2012, 194(8):2104. DOI: 10.1128/JB.00079-12.
Edwards, Zheng Wang, Gary J. Vora and Bruno Gómez-Gil
Iliana Espinoza-Valles, Sonia Soto-Rodríguez, Robert A.
Pathogen Vibrio harveyi CAIM 1792
Draft Genome Sequence of the Shrimp
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Draft Genome Sequence of the Shrimp Pathogen Vibrio harveyi Download full-text
Iliana Espinoza-Valles,aSonia Soto-Rodríguez,aRobert A. Edwards,b,dZheng Wang,cGary J. Vora,cand Bruno Gómez-Gila
CIAD A.C. Mazatlan Unit for Aquaculture and Environmental Management, Sinaloa, Méxicoa; Department of Biology and Department of Computer Science, San Diego
State University, San Diego, California, USAb; Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, Washington, DC, USAc; and Mathematics and
Computer Science Division, Argonne National Laboratory, Argonne, Illinois, USAd
Vibrio harveyi is a Gram-negative bacterium found in tropical and temperate marine environments as a free-living organism or
agent of the “bright red” syndrome of the Pacific white shrimp Litopenaeus vannamei.
toinduction (6) and bioluminescence (3). It is also an important
pathogen of marine fish and invertebrates (1), especially for
shrimp (5). Strain CAIM 1792 has caused recurrent outbreaks of
vibriosis known as “bright red” syndrome in Litopenaeus van-
namei shrimp farms in northwestern Mexico since 2005 (7).
anisms responsible for V. harveyi, the recent discovery of the mis-
genomes were sequenced demonstrated that there is a lack of a
representative V. harveyi genome (4).
Strain CAIM 1792 was sequenced using a 454 GS-FLX pyrose-
quencing approach (Life Sciences/Roche, Branford, CT). The
high-throughput sequencing resulted in ?18-fold coverage
bled using the Newbler software (version 2.5.3) into 87 contigs. A
genome-scale assembly was constructed with Mauve Genome
Alignment software (version 2.3.1; Genome Evolution Labora-
tory, University of Wisconsin—Madison [http://asap.ahabs.wisc
.edu]). The ordering of the contigs was tested by using the Scaf-
ted for publication) and with the completed Vibrio campbellii
ATCC BAA-1116 genome as a reference. BlastX queries were per-
formed to validate assemblies containing coding sequences
that are in the process of closure via PCR amplicon sequencing.
The assembled genome of CAIM 1792 is 5.84 Mbp in size with
5,328 RAST server-annotated CDS (2), and it has two chromo-
somes and a plasmid. The 3.50-Mbp chromosome I (Chr I) is
contains eight rRNA operons and at least 47 tRNAs. In compari-
son, the 2.24-Mbp chromosome II (Chr II) is composed of four
supercontigs with seven gaps and contains one rRNA operon and
harveyi CAIM 1792 has a superintegron located in Chr I that is
87.2 Kbp in size and contains ?130 gene cassettes, of which 97
?100 genes that encode putative virulence factors (e.g., hemoly-
III, IV, and VI secretion systems, RTX toxins, and vibriolysin)
ibrio harveyi is a member of the Vibrio core group and an
organism with an important role in the study of bacterial au-
that, when combined with additional comparative genomic anal-
yses with sequenced sister species such as V. campbellii, V. para-
haemolyticus, V. rotiferianus, and V. owensii, will aid in revealing
the underlying genetic assemblages responsible for pathogenicity,
host range, environmental adaptation, and evolution within V.
harveyi and the Vibrio core group.
Nucleotide sequence accession numbers. Vibrio harveyi
CAIM 1792 has been deposited in the Collection of Aquatic Im-
portant Microorganisms (CAIM; www.ciad.mx/caim), and the
genome sequence has been deposited in the GenBank database
under accession number AHHQ00000000. The version described
in this study is the first version, AHHQ01000000.
This work was supported by CONACYT (I.E.-V., S.S.-R., and B.G.-G.),
NSF grant DBI 0850356 from the Division of Biological Infrastructure
(R.A.E.), and the Office of Naval Research via U.S. Naval Research Labo-
ratory core funds (Z.W. and G.J.V.).
and are not to be construed as those of the U.S. Navy, military service at
large, or U.S. Government.
vertebrates and invertebrates. Lett. Appl. Microbiol. 43:119–124.
2. Aziz RK, et al. 2008. The RAST server: Rapid Annotations using Subsys-
tems Technology. BMC Genomics 9:75.
3. Belas R, et al. 1982. Bacterial bioluminescence: isolation and expression of
the luciferase genes from Vibrio harveyi. Science 218:791–793.
4. Lin B, et al. 2010. Comparative genomic analyses identify the Vibrio har-
veyi genome sequenced strains BAA-1116 and HY01 as Vibrio campbellii.
Environ. Microbiol. Rep. 2:81–89.
ponds. Microbiol. Aust. 19:22–27.
6. Nealson KH, Platt T, Hastings JW. 1970. Cellular control of the synthesis
and activity of the bacterial luminescent system. J. Bacteriol. 104:313–322.
7. Soto-Rodriguez S, Gómez-Gil B, Lozano R. 2010. ‘Bright-red’ syndrome
in Pacific white shrimp Litopenaeus vannamei is caused by Vibrio harveyi.
Dis. Aquat. Org. 92:11–19.
Received 1 February 2012 Accepted 6 February 2012
Address correspondence to Bruno Gómez-Gil, firstname.lastname@example.org.
Copyright © 2012, American Society for Microbiology. All Rights Reserved.
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