37 research outputs found
Genetic Susceptibility of Cultured Shrimp (\u3ci\u3ePenaeus vannamei\u3c/i\u3e) to Infectious Hypodermal and Hematopoietic Necrosis Virus and \u3ci\u3eBaculovirus penaei\u3c/i\u3e: Possible Relationship with Growth Status and Metabolic Gene Expression
Offspring of four crosses (I, II, III, and IV) of Penaeus vannamei from known high- and low-growth families were challenged with infectious hypodermal and hematopoietic necrosis virus (IHHNV) and Baculovirus penaei (BP) to compare their susceptibility to these viral agents and examine the genetic component involved in disease resistance or susceptibility. Family crosses were made using broodstock from five families developed by the U.S. Marine Shrimp Farming Program. The prevalence of IHHNV infection was highest in cross I and lowest in cross III. Cross I was developed using male and female broodstock from the low-growth family 1.6, and cross III was developed using a female from the high-growth family 1.3 and a male from the low-growth family 1.6. The prevalence of BP infection at Day 4 was highest (100%) in cross IV, which was developed using a female from the low-growth family 1.4 and a male from the high-growth family 1.5. The reciprocal cross, cross III, had the lowest (68%) prevalence at Day 4 postexposure. Both crosses I and II had 88% prevalence of infection at Day 4. Despite 100% prevalence of BP infection in cross IV at 4 days, animals from this cross and cross II exhibited high survival by Day 18 (85 and 77%). On the other hand, crosses I and III (with 88 and 68% prevalence at Day 4, respectively) showed low survival at Day 18 (19 and 24%). On the basis of prevalence of infection and mortality rates, it was concluded that the susceptibility to BP in penaeid shrimp is governed by the genetic background of the parental crosses. The random amplified polymorphic DNA polymorphisms for crosses I, II, III, and IV, were 43, 45, 53, and 51%, respectively, showing no clear relationship between IHHNV and BP prevalence of infection and levels of nuclear genetic diversity. Though the mtDNA haplotypes in offspring from the different crosses were the same, major differences were observed in both steady-state levels and patterns of expression of the mitochondrial 12s rRNA in offspring obtained at various early developmental stages from each of the four crosses. The possible relationship among disease susceptibility, growth status, and expression of mitochondrial 12s rRNA is discussed in the context of a complex nuclear-cytoplasmic genetic system involved in the regulation of gene expression
Penaeid shrimp genome provides insights into benthic adaptation and frequent molting
Crustacea, the subphylum of Arthropoda which dominates the aquatic environment, is of major importance in ecology and fisheries. Here we report the genome sequence of the Pacific white shrimp Litopenaeus vannamei, covering similar to 1.66 Gb (scaffold N50 605.56 Kb) with 25,596 protein-coding genes and a high proportion of simple sequence repeats (>23.93%). The expansion of genes related to vision and locomotion is probably central to its benthic adaptation. Frequent molting of the shrimp may be explained by an intensified ecdysone signal pathway through gene expansion and positive selection. As an important aquaculture organism, L. vannamei has been subjected to high selection pressure during the past 30 years of breeding, and this has had a considerable impact on its genome. Decoding the L. vannamei genome not only provides an insight into the genetic underpinnings of specific biological processes, but also provides valuable information for enhancing crustacean aquaculture
De novo assembly and characterization of a maternal and developmental transcriptome for the emerging model crustacean Parhyale hawaiensis
