Shrimp aquaculture contributes significantly to global economic growth, and the whiteleg shrimp, Penaeus vannamei, is a leading species in this industry. However, Vibrio parahaemolyticus infection poses a major challenge in ensuring the success of P. vannamei aquaculture. Despite its significance in this industry, the biological knowledge of its pathogenesis remains unclear. Hence, this study was conducted to identify the interaction sites and binding affinity between several immune-related proteins of P. vannamei with V. parahaemolyticus proteins associated with virulence factors. Potential interaction sites and the binding affinity between host and pathogen proteins were identified using molecular docking and dynamics (MD) simulation. The P. vannamei-V. parahaemolyticus protein-protein interaction of Complex 1 (Ferritin-HrpE/YscL family type III secretion apparatus protein), Complex 2 (Protein kinase domain-containing protein-Chemotaxis CheY protein), and Complex 3 (GPCR-Chemotaxis CheY protein) was found to interact with -4319.76, -5271.39, and -4725.57 of the docked score and the formation of intermolecular bonds at several interacting residues. The docked scores of Complex 1, Complex 2, and Complex 3 were validated using MD simulation analysis, which revealed these complexes greatly contribute to the interactions between P. vannamei and V. parahaemolyticus proteins, with binding free energies of -22.50 kJ/mol, -30.20 kJ/mol, and -26.27 kJ/mol, respectively. This finding illustrates the capability of computational approaches to search for molecular binding sites between host and pathogen, which could increase the knowledge of Vibrio spp. infection on shrimps, which then can be used to assist in the development of effective treatment.
The invasive freshwater crayfish Orconectes limosus mitogenome was recovered by genome skimming. The mitogenome is 16,223 base pairs in length consisting of 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs, and a non-coding AT-rich region. The O. limosus mitogenome has an AT bias of 71.37% and base composition of 39.8% for T, 10.3% for C, 31.5% for A, and 18.4% for G. The mitogene order is identical to two other genera of northern hemisphere crayfish that have been sequenced for this organelle.
The complete mitochondrial genome of the Bass yabby Trypaea australiensis was obtained from a partial genome scan using the MiSeq sequencing system. The T. australiensis mitogenome is 16,821 bp in length (70.25% A + T content) made up of 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs and a putative 1977 bp non-coding AT-rich region. This Trypaea mitogenome sequence is the 5th for the family Callianassidae and represents a new gene order for the Decapoda involving protein-coding, rRNA and tRNA genes and the control region.
The mitochondrial genome sequence of the Australian freshwater shrimp, Paratya australiensis, is presented, which is the fourth for genera of the superfamily Atyoidea and the first atyid from the southern hemisphere. The base composition of the P. australiensis, mitogenome is 33.55% for T, 18.24% for C, 35.16% for A, and 13.06% for G, with an AT bias of 71.58%. It has a mitogenome of 15,990 base pairs comprised of 13 protein-coding, 2 ribosomal subunit and 22 transfer RNAs genes and a non-coding AT-rich region. The mitogenome gene order for the species is typical for atyid shrimps, which conform to the primitive pan crustacean model.
The complete mitochondrial genome of the hermit crab Clibanarius infraspinatus was recovered by genome skimming using Next-Gen sequencing. The Clibanarius infraspinatus mitogenome has 16,504 base pairs (67.94% A + T content) made up of 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs and a putative 1500 bp non-coding AT-rich region. The Clibanarius infraspinatus mitogenome sequence is the first for the family Diogenidae and the second for the superfamily Paguroidea and exhibits a translocation of the ND3 gene not previously reported for the Decapoda.
The mitochondrial genome sequence of the stone crab, Myomenippe fornasinii, second of the superfamily Eriphioidea is documented. Myomenippe fornasinii has a mitogenome of 15,658 base pairs consisting of 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs and a non-coding AT-rich region. The base composition of the M. fornasinii mitogenome is 36.10% for T, 18.52% for C, 35.48% for A, and 9.90% for G, with an AT bias of 71.58%. The mitogenome gene order conforms to what is the standard arrangement for brachyuran crabs.
