This document summarizes the discovery of a fossilized White Spot Syndrome Virus (WSSV)-like element (DNAV-1_LVa) integrated into the genome of the original specific pathogen-free (SPF) shrimp (Penaeus vannamei) domesticated by the US Marine Shrimp Farming Program. Analysis found approximately 42 copies of a complete 279-kb DNAV-1_LVa sequence present in the shrimp genome. DNAV-1_LVa appears to preferentially insert at telomeric sequences and encodes at least 66 proteins, 15 of which show similarity to WSSV proteins. This represents the first characterization of a new lineage of WSSV-like virus integrated into

1. A fossilized White Spot Syndrome Virus-like element (DNAV-1_LVa)
in the genome of the original specific pathogen-free (SPF) shrimp Penaeus
(Litopenaeus) vannamei domesticated by the breeding program of the U.S.
Marine Shrimp Farming Program (USMSFP) from Hawaii, USA
Weidong Bao1*
,Acacia Alcivar-Warren2,3*
, Robert Bogden4
, Quanzhou Tao4
, Suresh Iyer4
, Galina Mikhaylenko4
,
Jon Wittendorp4
,Amy Mraz4
, Evan Hart4
, Emily Hatas5
, Steven Kujawa5
, Joan Wilson5
, KarlVoss5
* weidong@girinst.org; environmentalgenomics.warren@gmail.com
1. Genetics Information Research Institute (GIRI), 465 Fairchild Drive, Suite 201,
Mountain View, CA 94043
2. FUCOBI Foundation, Quito, Ecuador, www.fucobi.org
3. Environmental Genomics Inc., P. O. Box 196, Southborough MA 01772 USA
4. Amplicon Express, Pullman, WA 99163 USA
5. Pacific Biosciences, Menlo Park, CA, USA
Introduction
Whiteleg shrimp, Penaeus vannamei or Litopenaeus van-
namei, is an important species in fishing industry. To under-
stand its genomic feature and the mechanisms underlying the
susceptibility to various bacterial and viral diseases, such as
White Spot Syndrome (WSS) and Acute Hepatopancreatic
Necrotsis Disease (AHPND), a broodstock of the first specific
pathogen-free (SPF) L. vannamei developed by the U.S. Ma-
rine Shrimp Farming Program (USMSFP) in 1992 was sub-
ject to a pilot whole genome sequencing using PacBio SMRT
method.
A total of 1.2 Gb sequences were generated, including
453,089 subreads from 89,710 genome loci. After removing
the redundant subreads, it is estimated 424 Mb, ~ 1/7 of the
genome (2.8 Gb), is covered at least once in this dataset.
WSS is caused by White Spot Syndrome Virus (WSSV),
the lone virus of the family Nimaviridae. Its genome is a giant
single circular double-stranded DNA (~300 Kb, AF369029.2),
coding for about 180-proteins. WSSV-like sequences are
known to be present in the genome of some decapod crusta-
ceans, but the complete genomes of these WSSV-like lineag-
es are still lacking.
Results & Discussion
• A complete ~279-kb consensus sequence, named as
DNAV-1_LVa, was rebuilt from the shrimp whole genome se-
quence. The depth of the consensus is composed of ~6X
nonredundant subreads, and the average sequence diversity
is ~10%.
• DNAV-1_LVa represents the complete sequences of a un-
characterized lineage of WSSV-like virus.
• It is estimated that 42 copies of DNAV-1_LVa are present
in the genome of this tested strain of shrimp.
• At least 66 CDS could be recognized in the current version
of DNAV-1_LVa. 15 of them show distant but significant simi-
larity to those of WSSV (Fig 1.).
• DNAV-1_LVa inserts preferentially, if not specificly, into the
telomeric sequnence (AGGTT)n (Fig. 1B).
• Shrimp genome is AT-rich (GC%=34%), and highly abun-
dant of various repeat sequences. Particualrly, simple satellites
account for more than 23% of the genome.
• It is intriguiing to know how widely DNAV-1_LVa is pres-
ent in other strains of shrimps, and whether DNAV-1_LVa ever
convey any immulogical benefit to the shrimp.