<p>Abstract</p> <p>Background</p> <p>Arthropods are the most diverse animal phylum, but their genomic resources are relatively few. While the genome of the branchiopod <it>Daphnia pulex </it>is now available, no other large-scale crustacean genomic resources are available for comparison. In particular, genomic resources are lacking for the most tractable laboratory model of crustacean development, the amphipod <it>Parhyale hawaiensis</it>. Insight into shared and divergent characters of crustacean genomes will facilitate interpretation of future developmental, biomedical, and ecological research using crustacean models.</p> <p>Results</p> <p>To generate a transcriptome enriched for maternally provided and zygotically transcribed developmental genes, we created cDNA from ovaries and embryos of <it>P. hawaiensis</it>. Using 454 pyrosequencing, we sequenced over 1.1 billion bases of this cDNA, and assembled them <it>de novo </it>to create, to our knowledge, the second largest crustacean genomic resource to date. We found an unusually high proportion of C2H2 zinc finger-containing transcripts, as has also been reported for the genome of the pea aphid <it>Acyrthosiphon pisum</it>. Consistent with previous reports, we detected trans-spliced transcripts, but found that they did not noticeably impact transcriptome assembly. Our assembly products yielded 19,067 unique BLAST hits against <b>nr </b>(E-value cutoff e-10). These included over 400 predicted transcripts with significant similarity to <it>D. pulex </it>sequences but not to sequences of any other animal. Annotation of several hundred genes revealed <it>P. hawaiensis </it>homologues of genes involved in development, gametogenesis, and a majority of the members of six major conserved metazoan signaling pathways.</p> <p>Conclusions</p> <p>The amphipod <it>P. hawaiensis </it>has higher transcript complexity than known insect transcriptomes, and trans-splicing does not appear to be a major contributor to this complexity. We discuss the importance of a reliable comparative genomic framework within which to consider findings from new crustacean models such as <it>D. pulex </it>and <it>P. hawaiensis</it>, as well as the need for development of further substantial crustacean genomic resources.</p
Penaeid shrimp genome provides insights into benthic adaptation and frequent molting
Crustacea, the subphylum of Arthropoda which dominates the aquatic environment, is of major importance in ecology and fisheries. Here we report the genome sequence of the Pacific white shrimp Litopenaeus vannamei, covering ~1.66 Gb (scaffold N50 605.56 Kb) with 25,596 protein-coding genes and a high proportion of simple sequence repeats (>23.93%). The expansion of genes related to vision and locomotion is probably central to its benthic adaptation. Frequent molting of the shrimp may be explained by an intensified ecdysone signal pathway through gene expansion and positive selection. As an important aquaculture organism, L. vannamei has been subjected to high selection pressure during the past 30 years of breeding, and this has had a considerable impact on its genome. Decoding the L. vannamei genome not only provides an insight into the genetic underpinnings of specific biological processes, but also provides valuable information for enhancing crustacean aquaculture
The Complete Genome of an Endogenous Nimavirus (Nimav-1_LVa) From the Pacific Whiteleg Shrimp Penaeus (Litopenaeus) Vannamei
White spot syndrome virus (WSSV), the lone virus of the genus Whispovirus under the family Nimaviridae, is one of the most devastating viruses affecting the shrimp farming industry. Knowledge about this virus, in particular, its evolution history, has been limited, partly due to its large genome and the lack of other closely related free-living viruses for comparative studies. In this study, we reconstructed a full-length endogenous nimavirus consensus genome, Nimav-1_LVa (279,905 bp), in the genome sequence of Penaeus (Litopenaeus) vannamei breed Kehai No. 1 (ASM378908v1). This endogenous virus seemed to insert exclusively into the telomeric pentanucleotide microsatellite (TAACC/GGTTA)n. It encoded 117 putative genes, with some containing introns, such as g012 (inhibitor of apoptosis, IAP), g046 (crustacean hyperglycemic hormone, CHH), g155 (innexin), g158 (Bax inhibitor 1 like). More than a dozen Nimav-1_LVa genes are involved in the pathogen-host interactions. We hypothesized that g046, g155, g158, and g227 (semaphorin 1A like) were recruited host genes for their roles in immune regulation. Sequence analysis indicated that a total of 43 WSSV genes belonged to the ancestral/core nimavirus gene set, including four genes reported in this study: wsv112 (dUTPase), wsv206, wsv226, and wsv308 (nucleocapsid protein). The availability of the Nimav-1_LVa sequence would help understand the genetic diversity, epidemiology, evolution, and virulence of WSSV
Genetic Susceptibility of Cultured Shrimp (\u3ci\u3ePenaeus vannamei\u3c/i\u3e) to Infectious Hypodermal and Hematopoietic Necrosis Virus and \u3ci\u3eBaculovirus penaei\u3c/i\u3e: Possible Relationship with Growth Status and Metabolic Gene Expression