The mitochondrial genome sequence of the Morton Bay bug, Thenus orientalis, is documented, which makes it the second mitogenome for species of the family Scyllaridae and the ninth for members of the superfamily Palinuroidae. Thenus orientalis has a mitogenome of 16,826 base pairs consisting of 13 protein-coding genes, 2 ribosomal subunit genes, 23 transfer RNAs, and a non-coding AT-rich region. The base composition of the T. orientalis mitogenome is 31.31% for T, 23.77% for C, 31.05% for A, and 13.87% for G, with an AT bias of 62.36%. In addition to a duplicated trnS1 and several other tRNA gene rearrangements, the mitogenome gene order has novel protein coding gene order with the nad6 and cob genes translocated as a block to a location downstream of the nad3 gene.
The complete mitochondrial genome of the swimming crab Thalamita crenata was obtained from a partial genome scan using the MiSeq sequencing system. The Thalamita crenata mitogenome has 15,787 base pairs (70% A+T content) made up of 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs, and a putative 897 bp non-coding AT-rich region. This Thalamita mitogenome sequence is the first for the genus and the eighth for the family Portunidae.
The complete mitochondrial genome of the moon crab Ashtoret lunaris was obtained from a partial genome scan using the MiSeq sequencing system. The Ashtoret lunaris mitogenome is 15,807 base pairs in length (70% A + T content) and made up of 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs, and a putative 956 bp non-coding AT-rich region. This A. lunaris mitogenome sequence is the first for the genus, as well as the family Matutidae and superfamily Calappoidea.
The emergence of cost-effective and rapid sequencing approaches has resulted in an exponential rise in the number of mitogenomes on public databases in recent years, providing greater opportunity for undertaking large-scale comparative genomic and systematic research. Nonetheless, current datasets predominately come from small and disconnected studies on a limited number of related species, introducing sampling biases and impeding research of broad taxonomic relevance. This study contributes 21 crustacean mitogenomes from several under-represented decapod infraorders including Polychelida and Stenopodidea, which are used in combination with 225 mitogenomes available on NCBI to investigate decapod mitogenome diversity and phylogeny. An overview of mitochondrial gene orders (MGOs) reveals a high level of genomic variability within the Decapoda, with a large number of MGOs deviating from the ancestral arthropod ground pattern and unevenly distributed among infraorders. Despite the substantial morphological and ecological variation among decapods, there was limited evidence for correlations between gene rearrangement events and species ecology or lineage specific nucleotide substitution rates. Within a phylogenetic context, predicted scenarios of rearrangements show some MGOs to be informative synapomorphies for some taxonomic groups providing strong independent support for phylogenetic relationships. Additional comparisons for a range of mitogenomic features including nucleotide composition, strand asymmetry, unassigned regions and codon usage indicate several clade-specific trends that are of evolutionary and ecological interest.
Two new species of Hesionidae, Parahesione pulvinata sp. nov. and Parahesione apiculata sp. nov. are described based on materials collected at tidal flats in Okinawa (Japan) from burrows of the ghost shrimps Neocallichirus jousseaumei and Glypturus armatus. The two new species are characterized by having eight enlarged cirri, dorsal cirrophores with dorsal foliose lobe and biramous parapodia, and by lacking median antenna. Parahesione apiculata sp. nov. has digitate lobes on the posterior margin of the dorsal foliose lobe (absent in P. pulvinata sp. nov.). The two new species were never found outside the ghost shrimp burrows, suggesting they are obligate symbionts. Phylogenetic analyses based on four concatenated genes suggest that the symbiotic lifestyle has evolved several times in Hesionidae.
Next-Gen sequencing was used to recover the complete mitochondrial genome of Cherax tenuimanus. The mitogenome consists of 15,797 base pairs (68.14% A + T content) containing 13 protein-coding genes, two ribosomal subunit genes, 22 transfer RNAs, and a 779 bp non-coding AT-rich region. Mitogenomes have now been recovered for all six species of Cherax native to Western Australia.
The present study describes the length-weight relationships (LWRs) of four Acetes species (Acetes indicus, A. serrulatus,
A. japonicus and A. sibogae) which were sampled from offshore trawling and inshore catches along the west coast of
Peninsular Malaysia. Morphometric measurements (total length, TL and wet weight, WW) were obtained from the samples
and LWRs were estimated. All LWRs were significant (p<0.05) for the four species, with the coefficient of determination, R2
>
0.659. The estimated b values for LWR were 2.432-3.403. The R2
value was >0.84 when the data was analysed according
to inshore and offshore samples. Male and female A. indicus and A. serrulatus demonstrated negative allometric growth
whilst male A. japonicus and A. sibogae showed isometric growth type. Positive allometric growth was depicted by a
combined group of male and female A. sibogae. This study has contributed to the knowledge of the offshore and inshore
distribution patterns of different populations of Acetes spp. in the Straits of Malacca. It also presents a comparison of
the LWRs between offshore and inshore catches of A. indicus and A. serrulatus, with the inshore catches of A. japonicus
and A. sibogae, which have not been previously reported. The findings of this study would contribute to the conservation
and management of this commercially important fisheries resource.
