Shrimp Genome Research Articles

Additional random, single to multiple genome fragments of Penaeus stylirostris densovirus in the giant tiger shrimp genome have implications for viral disease diagnosis

Scattered reports of viral inserts in shrimp and insect genomes led to the hypothesis that random, autonomous insertion of such sequences occurs in these organisms and leads to specific, heritable immunity. To test the prediction regarding random insertion of viral sequences into the shrimp genome, we examined the giant tiger shrimp for random genomic insertions of Penaeus stylirostris densovirus (also called IHHNV). By PCR analysis using a set of 7 overlapping primer pairs to cover the whole IHHNV genome (4kb), PCR failure with some pairs indicated sequence gaps that revealed a random pattern of putative viral inserts in the genomes of individual shrimp. Targeting a putative insert from one arbitrarily selected specimen, we used genome walking to reveal a viral insert linked to a host microsattelite-like fragment. This differed from 2 previously reported inserted fragments of IHHNV in P. monodon. In one specimen, 2 slightly different inserts were revealed, probably on paired chromosomes. By design and use of chimeric shrimp/virus primer pairs we proved that similar insertions occurred in several shrimp specimens, including those infected with IHHNV but showing no signs of disease. For the infected specimens, the inserts gave false positive PCR test results using 309F/R primers and a new IQ2000 test protocol currently recommended for detection of infectious IHHNV. This is the first experimental support for the hypothesis-based prediction that a random number and length of sequence fragments from a single virus genome may occur in the shrimp genome. Since some inserts can give false positive results for infectious IHHNV with the recommended methods above, they may have a negative effect on international seafood trade. In addition, discard of domesticated shrimp breeding stocks based on such false positive results might have negative consequences, if such inserts are related to shrimp viral disease tolerance, as also hypothesized.

Involvement of WSSV–shrimp homologs in WSSV infectivity in kuruma shrimp: Marsupenaeus japonicus

White spot syndrome virus (WSSV) is pathogenic and specific to shrimp, and is capable of producing a persistent infection in the host. Moreover, shrimp are capable of persistently carrying a single or multiple viruses, allowing them to survive for long periods with latent infections. In order to identify genes that are specially involved in the intricate WSSV–shrimp association, we focused on homologs between the WSSV and shrimp genomes. We here investigated whether homologous WssvORFs ( WssvORF285, WssvORF332) and their homologs in the kuruma shrimp genome ( MjORF16, MjORF18) are important for WSSV infectivity by utilizing dsRNA-mediated RNA interference, and further proposed potential roles of homologous WssvORFs associated with the persistent viral infection stage. Homologous MjORFs were found to be highly up-regulated in several tested tissues upon WSSV infection. Injection of dsRNAs specific to homologous MjORFs, followed by WSSV challenge, led to reduced and delayed shrimp mortality when compared to that of shrimp without dsRNA injection. Silencing of homologous WssvORFs by specific dsRNAs sharply increased shrimp survival. WssvORF332 may function as a latency gene especially associated with the persistent WSSV infection stage while WssvORF285 may be classified into the same group as WssvVP28 and may play a role in virus penetration during the infection. Our results suggest that WSSV–shrimp homologs are involved in WSSV infectivity and support the hypothesis that homologous WssvORFs are related to WSSV latency and pathogenesis.

A gene‐based SNP linkage map for pacific white shrimp, Litopenaeus vannamei

Pacific white shrimp (Litopenaeus vannamei) are of particular economic importance to the global shrimp aquaculture industry. However, limited genomics information is available for the penaeid species. We utilized the limited public information available, mainly single nucleotide polymorphisms (SNPs) and expressed sequence tags, to discover markers for the construction of the first SNP genetic map for Pacific white shrimp. In total, 1344 putative SNPs were discovered, and out of 825 SNPs genotyped, 418 SNP markers from 347 contigs were mapped onto 45 sex-averaged linkage groups, with approximate coverage of 2071 and 2130 cm for the female and male maps, respectively. The average-squared correlation coefficient (r(2)), a measure of linkage disequilibrium, for markers located more than 50 cm apart on the same linkage group, was 0.15. Levels of r(2) increased with decreasing inter-marker distance from approximately 80 cm, and increased more rapidly from approximately 30 cm. A QTL for shrimp gender was mapped on linkage group 13. Comparative mapping to model organisms, Daphnia pulex and Drosophila melanogaster, revealed extensive rearrangement of genome architecture for L. vannamei, and that L. vannamei was more related to Daphnia pulex. This SNP genetic map lays the foundation for future shrimp genomics studies, especially the identification of genetic markers or regions for economically important traits.

