ASM373033v1 of P. vannamei F1 breed from China (GCA_003730335), but is not present in the large scaffold-based genome assembly of P. vannamei breed Kehai No.1 farmed in China (GCA_003789085; 1.7-Gb) or in the recently published assembly ASM3358929v1 (GCA_033589295.1, 1.9-Gb). Similar results were found in the 3’end of Wenzhou shrimp virus 8 strain (KX883984 and OK662577), suggesting putative endogenous viral elements (EVE) of PvSV (PvSV-EVE) present in P. vannamei genome. WGS searches of 16 databases for Penaeoidea (taxid:111520) confirmed that these EVEs are specific for P. vannamei.
Considering that the estimated genome size for the first SPF P. vannamei produced by the USMSFP is 2.83-Gb, a new, contiguous, whole reference genome for P. vannamei is needed to confirm presence of these endogenous virus sequences.