shrimpENCODE: Sequencing of First Specific Pathogen-Free (SPF) Pacific Whiteleg Shrimp, Litopenaeus vannamei from the United States - Update

Various genome sequencing projects are underway for the Pacific whiteleg shrimp, Litopenaeus vannamei, but a fully assembled genome sequence is not yet publicly available. At PAG Asia 2014, Prof. Jianhai Xiang and collaborators from China presented an excellent overview of their research efforts on mapping and sequencing the L. vannamei genome. He also stated that the white spot syndrome virus (WSSV)-like ORFs that some of us have identified in transcriptome projects are not present in his L. vannameisequence, suggesting variation in the commercial breeding stocks being used for sequencing.

As part of ‘The Shrimp Epigenome (shrimpENCODE) Project’, we investigate epigenetic mechanisms associated with susceptibility of L. vannamei to Acute Hepatopancreatic Necrosis Disease (AHPND), also known as Early Mortality Syndrome (EMS), that is causing serious economic losses to the shrimp industry in Asia, Mexico and Central America, and have begun sequencing the genome of the first true SPF stocks of L. vannamei produced by the breeding program of the US Marine Shrimp Farming Program, which were maintained at the Oceanic Institute in Oahu, Hawaii:  https://www.was.org/meetings/ShowAbstract.aspx?Id=35064. 

A pilot sequencing project was initiated with help from Robert Bogden of Amplicon Express and Emily Hatas of Pacific Biosciences. HMW DNA prepared 12 years ago for construction of a BAC library was used for making 20Kb PacBio SMRTCell libraries and running on the Pacific Bioscience RSII platform with P5 chemistry.  Preliminary review of this data by Weidong Bao of Genetic Information Research Institute confirmed the complexity of the genome, with ~55% of repetitive sequences in 9.6 Mb of raw sequences (GC%=35.7%), 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%). 76 transposable element (TE) families were identified, with the most abundant TE family represented by the non-LTR retrotransposon RTE-3_LVa, the TE associated with the endogenous virus IHHNV (DQ228358), linked to sex locus – previously reported as ovary microsatellites (LG4, ShrimpMap2, EGI) and SNP for High Growth/TSV susceptible SPF L. vannamei (TranposoShrimp, EGI).  Although multiple duplications of large DNA segments and a complex transcriptome hs been reported for SPF L. vannamei, the genome of 2.89 pg/nucleus does not appear to be duplicated (Jeffery et al. 2014).

Sequence information will also be presented from various gDNA libraries obtained from ovaries at different maturation stages of founder broodstock from the SPF L. vannamei used for the selective breeding program of the US Marine Shrimp Farming Program. We confirm that homologs of sex differentiation markers reported for P. monodon and L. vannamei via transcriptome analyses, and the piwiRNA involved in sex determination of Bombyx mori, are present in the genome of SPF L. vannamei. Additional high quality NGS data are being obtained in order to generate a good sequence assembly of this difficult genome.  Using all the available genome sequences of L. vannamei up to now, including all SRA databases, no significant homology with any bacterial transposases and the AHPND-causing plasmid KM06790 sequences was found.