Transcriptome characterization of the South African abalone Haliotis midae using sequencing-by-synthesis

<p>Abstract</p> <p>Background</p> <p>Worldwide, the genus <it>Haliotis </it>is represented by 56 extant species and several of these are commercially cultured. Among the six abalone species found in South Africa, <it>Haliotis midae </it>is the only aquacultured species. Despite its economic importance, genomic sequence resources for <it>H. midae</it>, and for abalone in general, are still scarce. Next generation sequencing technologies provide a fast and efficient tool to generate large sequence collections that can be used to characterize the transcriptome and identify expressed genes associated with economically important traits like growth and disease resistance.</p> <p>Results</p> <p>More than 25 million short reads generated by the Illumina Genome Analyzer were <it>de novo </it>assembled in 22,761 contigs with an average size of 260 bp. With a stringent <it>E</it>-value threshold of 10^-10, 3,841 contigs (16.8%) had a BLAST homologous match against the Genbank non-redundant (NR) protein database. Most of these sequences were annotated using the gene ontology (GO) and eukaryotic orthologous groups of proteins (KOG) databases and assigned to various functional categories. According to annotation results, many gene families involved in immune response were identified. Thousands of simple sequence repeats (SSR) and single nucleotide polymorphisms (SNP) were detected. Setting stringent parameters to ensure a high probability of amplification, 420 primer pairs in 181 contigs containing SSR loci were designed.</p> <p>Conclusion</p> <p>This data represents the most comprehensive genomic resource for the South African abalone <it>H. midae </it>to date. The amount of assembled sequences demonstrated the utility of the Illumina sequencing technology in the transcriptome characterization of a non-model species. It allowed the development of several markers and the identification of promising candidate genes for future studies on population and functional genomics in <it>H. midae </it>and in other abalone species.</p

The Structural Diversity of Carbohydrate Antigens of Selected Gram-Negative Marine Bacteria

Marine microorganisms have evolved for millions of years to survive in the environments characterized by one or more extreme physical or chemical parameters, e.g., high pressure, low temperature or high salinity. Marine bacteria have the ability to produce a range of biologically active molecules, such as antibiotics, toxins and antitoxins, antitumor and antimicrobial agents, and as a result, they have been a topic of research interest for many years. Among these biologically active molecules, the carbohydrate antigens, lipopolysaccharides (LPSs, O-antigens) found in cell walls of Gram-negative marine bacteria, show great potential as candidates in the development of drugs to prevent septic shock due to their low virulence. The structural diversity of LPSs is thought to be a reflection of the ability for these bacteria to adapt to an array of habitats, protecting the cell from being compromised by exposure to harsh environmental stress factors. Over the last few years, the variety of structures of core oligosaccharides and O-specific polysaccharides from LPSs of marine microrganisms has been discovered. In this review, we discuss the most recently encountered structures that have been identified from bacteria belonging to the genera Aeromonas, Alteromonas, Idiomarina, Microbulbifer, Pseudoalteromonas, Plesiomonas and Shewanella of the Gammaproteobacteria phylum; Sulfitobacter and Loktanella of the Alphaproteobactera phylum and to the genera Arenibacter, Cellulophaga, Chryseobacterium, Flavobacterium, Flexibacter of the Cytophaga-Flavobacterium-Bacteroides phylum. Particular attention is paid to the particular chemical features of the LPSs, such as the monosaccharide type, non-sugar substituents and phosphate groups, together with some of the typifying traits of LPSs obtained from marine bacteria. A possible correlation is then made between such features and the environmental adaptations undertaken by marine bacteria

Mass mortality of flat oysters (Ostrea rivularis) associated with a bloom of Procentrum sp. in the port of Zhangiang, South China

No description availabl

Rock Lobster Enhancement and Aquaculture Sub-Program: Health assurance of Southern Rock Lobsters

No description availabl

Assessment over time of the infectivity of gill-derived and seawater dispersed Neoparamoeba permaquidensis (Page, 1987)

A laboratory infection trial tested if Neoparamoeba pemaquidensis, the protozoan responsible for AGD, remained infectious for up to 14 days when out of contact with host tissues. In the infection trial, 14 Atlantic salmon (Salmo salar) were exposed to gill-derived paramoebae, which had been out of contact with hosts for up to 14 days. At the conclusion of the trial fish tested immunodot blot positive and were positive for histology. This implies that infection occurs from water to fish and the zone of infection around salmon farms may be very extensive

Clubbing and necrosis gill (CNG) syndrome in sea-caged Atlantic salmon, Salmo salar L., in Tasmania: an initial report

In autumn 1993, an outbreak of gill disease occurred in Atlantic salmon, Salmo salar L., smolts farmed in the Huon estuary in southern Tasmania, Australia. Histologically, the presumptive primary lesion appeared as focal, sometimes full thickness, gill necrosis, which showed no host reaction in the initial stages. Healing of these damaged areas gave rise to conspicuous expanded tips or clubbing of gill filaments. The term clubbing and necrosis gill (CNG) syndrome is suggested to include both these histological features. Fusion of lamellae proximally along the filament, often with vascular dilation, was also a feature of the condition. Similar lesions have been described previously in the literature, but the initial necrosis followed by the very prominent clubbing of filaments was sufficiently different from previous descriptions to warrant designation of this condition as a distinct entity