As part of our efforts to understand the epigenetic mechanisms associated with susceptibility of Penaeus vannamei to bacterial and viral diseases, we proposed that horizontal transfer (HT) and methylation of transposable elements (TEs) are potential mechanisms involved in susceptibility to Acute Hepatopancreatic Necrosis Disease (AHPND), white spot syndrome virus (WSSV), and Infectious hypodermal and hematopoietic necrosis virus (IHHNV) . To test this hypothesis, we needed access to a fully assembled P. vannamei genome sequence (expected size is 2.8 Gb) , but none is currently available in the NCBI genome databases. The only genome sequence available for P. vannamei is a 1.6 Gb draft prepared with muscle DNA of male shrimp of Kehai isolate from China (GCA_003789085.1; breed Kehai No. 1) originally from the United States.
A pilot genome sequencing effort was initiated through ‘The Shrimp Epigenome (ShrimpENCODE) Project ’ of the FUCOBI Foundation of Ecuador and Environmental Genomics Inc., MA, USA, with help from Amplicon Express and Pacific Biosciences collaborators. High molecular weight DNA from offspring of SPF Kona Line P. vannamei domesticated by the breeding program of the U.S. Marine Shrimp Farming Program (USMSFP) maintained at the Oceanic Institute in Kona and Oahu, HI were used for sequencing.
A total of 312 TEs were identified in a partial genome sequence (~470 Mb) belonging either to Class I [Long terminal repeat (LTR) retrotransposons and non-LTR retrotransposons] or Class II (DNA transposons). These included: 105 DNA transposons [EnSpm (1), Harbinger(11), hAT (13), Kolobok (2), Mariner/Tc1(10), Merlin(12), MuDR (1), P(1), piggyBac(8), Polinton (3), Transib(2), unclassified(41)]; 119 LTR retrotransposons [BEL(15), Copia(2), Gypsy(92), unclassified(10)]; 76 non-LTR retrotransposons [CR1(7), Daphne(7), Ingi(4), Jockey(4), Nimb(7), Penelope(18), Proto2(2), RTE(9), R4(2), Vingi(2), SINE2(3), unclassified(11)]; 1 integrated Nimavirus , Nimav-1_LVa (279,905 bp), and 11 unclassified . All sequences are deposited in Repbase (https://pubmed.ncbi.nlm.nih.gov/31947590/). Future research will focus on (a) sequencing a continuous, fully assembled reference genome from either brood stocks of the original SPF P. vannamei produced by the USMSFP or wild shrimp from Ecuador, and (b ) understanding the epigenetic mechanisms associated with HT of retrotransposons.