The intra- and inter-specific variation of Acetes shrimps were evaluated based on samples collected from in-shore catches and off-shore trawling around the west coast of Peninsular Malaysia. Species captured were identified as Acetes indicus, A. serrulatus, A. japonicus and A. sibogae. A region of the mitochondrial cytochrome c oxidase subunit I (COI) gene comprising 552 base pairs (bp) was amplified from 159 Acetes specimens. The sequence alignment analysis generated phylogenetic trees which depicted the four major clades that were consistent with the species identified morphologically. These four species varied considerably for haplotype and nucleotide diversity, with A. indicus and A. serrulatus showing different demographic histories. Furthermore, the observation of two clades in the A. indicus and A. sibogae lineages, with relatively high levels of intraspecific divergence, suggests that cryptic diversity is possibly present in these two taxa. This study has contributed to the knowledge of the distribution patterns and molecular phylogenetics of four Acetes spp. in the Straits of Malacca.
Detection of diatom frustules in bone marrow (diatom test) is used for diagnosing ante-mortem drowning where the usual signs of drowning are not present in dead bodies recovered from water. However, controversies over the reliability of diatom test results are continuing. There have been indications on the possibilities of diatoms entering into systemic circulation from atmospheric air, food and drink. While diatoms have been demonstrated in the gut content of edible marine forms such as shrimps and clams, the present study, for the first time, provides empirical evidence on the prevalence as well as abundance of diatom frustules in the samples of cooked non-vegetarian foodstuffs that impend human consumption in Kelantan, Malaysia. It is found that 50 g each of cleaned and cooked prawns and of clams impending human consumption contain about 8360 and 29,054 diatom frustules, respectively. A person accustomed to prawn and clam food would be ingesting an estimated 2 million diatoms in a single year. Considering the suggestion that detection of five diatom frustules in 10 g of bone marrow would suffice for concluding drowning as mode of death, and the fact that there is yet no proof that diatom frustules do not enter into the human systemic circulation through the digestive tract, the estimated number of diatom frustules routinely ingested acquires significance since entry of a few of such ingested frustules into the systemic circulation can lead to false positive test results. The findings of this research raise two important issues: first, population based routine food related diatom ingestion requires to be estimated, and, second, studies have to be initiated to categorically prove or disprove the possibility of entry of diatom frustules into the systemic circulation via the digestive tract.
Majority of the studies on the effect of chitin and chitosan on growth and carcass characteristics of broiler chickens has concentrated more on shrimp chitin and shrimp chitosan, and often with contradictory results. Therefore, the objective of this present study is to evaluate and compare the effect of dietary chitin and chitosan from cricket and shrimp on growth performance, carcass, and organ characteristics of broiler chickens. One hundred fifty-day-old male Cobb500 broiler chicks of similar average weight were randomly allotted into one of the five dietary treatments with three replicates. Treatment 1 (T1) chicks were fed basal diet only (control), treatment 2 and 3 (T2 and T3) chicks were given basal diet with 0.5 g/kg diet of cricket chitin and cricket chitosan, respectively, while treatment 4 and 5 (T4 and T5) chicks were served basal diet with 0.5 g/kg diet of shrimp chitin and shrimp chitosan respectively. No significant variation occurred between cricket chitin and shrimp chitin, although data on growth performance were higher in cricket chitin, but growth performance varied significantly between cricket chitosan and shrimp chitosan. This study revealed that cricket chitin at 0.5 g/kg significantly improved growth performance, carcass quality, and organ characteristics of broilers more than chitosan. Birds fed basal diet alone, although gained more weight, also accumulated more fat having the poorest feed conversion ratio (FCR) and the highest mortality. However, carcass of birds fed cricket chitin was the leanest and thus economically beneficial as they consumed the least amount of feed with the best FCR.