Shrimp Molecular Responses to Viral Pathogens

From almost negligible amounts in 1970, the quantity of cultivated shrimp (~3 million metric tons in 2007) has risen to approach that of the capture fishery and it constitutes a vital source of export income for many countries. Despite this success, viral diseases along the way have caused billions of dollars of losses for shrimp farmers. Desire to reduce the losses to white spot syndrome virus in particular, has stimulated much research since 2000 on the shrimp response to viral pathogens at the molecular level. The objective of the work is to develop novel, practical methods for improved disease control. This review covers the background and limitations of the current work, baseline studies and studies on humoral responses, on binding between shrimp and viral structural proteins and on intracellular responses. It also includes discussion of several important phenomena (i.e., the quasi immune response, viral co-infections, viral sequences in the shrimp genome and persistent viral infections) for which little or no molecular information is currently available, but is much needed.

Mining ESTs to Determine the Usefulness of SNPs Across Shrimp Species

Expressed sequence tag (EST) libraries from members of the Penaeidae family and brine shrimp (Artemia franciscana) are currently the primary source of sequence data for shrimp species. Penaeid shrimp are the most commonly farmed worldwide, but selection methods for improving shrimp are limited. A better understanding of shrimp genomics is needed for farmers to use genetic markers to select the best breeding animals. The ESTs from Litopenaeus vannamei have been previously mined for single nucleotide polymorphisms (SNPs). This present study took publicly available ESTs from nine shrimp species, excluding L. vannamei, clustered them with CAP3, predicted SNPs within them using SNPidentifier, and then analyzed whether the SNPs were intra- or interspecies. Major goals of the project were to predict SNPs that may distinguish shrimp species, locate SNPs that may segregate in multiple species, and determine the genetic similarities between L. vannamei and the other shrimp species based on their EST sequences. Overall, 4,597 SNPs were predicted from 4,600 contigs with 703 of them being interspecies SNPs, 735 of them possibly predicting species' differences, and 18 of them appearing to segregate in multiple species. While sequences appear relatively well conserved, SNPs do not appear to be well conserved across shrimp species.

Hyper-expansion of large DNA segments in the genome of kuruma shrimp, Marsupenaeus japonicus

BackgroundHigher crustaceans (class Malacostraca) represent the most species-rich and morphologically diverse group of non-insect arthropods and many of its members are commercially important. Although the crustacean DNA sequence information is growing exponentially, little is known about the genome organization of Malacostraca. Here, we constructed a bacterial artificial chromosome (BAC) library and performed BAC-end sequencing to provide genomic information for kuruma shrimp (Marsupenaeus japonicus), one of the most widely cultured species among crustaceans, and found the presence of a redundant sequence in the BAC library. We examined the BAC clone that includes the redundant sequence to further analyze its length, copy number and location in the kuruma shrimp genome.ResultsMj024A04 BAC clone, which includes one redundant sequence, contained 27 putative genes and seemed to display a normal genomic DNA structure. Notably, of the putative genes, 3 genes encode homologous proteins to the inhibitor of apoptosis protein and 7 genes encode homologous proteins to white spot syndrome virus, a virulent pathogen known to affect crustaceans. Colony hybridization and PCR analysis of 381 BAC clones showed that almost half of the BAC clones maintain DNA segments whose sequences are homologous to the representative BAC clone Mj024A04. The Mj024A04 partial sequence was detected multiple times in the kuruma shrimp nuclear genome with a calculated copy number of at least 100. Microsatellites based BAC genotyping clearly showed that Mj024A04 homologous sequences were cloned from at least 48 different chromosomal loci. The absence of micro-syntenic relationships with the available genomic sequences of Daphnia and Drosophila suggests the uniqueness of these fragments in kuruma shrimp from current arthropod genome sequences.ConclusionsOur results demonstrate that hyper-expansion of large DNA segments took place in the kuruma shrimp genome. Although we analyzed only a part of the duplicated DNA segments, our result suggested that it is difficult to analyze the shrimp genome following normal analytical methodology. Hence, it is necessary to avoid repetitive sequence (such as segmental duplications) when studying the other unique structures in the shrimp genome.

