scholarly journals Genetic diversity ofVibrio parahaemolyticusstrains isolated from farmed Pacific white shrimp and ambient pond water affected by acute hepatopancreatic necrosis disease outbreak in Thailand

2015 ◽  
Vol 363 (2) ◽  
pp. fnv222 ◽  
Author(s):  
Kaknokrat Chonsin ◽  
Shigeaki Matsuda ◽  
Chonchanok Theethakaew ◽  
Toshio Kodama ◽  
Jiraphan Junjhon ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Pond Water ◽  
Disease Outbreak ◽  
Pacific White Shrimp ◽  
White Shrimp ◽  
Acute Hepatopancreatic Necrosis Disease

scholarly journals Microbiome analysis of Pacific white shrimp gut and rearing water from Malaysia and Vietnam: implications for aquaculture research and management

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5826 ◽  
Author(s):  
Muhammad Zarul Hanifah Md Zoqratt ◽  
Wilhelm Wei Han Eng ◽  
Binh Thanh Thai ◽  
Christopher M. Austin ◽  
Han Ming Gan
Keyword(s):  
16S Rrna ◽  
Microbial Diversity ◽  
Pond Water ◽  
Pacific White Shrimp ◽  
White Shrimp ◽  
Rrna Gene ◽  
Early Mortality Syndrome ◽  
The Pacific ◽  
High Sequence Conservation ◽  
Clustering Approach

Aquaculture production of the Pacific white shrimp is the largest in the world for crustacean species. Crucial to the sustainable global production of this important seafood species is a fundamental understanding of the shrimp gut microbiota and its relationship to the microbial ecology of shrimp pond. This is especially true, given the recently recognized role of beneficial microbes in promoting shrimp nutrient intake and in conferring resistance against pathogens. Unfortunately, aquaculture-related microbiome studies are scarce in Southeast Asia countries despite the severe impact of early mortality syndrome outbreaks on shrimp production in the region. In this study, we employed the 16S rRNA amplicon (V3–V4 region) sequencing and amplicon sequence variants (ASV) method to investigate the microbial diversity of shrimp guts and pond water samples collected from aquaculture farms located in Malaysia and Vietnam. Substantial differences in the pond microbiota were observed between countries with the presence and absence of several taxa extending to the family level. Microbial diversity of the shrimp gut was found to be generally lower than that of the pond environments with a few ubiquitous genera representing a majority of the shrimp gut microbial diversity such as Vibrio and Photobacterium, indicating host-specific selection of microbial species. Given the high sequence conservation of the 16S rRNA gene, we assessed its veracity at distinguishing Vibrio species based on nucleotide alignment against type strain reference sequences and demonstrated the utility of ASV approach in uncovering a wider diversity of Vibrio species compared to the conventional OTU clustering approach.

scholarly journals Genomic characterization of Vibrio parahaemolyticus from Pacific white shrimp and rearing water in Malaysia reveals novel sequence types and structural variation in genomic regions containing the Photorhabdus insect-related (Pir) toxin-like genes

2019 ◽  
Vol 366 (17) ◽  
Author(s):  
Chrystine Zou Yi Yan ◽  
Christopher M Austin ◽  
Qasim Ayub ◽  
Sadequr Rahman ◽  
Han Ming Gan
Keyword(s):  
Vibrio Parahaemolyticus ◽  
Illumina Miseq ◽  
Pacific White Shrimp ◽  
White Shrimp ◽  
Phylogenomic Analysis ◽  
Genomic Characterization ◽  
Genomic Resource ◽  
Acute Hepatopancreatic Necrosis Disease ◽  
Genomic Regions

ABSTRACT The Malaysian and global shrimp aquaculture production has been significantly impacted by acute hepatopancreatic necrosis disease (AHPND) typically caused by Vibrio parahaemolyticus harboring the pVA plasmid containing the pirAVp and pirBVp genes, which code for Photorhabdus insect-related (Pir) toxin. The limited genomic resource for V. parahaemolyticus strains from Malaysian aquaculture farms precludes an in-depth understanding of their diversity and evolutionary relationships. In this study, we isolated shrimp-associated and environmental (rearing water) V. parahaemolyticus from three aquaculture farms located in Northern and Central Malaysia followed by whole-genome sequencing of 40 randomly selected isolates on the Illumina MiSeq. Phylogenomic analysis and multilocus sequence typing (MLST) reveal distinct lineages of V. parahaemolyticus that harbor the pirABVp genes. The recovery of pVA plasmid backbone devoid of pirAVp or pirABVp in some V. parahaemolyticus isolates suggests that the toxin genes are prone to deletion. The new insight gained from phylogenomic analysis of Asian V. parahaemolyticus, in addition to the observed genomic instability of pVa plasmid, will have implications for improvements in aquaculture practices to diagnose, treat or limit the impacts of this disease.

scholarly journals Complete Genome Sequence of a Deletion Mutant of Vibrio parahaemolyticus from Pacific White Shrimp (Penaeus vannamei)

2018 ◽  
Vol 6 (25) ◽  
Author(s):  
Siddhartha Kanrar ◽  
Arun K. Dhar
Keyword(s):  
Genome Sequence ◽  
Vibrio Parahaemolyticus ◽  
Deletion Mutant ◽  
Pacific White Shrimp ◽  
White Shrimp ◽  
Penaeus Vannamei ◽  
Content Type ◽  
A Genome ◽  
Acute Hepatopancreatic Necrosis Disease ◽  
Experimental Challenge

ABSTRACT Vibrio parahaemolyticus carrying the toxin genes pirA and pirB causes acute hepatopancreatic necrosis disease in shrimp. A genome sequence of V. parahaemolyticus strain R13 was determined that showed deletions of the entire pirA gene and the 5ʹ end of the pirB gene and does not cause the disease in experimental challenge.

scholarly journals Genetic diversity within and between broodstocks of the white shrimp Litopenaeus vannamei (Boone, 1931) (Decapoda, Penaeidae) and its implication for the gene pool conservation

2007 ◽  
Vol 67 (4 suppl) ◽  
pp. 939-943 ◽  
Author(s):  
PD. Freitas ◽  
MR. Calgaro ◽  
PM. Galetti Jr.
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Litopenaeus Vannamei ◽  
Gene Pool ◽  
Rapd Analysis ◽  
Pacific White Shrimp ◽  
White Shrimp ◽  
Brazilian Coast ◽  
The Pacific ◽  
Improvement Programs

Genetic variation within and between fifteen closed broodstock lines of the Pacific white shrimp Litopenaeus vannamei, reared at different hatcheries in the Brazilian coast, was assessed by RAPD analysis. Fifty two polymorphic loci were identified when a set of five decamer primers was used in PCR. The genetic diversity analysis within lines evidenced genetic variation loss probably related to bottleneck effects and inbreeding. In addition, the genetic divergence values between the different samples appear to reflect the initial founder composition of such stocks, in some cases, sharing a common origin, suggesting a putative importance of interbreeding for the establishment of genetic improvement programs for these broodstocks. The genetic variation monitoring appears to be helpful to the gene pool conservation of this aquaculture species, mainly if considered its exotic status in Brazil and the current impossibility of new introduction of wild individuals.

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