Aquaculture 2022

February 28 - March 4, 2022

San Diego, California

PRELIMINARY SURVEY OF TRANSPOSABLE ELEMENTS FROM THE FIRST SPECIFIC PATHOGEN FREE (SPF) SHRIMP Penaeus vannamei PRODUCED IN THE UNITED STATES

 

Gladys Zuniga* , Acacia Alcivar-Warren

 

The Shrimp Epigenome (ShrimpENCODE) Project

Environmental Genomics Inc., Southborough, MA, 01772 USA, and

 Fundación para la Conservación de la Biodiversidad (FUCOBI) , Quito, Ecuador

 

fucobi@gmail.com

 



 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.