Simultaneous presence of infectious hypodermal and hematopoietic necrosis virus (IHHNV) and Type A virus-related sequence in Penaeus monodon from India

Detection of infectious hypodermal and hematopoietic necrosis virus (IHHNV) in shrimp is complicated by the fact that certain virus-related sequences are integrated into the genome of Penaeus monodon in some parts of the world, which has been reported so far from Africa and Australia. In this study, we evaluated the highly specific and sensitive diagnostic primer sets for detection of infectious IHHNV and integrated virus-related sequence in 177 samples of P. monodon from India. A nested primer set, IHHNV648F/R and IHHNV309F/R was used to specifically detect infectious IHHNV and not the virus-related sequences. IHHNV was detected in 67.4% postlarvae (PL) and 34% adult samples using this primer set. The OIE recommended primers IHHNV392F/R and IHHNV389F/R gave positive reaction for 86.7% PL and 67% adult samples, while the primer pair 77012F and 77353R gave positive reaction with 46.7% PL and 20% adult samples. These primers were found to detect virus-related sequence integrated into the shrimp genome. The analysis of virus-related sequence by MG831F/R primers showed that 33.7% PL and 31.7% adult shrimp possessed Type A virus-related sequence. 22.8% PL and 10.5% adults had both IHHNV and Type A virus-related sequence. Cloning and sequencing 832 bp virus-related sequence from P. monodon from India revealed presence of five shrimp DNA markers between 439 and 825 bp. This study is the first conclusive report on the presence of Type A virus-related sequence in P. monodon from India.

In silico analysis of polymorphic microsatellites in penaeid shrimp and construction of a free-access database

We performed an in silico analysis of all microsatellites so far described for penaeid shrimp and for which the polymorphic behavior has previously been analyzed. The objective of the study was to evaluate the structural characteristics of these microsatellites and identifying patterns which allow the characterization of the nature of these sequences in the penaeid genome. All data were compiled in a free-access database specially constructed for this study. Three hundred non-mononucleotide polymorphic microsatellite loci described for 12 shrimp species belonging to the family Penaeidae were analyzed and simple and compound microsatellites with di-, tri-, tetra-, penta- and hexanucleotide motifs were found. Dinucleotides and trinucleotides were the most frequent motifs among both the simple and the compound microsatellites. Although a certain bias related to different microsatellite isolation methodology could not be discarded, it is possible that part of this microsatellite abundance reflects some degree of conservation of microsatellite motifs among the different species. There was a pronounced motif variability within and between species, indicating high differentiation dynamism of these repetitions in this animal group. This study not only sheds light on the structure of the microsatellites present in the penaeid shrimp genome but also resulted in the free-access Penaeid Shrimp Microsatellite Database (available at http://www.shrimp.ufscar.br) which may be very useful for optimizing the use of these microsatellites.

Infectious hypodermal and hematopoietic necrosis virus (IHHNV)-related sequences in the genome of the black tiger prawn Penaeus monodon from Africa and Australia

We found an infectious hypodermal and hematopoietic necrosis virus (IHHNV)-related sequence within the shrimp genome in populations of Penaeus monodon from Africa and Australia. IHHNV is a singlestranded DNA virus that has caused severe mortality and stunted growth in penaeid shrimp. Recently, IHHNV-related sequences were found in samples of P. monodon from Madagascar and Tanzania. These sequences vary considerably (14 and 8%, respectively) from that of IHHNV found in association with viral epidemics. Laboratory bioassays were carried out with P. monodon and Litopenaeus vannamei to determine if either of these IHHNV-related sequences is infectious. We used juvenile and adult P. monodon containing the virus-related sequences from four geographic regions to generate inocula and tissues for feeding. Specific pathogen free P. monodon and L. vannamei were used as indicator shrimp. During the 2–4 week bioassays, none of the indicator shrimp showed signs of infection or disease. Results of both PCR assays and histological examination of the indicator shrimp were negative for IHHNV infection, indicating that the Africa type IHHNV-related sequences are not infectious. With the shrimp containing the Madagascar type IHHNV-related sequence (designated as type A), we performed genome walking at the 3′ end of the virus-related sequence and found that this virus-related sequence is part of the P. monodon genome. A fragment of 1.9 kb flanking sequence was cloned and sequenced. Sequence analysis showed that this flanking sequence contains shrimp microsatellite DNA. Also, its translated amino acid sequence was highly similar to a retrotransposon. This result provides molecular evidence that the type A IHHNV-related sequence is shrimp DNA. This sequence was found in the P. monodon collected from Africa and Australia.

