Transposable Elements in the Genome of Litopenaeus vannamei

As part of our efforts to understand the epigenetic mechanisms associated with susceptibility of Litopenaeus vannamei to Acute Hepatopancreatic Necrosis Disease (AHPND), we began sequencing the genome of the first SPF L. vannamei stocks produced by the breeding program of the US Marine Shrimp Farming Program maintained at the Oceanic Institute in Oahu, Hawaii.  AHPND is caused by Vibrio parahaemolyticus (Vp) isolates containing a ~69 kb conjugative plasmid (plasmid pVPA3-1, Genbank access.# KM067908). The plasmid encode Pir (Photorhabdus insect related) toxin-like proteins that belong to the delta endotoxin_N (N-terminal domain) family, members of which include insecticidal toxins produced by Bacillus species, involved in membrane insertion and pore formation. Other virulence-associated proteins share conserved domains with VirB2-VirB11 present in Agrobacterium tumefaciens, involved in type IV DNA secretion systems (T4SS) which mediate the translocation of virulence factors from Gram-negative bacteria into eukaryotic cells. On plasmid pVPA3-1, the two Pir genes are located within a 3.5 kb-long insertion element (IS) flanked with inverted repeats. Comparison of KM607908 with the genome of Vp strain M0605 from Mexico (Gomez-Gil et al. 2014) revealed that these inverted repeats are from an insertion element of IS903 family (1-4986 nt of contig34 JALL01000066). Mobile/transposable elements (TEs) such as IS5 family are involved in the spread of pathogenicity via horizontal gene transfer (HGT). It is possible that both genetic (receptor-binding, mutations) and epigenetic (DNA and histone methylation, chromatin modification, non-coding RNAs silencing transposition of TEs) mechanisms are involved in susceptibility to AHPND. No genome sequence of L. vannamei is publicly available to test the hypothesis.

We report results from a pilot genome sequence (1.7 Mb) of SPF L. vannamei assembled from a total of 9.6 Mb of raw sequences (GC% = 35.7%), using 20Kb PacBio SMRTCell libraries and running on the Pacific Bioscience RSII platform with P5 chemistry. Approximately 55% of the 9.6 Mb is repetitive sequences, of which ~50% is simple or satellite sequences, AT-rich (GC% = 15.5%), and another half consists of interspersed transposons, GC-rich (GC% = 45.3%). A total of 76 TEs families were identified that belong to 2 LTR retrotransposons clades (Gypsy, BEL), 8 non-LTR retrotransposons clades (RTE, Penelope, Jockey, Ingi, Nimb, Proto2, Vingi, SINE), 4 DNA transposons superfamilies (Harbinger, Mariner, piggyback, Merlin) and a few other unclassified types. The most common repeat is from the non-LTR retrotransposon group (>12% of the genome). RTE-3_LVa is the most abundant TE family (3.5%), and is the TE reported associated with the endogenous virus IHHNV (DQ228358), sex locus (LG4, ShrimpMap2, EGI) and High Growth but TSV susceptible SPF L. vannamei (TranposoShrimp, EGI). The TEs are deposited in Repbase Update (Repbase Reports, 2015, Vol. 15, Issue 4). A complete TE data set with high quality consensus and annotation will be made available when the sequence and assembly of the genome is completed. Up to now, the available genomic sequences show no significant homology with any bacterial transposases and the plasmid KM067908 sequences.