Fig 1. A) At least 66 ORFs are able to be recognized in DNAV-1_LVa
consensus on both strands, though the quality of the consensus se-
quence is very low in some areas. 15 ORFs show significant similarity
(E-Value < 0.005), and 6 ORFs show marginal similariy, with the pro-
tein sequences encode by WSSV. B) Majority of DNAV-1_LVa copies
show that it inserts preferentially, if not specificly, at (AGGTT)n micro-
satellite, which is believed to be the telomeric sequence in shrimp.
9 16
10
6517
18 19 20 24 28 40 45
46 48
49 55
58 59
60 61
64
DNAV-1_LVa (279 Kb)
15 significant WSSV homologs (E-Value < 0.005) 6 marginal WSSV homologs (0.017 < E-Value < 1.9)
A
B
45p (DNAV-1_LVa)
100
91
wsv289-like protein: BBD20110.1
(Marsupenaeus japonicus)
capsid protein: GAV93240.1
(Chionoecetes opilio bacilliform virus)
wsv289-like protein: AKS10638.1
(Metopaulias depressus)
ORF1005: ATU83357.1 (WSSV)
45p LTNMPDNLYI YVPIFPTSFL MAEQ---IKS VLEIAKDKIK HVVKHREYQS TVIRDCNDEI
BBD20110.1 LMNMPDNLHI YVPTLPTSFL MAEQ---IKS ILDIAKDKTK HLIANKKEQS DLIEKHKNEI
AKS10638.1 SVNFSSSQYI YVPINPKHIL THMQWLECMS VIEAATRDSA KAVRHFEEAA GGTLEELKKL
ATU83357.1 DLNFSPAQNL FVPVNPRHIL TDMQWLNCIS IIETATRDSA IVMQSFQEQA DKTTTQLEEL
GAV93240.1 SQNFSSAQHL FVPINPRRLL LNAQWLECVA LIGVGTEHFV KALKKLETRI KDNNEELKTL
45p QKRFVDIWGS YNSQDKIQEA INLDILSVQT RKQDIAI--- ---KNKKLLS SLPVCLDIST
BBD20110.1 NEQFMTIWGN SGRLNKLEEA FRQDFLSVLK GKQNIAI--- ---KNKKLFF NLPFLLDLVQ
AKS10638.1 LEQWDDIVKQ VTSTESPAVL SLLKLEWMDK EATRIAKLRD EAERSRVALA VQGKVVNIEK
ATU83357.1 LSQWNNIVSQ VTDEKSPAYV SSVKLEWLNN EASRIAAIRE NSEKSKIVMG VQGKIVNIDE
GAV93240.1 LKLWKQRTNM STGTDDTVF- --LELDWVQQ QAKRLIKLRE HLERTYAAIV VRSIPINIDK
45p YRLHLAIKSM MDIDYYIKVP NFWRLMDIEE MLQFAVSVML ITLQKLVDVG LNTARRYSEV
BBD20110.1 YQLHLAIRSV TDIDYYIKVP NFWRMMDIDE MLKFAISLML ITLEKLVNVG LNTAKRFSEI
AKS10638.1 YGIIAVSRSL IDVDFYVKLP NSWPSGNWRE LVYSAVSLAS IPLQVNISKG IMAASQATMV
ATU83357.1 LGIVAVARSI VDVDFYIKMP NVWASRDWKN LIYYAVNIAA TPLINNISRG IMAASQTSVL
GAV93240.1 YSITAIARSL SDVDYYLKVP NPWINMDWHD VMYSALLLTI LPLNLNISRG IILASNASVL
Fig 2. A) Evolutionary relationship based on the sequences of
45p encoded by DNAV-1_LVa and its homologs (ATU83357.1,
GAV93240.1, AKS10638.1, BBD20110.1) in WSSV, Chionoecetes
opilio bacilliform virus, and the genome-integrated, fossilized WS-
SV-like viruses found in Metopaulias depressus (reddish-brown crab),
Marsupenaeus japonicus (Japanese tiger prawn).B) Illustration of the
multiple alignment on the C-terminal region.
A
B