Offspring of four crosses (I, II, III, and IV) of Penaeus vannamei from known high- and low-growth families were challenged with infectious hypodermal and hematopoietic necrosis virus (IHHNV) and Baculovirus penaei (BP) to compare their susceptibility to these viral agents and examine the genetic component involved in disease resistance or susceptibility. Family crosses were made using broodstock from five families developed by the U.S. Marine Shrimp Farming Program. The prevalence of IHHNV infection was highest in cross I and lowest in cross III. Cross I was developed using male and female broodstock from the low-growth family 1.6, and cross III was developed using a female from the high-growth family 1.3 and a male from the low-growth family 1.6. The prevalence of BP infection at Day 4 was highest (100%) in cross IV, which was developed using a female from the low-growth family 1.4 and a male from the high-growth family 1.5. The reciprocal cross, cross III, had the lowest (68%) prevalence at Day 4 postexposure. Both crosses I and II had 88% prevalence of infection at Day 4. Despite 100% prevalence of BP infection in cross IV at 4 days, animals from this cross and cross II exhibited high survival by Day 18 (85 and 77%). On the other hand, crosses I and III (with 88 and 68% prevalence at Day 4, respectively) showed low survival at Day 18 (19 and 24%). On the basis of prevalence of infection and mortality rates, it was concluded that the susceptibility to BP in penaeid shrimp is governed by the genetic background of the parental crosses. The random amplified polymorphic DNA polymorphisms for crosses I, II, III, and IV, were 43, 45, 53, and 51%, respectively, showing no clear relationship between IHHNV and BP prevalence of infection and levels of nuclear genetic diversity. Though the mtDNA haplotypes in offspring from the different crosses were the same, major differences were observed in both steady-state levels and patterns of expression of the mitochondrial 12s rRNA in offspring obtained at various early developmental stages from each of the four crosses. The possible relationship among disease susceptibility, growth status, and expression of mitochondrial 12s rRNA is discussed in the context of a complex nuclear-cytoplasmic genetic system involved in the regulation of gene expression
Multidimensional Fluorescence Fingerprinting for Classification of Shrimp by Location and Species
Parallel factor analysis with soft independent modeling
by class
analogy (PARAFAC-SIMCA) was used to analyze fluorescence data from
shrimp extracts (organic and aqueous phases) to create classification
schemes for two species of shrimp from four different countries. Twenty-four
shrimp (six from each location: Ecuador, Philippines, Thailand, and
United States) were studied; two were classified as statistical outliers.
Using PARAFAC scores from the two aqueous fluorescent components and
the strongest four components from the organic phase, country of origin
was correctly identified at the 95% confidence level for all 22 remaining
specimens; three false positives, at lower confidence levels than
the true positives, were also indicated. A classification scheme which
used all eight fluorescent components reproduced the 22 correct classifications
and reduced the number of false positives to one. Finally, a scheme
using PARAFAC scores from the two aqueous fluorescent components and
the strongest four components from the organic phase, designed to
classify according to species, produced 22 correct matches with no
false positives. Spectral similarities between known chemical species
and the components identified by PARAFAC are suggested for most cases.
The results indicate that environmental effects appear in the fluorescence
fingerprints of shrimp collected in different locations; therefore,
fluorescence measurements on shrimp have the potential to permit geographical
classification of shrimp or, conversely, to permit inferences to be
made about the animal’s environment
Aquatic Invertebrates
This chapter presents an overview of the clinical signs and major disease syndromes affecting captive and wild invertebrates. This grouping includes all animal groups not in the subphylum Vertebrata. Covered in this chapter are the Porifera (sponges), coelenterates (jellyfish, anemones, corals – wild and in cultivation), mollusks (bivalves), gastropods (abalone), cephalopods, crustaceans, and urochordates