While studying Infectious hypodermal and hematopoietic necrosis virus (IHHNV), now called Decapod penstylhamaparvovirus 1, one of the major viral pathogens of penaeid shrimps that can result in runt deformity syndrome (slow growth), a Type-A non-infectious endogenous IHHNV related sequence (DQ228358, 4,655bp; Tang & Ligthner 2006) was previously identified in the genome of P. monodon from Madagascar and demonstrated integrated into an RTE-like non-LTR retrotransposon. The 3’-flanking sequence of the integrated IHHNV, nucleotides 3262-4655 of DQ228358, shows 98% identity to nucleotides 1531-2924 of a P. monodon repeat family RTE-2_PMon (3,656-bp) which shares 85% sequence identity along the whole length with RTE-3_LVa non-LTR retrotransposon (3,654-bp; www.girinst.org).
RTE-3_LVa was characterized from a pilot genome sequence (total length of ~470 Mb) from the first SPF P. vannamei produced by the breeding program of the U.S. Marine Shrimp Farming Program (USMSFP) maintained in Kona and Oahu, Hawaii, USA. Thirteen microsatellites isolated from ovary of SPF P. vannamei are homologous to RTE-3_LVa, two located onto the sex linkage group 4 (LG4, ShrimpMap2) of SPF P. vannamei.
Homology searches using the whole genome sequences databases in GenBank revealed that RTE-3_LVa has many copies in various scaffolds of P. vannamei breed Kehai No.1 assembly including in LG18 associated with sex differentiation. PCR amplification of DNA from adult SPF P. vannamei using primers from two of the microsatellites similar to RTE-3_LVa showed sex-specific bands, suggesting that RTE-3_LVa is a potential sex marker for shrimp. Results should be confirmed in cultured and wild shrimp.
RTE-3_LVa is also present in various chromosomes of other penaeid species like P. monodon from Thailand . Considering the variability in genome sizes of current penaeids assemblies [P. monodon from China and Vietnam (~1.4-~1.6 Gb), P. chinensis from China (~1.6 Gb), P. indicus from India (~1.6 Gb), P. japonicus from China and Japan (~1.7 Gb)], which are smaller than the expected ~2.87 Gb genome size of SPF P. vannamei from a breeding company in Florida, USA, a new, continuous, whole reference genome sequence is urgently needed from both the founding parents of the SPF P. vannamei breeding program of the USMSFP and wild P. vannamei to study organization and evolution of integrated viruses like IHHNV, expression of RTE-3_LVa, and mechanisms of sex determination and differentiation. This research will lead to sustainable production of “ALL-FEMALE P. vannamei”.