Limited information is available on the content of repetitive elements [REs] in Penaeid shrimp. A pilot genome sequence (470 Mb) from the first specific pathogen-free (SPF) Penaeus vannamei produced by the breeding program of the U. S. Marine Shrimp Farming Program (USMSFP) generated 479 REs representing 269 long terminal repeat (LTR) retrotransposons, 83 non-LTR retrotransposons, and 127 DNA transposons. Sixty elements were also obtained from the genome assembly of P. vannamei farmed in China (ASM378908v1: 1.66 Gb). Some REs show similarity to SPF P. vannamei microsatellites including the telomeric pentanucleotide (TAACC/GGTTA)n repeats, the site of insertion of nimavirus Nimav-1_LVa (https://pubmed.ncbi.nlm.nih.gov/31947590/). The non-LTR retrotransposon Outcast-1_LVa (6,180 bp) is further characterized.
A genomic locus [KC179708, 4101-bp] comprising 4-kb nucleotides derived from the 1,974-6,062 of Outcast-1_LVa, shows 96.9% identity to the consensus sequence of Outcast-1_LVa stored in Repbase (www.girinst.org). KC179708 locus was putatively associated with Abdominal Segment Deformity Disease (ASDD) of farmed P. vannamei from Thailand. Researchers suggested that ASDD may be related to inbreeding and use of eyestalk ablation (EA) in female broodstock. In the ASM378908v1 genome assembly 632 Outcast-1_LVa loci are identified in 43 scaffolds and is actively expressed in P. vannamei transcriptomes from various developmental stages and adult tissues. Expression changes were observed in ovaries six days after EA.
Considering that the genome size of SPF P. vannamei was estimated at 2.89 Gb, a new contiguous whole reference genome for P. vannamei is needed to fully characterize its repeatome, study molecular and epigenetics mechanisms involved in growth and disease susceptibility or tolerance/resistance and determine whether expression of Outcast-1_LVa is associated with EA and inbreeding.