Analysis of tandem repeats in the genome of Chinese shrimp Fenneropenaeus chinensis

Through random sequencing, we found a total of 884000 base-pairs (bp) of random genomic sequences in the genome of Chinese shrimp (Fenneropenaeus chinensis). Using bio-soft Tandem Repeat Finder (TRF) software, 2159 tandem repeats were found, in which there were 1714 microsatellites and 445 minisatellites, accounting for 79.4% and 20.6% of repeat sequences, respectively. The cumulative length of repeat sequences was found to be 116685 bp, accounting for 13.2% of the total DNA sequence; the cumulative length of microsatellites occupied 9.78% of the total DNA sequence, and that of minisatellites occupied 3.42%. In decreasing order, the 20 most abundant repeat sequence classes were as follows: AT (557), AC (471), AG (274), AAT (92), A (56), AAG (28), ATC (27), ATAG (27), AGG (18), ACT (15), C (11), AAC (11), ACAT (11), CAGA (10), AGAA (9), AGGG (7), CAAA (7), CGCA (6), ATAA (6), AGAGAA (6). Dinucleotide repeats, not only in the aspect of the number, but also in cumulative length, were the preponderant repeat type. There were few classes and low copy numbers of repeat units of the pentanucleotide repeat type, which included only three classes: AGAGA, GAGGC and AAAGA. The classes and copy numbers of heptanucleotide, eleven-nucleotide and thirteen-nucleotide primer-number-composed repeats were distinctly less than that of repeat types beside them.

The shrimp FAMeT cDNA is encoded for a putative enzyme involved in the methylfarnesoate (MF) biosynthetic pathway and is temporally expressed in the eyestalk of different sexes

Methylfarnesoate (MF), an analogue of the insect juvenile hormone III, has been implicated to play a vital role in the regulation of the growth and reproductive development in crustaceans. Farnesoic acid O-methyltransferase (FAMeT) is the key enzyme involved in catalyzing the final step in the MF biosynthetic pathway. In this study, we report the cloning and characterization of the cDNA encoding the putative FAMeT of the shrimp Metapenaeus ensis. FAMeT comprises 280 amino acid residues with a predicted molecular weight of 32 kDa. The predicted putative FAMeT protein reveals a high degree of structural conservation of FAMeT with the lobsters. It shares 79 and 70% sequence identities with the putative FAMeTs of Homarus americanus and Panulirus interruptus, respectively. As revealed by the Southern blot analysis and genomic PCR, only one gene exists in the shrimp genome and the gene is uninterrupted in the coding region. The shrimp FAMeT mRNA is widely distributed in many tissues with the highest expression level observed in the central nervous system. A constant level of FAMeT expression is recorded in the ventral nerve cord of the juveniles and the mature females during the reproductive cycle. Unlike the ventral nerve cord, the eyestalk of the juvenile male, but not the female, expresses FAMeT. Further study shows that the eyestalk of the mature female expresses FAMeT during all stages of ovarian maturation. We spectulate that FAMeT may be important for the regulation of eyestalk neuropeptides. This is the first extensive study on the molecular characterization, structural analysis and expression of the crustacean FAMeT.

Molecular characterization of an additional shrimp hyperglycemic hormone: cDNA cloning, gene organization, expression and biological assay of recombinant proteins

The crustacean eyestalk CHH/MIH/GIH neurohormone gene family represents a unique group of neuropeptides identified mainly in crustaceans. In this study, we report the cloning and characterization of the cDNA and the gene encoding the hyperglycemic hormone (MeCHH-B) of the shrimp Metapenaeus ensis. The amino acid sequence of MeCHH-B shows 85% identity to that of MeCHH-A (formerly MeCHH-like neuropeptide). Two separate but identical MeCHH-B genes were identified in the genome of shrimp by library screening and they are located on different CHH gene clusters. The organization of the MeCHH-B gene is identical to other members of the CHH/MIH/GIH neurohormone family. MeCHH-B is expressed at a constant level in the eyestalks of juveniles and mature females. Unlike the MeCHH-A gene, a low level of MeCHH-B transcripts can also be detected in the central nervous system. Interestingly, the expression pattern of MeCHH-B in the eyestalk of vitellogenic females is reversed to that of the MeCHH-A gene. At the middle stage of gonad maturation, a minimum level of MeCHH-B transcript was recorded and a maximum level of MeCHH-A transcript was detected. Recombinant proteins for MeCHH-A and MeCHH-B were produced by a bacterial expression system. The hemolymph glucose level of bilaterally eyestalk-ablated shrimp increased two-fold 1 h after the rCHH injection and then returned to normal after 2 h. The hyperglycemic effect of these fusion proteins is comparable to that of de-stalked shrimp injected with crude extract from a single sinus gland.