The vp28 gene encoding an envelope protein (28 kDa) of white spot syndrome virus (WSSV) was amplified from WSSV-infected tiger shrimp that originated from Malaysia. Recombinant VP28 protein (r-28) was expressed in Escherichia coli and used as an antigen for preparation of monoclonal antibodies (MAbs). Three murine MAbs (6F6, 6H4 and 9C10) that were screened by r-28 antigen-based enzyme-linked immunosorbent assay (ELISA) were also able to recognize viral VP28 protein as well as r-28 on Western blot. Three non-overlapping epitopes of VP28 protein were determined using the MAbs in competitive ELISA; thus, an antigen-capture ELISA (Ac-ELISA) was developed by virtue of these MAbs. Ac-ELISA can differentiate WSSV-infected shrimp from uninfected shrimp and was further confirmed by a polymerase chain reaction (PCR) and Western blot. Approximately 400 pg of purified WSSV sample and 20 pg of r-28 could be detected by Ac-ELISA, which is comparable in sensitivity to PCR assay but more sensitive than Western blot in the detection of purified virus. Hemolymph and tissue homogenate samples collected from a shrimp farm in Malaysia during December 2000 and July 2001 were also detected by Ac-ELISA and PCR with corroborating results.
Intensive research on the effectiveness of chemoattractants has been widely explored to improve the feed qualities in expanding crustacean farming. Taste preferences in slipper lobster remained unknown despite their significant contribution to the lobster fisheries. Chemoattractants allow better performance in aquaculture species by increasing food attractiveness and palatability. Amino acids (AA) have been leading in previous research on crustacean feeding behavior. Given that slipper lobster possesses chemoreceptors to detect and orient towards food, this study investigated an approach to identify the AA with the most potent chemoattractant in eliciting a response from slipper lobster. Behavioral assays were performed to evaluate the responses of slipper lobster Thenus orientalis (carapace length, 52.34 ± 1.52 mm) on 15 crystalline AA and three derivatives of AA (DAA) at three concentrations between 10-1 and 10-3 M as test substances (TS). Meretrix sp. extract was used as a positive control and clean filtered seawater as a negative control. The behavioral responses of 14 T. orientalis were evaluated based on their antennular flicking rate, third maxillipeds activity, and substrate probing by the pereiopods. T. orientalis responded to the solutions of single AA down to a concentration of 10-3 M, excluding histidine and serine. The behavioral activity displayed by T. orientalis increased with the TS concentrations. L-glutamic acid monosodium salt monohydrate, betaine, and glycine solutions elicited the most behavioral responses, whereas histidine exhibited the lowest behavioral responses. Conclusively, L-glutamic acid monosodium salt monohydrate, betaine, and glycine can be potential chemoattractants for T. orientalis.
Discovery of species-specific interaction between the host and virus has drawn the interest of many researchers to study the evolution of the newly emerged virus. Comparative genome analysis provides insights of the virus functional genome evolution and the underlying mechanisms of virus-host interactions. The analysis of nucleotide composition signified the evolution of nodavirus towards host specialization in a host-specific mutation manner. GC-rich genome of betanodavirus was significantly deficient in UpA and UpU dinucleotides composition, whilst the AU-rich genome of gammanodavirus was deficient in CpG dinucleotide. The capsid of MrNV and PvNV of gammanodavirus retains the highest abundance of adenine and uracil at the second codon position, respectively, which were found to be very distinctive from the other genera. ENC-GC3 plot inferred the influence of natural selection and mutational pressure in shaping the evolution of MrNV RdRp and capsid, respectively. Furthermore, CAI/eCAI analysis predicts a comparable adaptability of MrNV in squid, Sepia officinalis than its natural host, Macrobrachium rosenbergii. Thus, further study is warranted to investigate the capacity of MrNV replication in S. officinalis owing to its high codon adaptation index.
The incidence of Vibrio parahaemolyticus in products of the Malaysian export shrimp processing industry was investigated through the stages from the catch to that of the cooked, peeled and frozen product. The organism was commonly found in freshly caught and landed shrimp, and could be detected by enrichment culture at all stages of processing. The number of V. parahaemolyticus in shrimp varied from nil to 4x10(4), and 19 of the 50 serotypes in the current antigenic scheme were found, O1-K38 and O1-K32 occurring most often. All the isolates were Kanagawa-negative; one strain was a sucrose-positive variant. The study indicated that specifications of 10(2) g-1 for V. parahaemolyticus in raw tropical shellfish are too stringent but that the Malaysian shrimp industry should be able to meet this requirement for cooked shrimp.