Molecular tracing of viral diseases in aquaculture

Molecular Tracing of Viral Diseases in Aquaculture = Traçage Moléculaire des Maladies Virales en Aquaculture : Colloque, Montpellier (FRA), 2015/01/27-29International audienc

De novo identification of viral pathogens from cell culture hologenomes

<p>Abstract</p> <p>Background</p> <p>Fast, specific identification and surveillance of pathogens is the cornerstone of any outbreak response system, especially in the case of emerging infectious diseases and viral epidemics. This process is generally tedious and time-consuming thus making it ineffective in traditional settings. The added complexity in these situations is the non-availability of pure isolates of pathogens as they are present as mixed genomes or hologenomes. Next-generation sequencing approaches offer an attractive solution in this scenario as it provides adequate depth of sequencing at fast and affordable costs, apart from making it possible to decipher complex interactions between genomes at a scale that was not possible before. The widespread application of next-generation sequencing in this field has been limited by the non-availability of an efficient computational pipeline to systematically analyze data to delineate pathogen genomes from mixed population of genomes or hologenomes.</p> <p>Findings</p> <p>We applied next-generation sequencing on a sample containing mixed population of genomes from an epidemic with appropriate processing and enrichment. The data was analyzed using an extensive computational pipeline involving mapping to reference genome sets and <it>de-novo </it>assembly. In depth analysis of the data generated revealed the presence of sequences corresponding to <it>Japanese encephalitis </it>virus. The genome of the virus was also independently <it>de-novo </it>assembled. The presence of the virus was in addition, verified using standard molecular biology techniques.</p> <p>Conclusions</p> <p>Our approach can accurately identify causative pathogens from cell culture hologenome samples containing mixed population of genomes and in principle can be applied to patient hologenome samples without any background information. This methodology could be widely applied to identify and isolate pathogen genomes and understand their genomic variability during outbreaks.</p

First evidence of the activation of Cg-timp, an immune response component of pacific oysters, through a damage-associated molecular pattern pathway

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A European epidemiological survey of Vibrio splendidus clade shows unexplored diversity and massive exchange of virulence factors

The Vibrio splendidus clade has previously been associated with epidemic outbreaks of various aquatic animals, as in the case of the cupped oyster, Crassostrea gigas. To investigate whether involved strains could present a clonal origin and to identify possible alternative background carriage animals or zooplankton, a large epidemiological survey was conducted on isolates of the splendidus clade. For this purpose, Vibrio strains were isolated from various samples including oysters, mussels, sediments, zooplankton, and sea water on the basis of a North/South gradient of the European sea water zone (Ireland, The Netherlands, France, Italy, and Spain). A total of 435 isolates were successfully associated to the V. splendidus clade using real time polymerase chain reaction with 16S specific primers and probes. A multiple-locus variable-number tandem-repeat analysis (VNTR) was conducted on all isolates based on a multiplex PCR-VNTR with a set of primer pairs designed from the V. tasmaniensis LGP32 genome. Preliminary validation of the primers on a set of collection strains from the V. splendidus clade confirmed that the former V. splendidus-related LGP32 and relative strains were related to V. tasmaniensis rather than to the type strain V. splendidus LMG 4042. The VNTR analysis was then successfully conducted on 335 isolates which led to the characterization of 87 different profiles. Our results showed that (1) the high diversity of VNTR did not enlighten significant correlation between a specific pattern and the origin of collected samples. However, populations isolated from animal samples tend to differ from those of the background environment; (2) oyster mortality events could not be linked to the clonal proliferation of a particular VNTR type. However, few different patterns seemed successively associated with samples collected during peaks of oyster's mortality. (3) Finally, no correlation could be seen between specific VNTR patterns and sequence phylogeny of the virulence factors vsm and ompU that were detected among strains isolated during as well as outside mortality events. These results, combined with incongruence observed between the ompU and vsm phylogenetic trees, suggested both large diffusion of strains and massive lateral gene transfer within the V. splendidus clade

Distribution of Medicago species and their microsymbionts in a saline region of Algeria

We studied symbiosis of Medicago ciliaris and Medicago polymorpha, two legumes of forage and ecological importance in Algeria, especially in saline soil regions. We report the spatial distribution of the two species and their microsymbionts along salinity gradient transects in the Sebkha of Misserghin (Algeria, North Africa). Seeds and root nodules were sampled from 10 sites. Twenty-seven rhizobial strains were isolated from root nodules and characterized as fast-growers and slime-producers on yeast mannitol agar. By partial sequencing of the gene coding for the 16 S ribosomal RNA, they were found to be affiliated to Rhizobium, Sinorhizobium, and Agrobacterium but several strains had sequences with separate positions. Interestingly one of these was further assigned to Phyllobacterium. Opposite to rhizobia, the distribution of the two Medicago species varied along the salinity gradient, M. ciliaris being dominant in the low NaCl concentration zones and M. polymorpha dominant in the most saline zones. Tolerance to salinity, of both bacterial and plant partners, was studied under laboratory conditions, showing that plants are susceptible to NaCl concentrations of 50mM, 15-fold lower than that of their associated rhizobia (800mM)

An ancient truncated duplication of the anti-Mullerian hormone receptor type 2 gene is a potential conserved master sex determinant in the Pangasiidae catfish family.

Evolution of sex determination (SD) in teleosts is amazingly dynamic, as reflected by the variety of different master sex-determining genes identified. Pangasiids are economically important catfishes in South-Asian countries, but little is known about their SD system. Here, we generated novel genomic resources for 12 Pangasiids and characterized their SD system. Based on a Pangasianodon hypophthalmus, chromosome-scale genome assembly we identified an anti-Müllerian hormone receptor type Ⅱ gene (amhr2) duplication, which was further characterized as being sex-linked in males and expressed only in testes. These results point to a Y chromosome male-specific duplication (amhr2by) of the autosomal amhr2a. Sequence annotation revealed that the P. hypophthalmus Amhr2by is truncated in its N-terminal domain, lacking the cysteine-rich extracellular part of the receptor that is crucial for ligand binding, suggesting a potential route for its neofunctionalization. Reference-guided assembly of 11 additional Pangasiids, along with sex-linkage studies, revealed that this truncated amhr2by duplication is a male-specific conserved gene in Pangasiids. Reconstructions of the amhr2 phylogeny suggested that amhr2by arose from an ancient duplication / insertion event at the root of the Siluroidei radiation that is dated around 100 million years ago. Altogether these results bring multiple lines of evidence supporting that amhr2by is an ancient and conserved master sex-determining gene in Pangasiids, a finding that highlights the recurrent usage of the transforming growth factor β pathway, which is often used for the recruitment of teleost master sex determination genes, and brings another empirical case towards the understanding of the dynamics of sex determination systems