Identification of abundant and informative microsatellites from shrimp (Penaeus monodon) genome.

Microsatellites were isolated from P. monodon genomic libraries by direct sequencing of recombinant clones without probe screening. Forty-nine out of 83 clones sequenced contained 99 microsatellite arrays of three or more repeats. When five or more and ten or more repeats were considered, 28 and 14 microsatellites were detected, respectively. The 99 microsatellites were classified as perfect (75%), imperfect (6%), compound perfect (3%) and compound imperfect (16%). The abundance of di-, tri-, tetra- and hexanucleotide repeats were 67%, 20%, 9% and 3%, respectively. The dinucleotide repeats included 36 (CT)n, 31 (GT)n, 17(AT)n and 3 (CG)n. One octanucleotide repeat (ATTTATTC)5 was found within a large repeat sequence. Optimal annealing temperatures were determined for PCR using 11 primer sets encompassing 15 microsatellites. Ten primer sets provided successful amplifications with allele sizes generally ranging from 139 to 410 bp. All these primers amplified polymorphic loci with PIC values ranging from 0.63 to 0.96. Two primer sets amplified additional bands which can easily be distinguished from the bands of the main locus. Three out of 10 P. monodon microsatellites also amplified alleles in P. vannamei. The abundance and informative nature of P. monodon microsatellites and their potential for cross-species amplification make them useful for genetic studies.

The shrimp hyperglycemic hormone-like neuropeptide is encoded by multiple copies of genes arranged in a cluster

The crustacean hyperglycemic hormone (CHH) plays an important role in the regulation of glucose metabolism. We have cloned and sequenced several cDNAs encoding the preproCHH-like of the shrimp, Metapenaeus ensis. The preproCHH-like peptide of the shrimp consists of a signal peptide, a CHH precursor-like peptide (CPRP) and the CHH-like peptide. Comparative analysis revealed that the signal peptide and the CPRP of the shrimp peptide are the shortest among all the CHHs reported. MeCHH-like is expressed in the eyestalk, but it is not expressed in the heart, hepatopancreas, muscle, nerve cord and pre-hatch embryo. To study the structural organization of the shrimp CHH-like gene, we have screened the genomic DNA library constructed from one shrimp. Three groups of overlapping genomic clones have been isolated. The results from both genomic Southern blot analysis and library screening indicate that the shrimp genome contains at least six copies of the CHH-like genes arranged in a cluster on the chromosome. The size of the CHH-like genes is 1.5–2.1 kb. DNA sequence determinations indicate that the CHH-like genes share 98–100% amino acid sequence identity. There are three exons and two introns in each CHH-like gene. The first intron separates the signal peptide and the second intron separates the mature peptide in the coding region. The 150–200 bp of the upstream 5′ flanking region of the CHH-like genes contains promoters with characteristics similar to most eukaryotic genes. Several putative cis-acting elements are also identified in the first 400 bp 5′ end upstream region. The organization of the shrimp CHH-like genes is similar to that of the molt inhibiting hormone gene of the same shrimp and the crab, Charybdis feriatus.

A novel satellite/microsatellite combination in the genome of the marine shrimp, Penaeus vannamei

In our studies of repeated sequences in the genome of the marine shrimp, Penaeus vannamei ( Pv), we have discovered a novel combination of sequence elements. We inserted restriction fragments of genomic DNA into a plasmid vector and screened for recombinant plasmids containing repeated sequences. Ten of the resulting isolates contained representatives of the same repeated element, a satellite sequence present in one or more blocks of tandemly repeated units. The cloned repeat units range in size from 139 to 188 bp. Embedded within each cloned repeat unit are 6–15 copies of a tandemly repeated pentanucleotide microsatellite. The genome of Pv contains approx. 1 000 000 copies of this satellite/microsatellite unit. Sequences that cross-hybridize strongly with this structure were found in the genomes of lobster and crayfish, but not in other species of the genus Penaeus.