Generation of the first BAC-based physical map of the common carp genome

<p>Abstract</p> <p>Background</p> <p>Common carp (<it>Cyprinus carpio</it>), a member of Cyprinidae, is the third most important aquaculture species in the world with an annual global production of 3.4 million metric tons, accounting for nearly 14% of the all freshwater aquaculture production in the world. Apparently genomic resources are needed for this species in order to study its performance and production traits. In spite of much progress, no physical maps have been available for common carp. The objective of this project was to generate a BAC-based physical map using fluorescent restriction fingerprinting.</p> <p>Result</p> <p>The first generation of common carp physical map was constructed using four- color High Information Content Fingerprinting (HICF). A total of 72,158 BAC clones were analyzed that generated 67,493 valid fingerprints (5.5 × genome coverage). These BAC clones were assembled into 3,696 contigs with the average length of 476 kb and a N50 length of 688 kb, representing approximately 1.76 Gb of the common carp genome. The largest contig contained 171 BAC clones with the physical length of 3.12 Mb. There are 761 contigs longer than the N50, and these contigs should be the most useful resource for future integrations with linkage map and whole genome sequence assembly. The common carp physical map is available at <url>http://genomics.cafs.ac.cn/fpc/WebAGCoL/Carp/WebFPC/</url>.</p> <p>Conclusion</p> <p>The reported common carp physical map is the first physical map of the common carp genome. It should be a valuable genome resource facilitating whole genome sequence assembly and characterization of position-based genes important for aquaculture traits.</p

A first generation BAC-based physical map of the rainbow trout genome

Background: Rainbow trout (Oncorhynchus mykiss) are the most-widely cultivated cold freshwater fish in the world and an important model species for many research areas. Coupling great interest in this species as a research model with the need for genetic improvement of aquaculture production efficiency traits justifies the continued development of genomics research resources. Many quantitative trait loci (QTL) have been identified for production and life-history traits in rainbow trout. A bacterial artificial chromosome (BAC) physical map is needed to facilitate fine mapping of QTL and the selection of positional candidate genes for incorporation in marker-assisted selection (MAS) for improving rainbow trout aquaculture production. This resource will also facilitate efforts to obtain and assemble a whole-genome reference sequence for this species.[br/] Results: The physical map was constructed from DNA fingerprinting of 192,096 BAC clones using the 4-color high-information content fingerprinting (HICF) method. The clones were assembled into physical map contigs using the finger-printing contig (FPC) program. The map is composed of 4,173 contigs and 9,379 singletons. The total number of unique fingerprinting fragments (consensus bands) in contigs is 1,185,157, which corresponds to an estimated physical length of 2.0 Gb. The map assembly was validated by 1) comparison with probe hybridization results and agarose gel fingerprinting contigs; and 2) anchoring large contigs to the microsatellite-based genetic linkage map.[br/] Conclusion: The production and validation of the first BAC physical map of the rainbow trout genome is described in this paper. We are currently integrating this map with the NCCCWA genetic map using more than 200 microsatellites isolated from BAC end sequences and by identifying BACs that harbor more than 300 previously mapped markers. The availability of an integrated physical and genetic map will enable detailed comparative genome analyses, fine mapping of QTL, positional cloning, selection of positional candidate genes for economically important traits and the incorporation of MAS into rainbow trout breeding programs

Mercury mobility in a salt marsh colonised by Halimione portulacoides

The present study intends to increase the knowledge on the mobility of mercury in a salt marsh colonised by Halimione portulacoides. Mercury distribution in the sediment layers and its incorporation into the plant biomass were assessed, as well as the potential export of mercury from the contaminated area to the adjacent environment. Mercury pools in the sediments ranged from 560 to 943 mg m-2 and are largely associated with the solid fraction, with just a small amount being associated with the pore waters. Estimated diffusive fluxes of reactive mercury ranged from 1.3 to 103 ng m-2 d-1. Despite the above ground biomass values being comparatively higher than below ground biomass values, the mercury pools were much higher in the root system (0.06-0.16 mg m-2 and 29-102 mg m-2, respectively). The annual bioaccumulation of mercury in above ground tissues was estimated in 0.11 mg m-2 y-1, while in below ground biomass the values were higher (72 mg m-2 y-1). The turnover rates of H. portulacoides biomass suggest higher mercury mobility within the plant rhizosphere. Taking into account the pools of mercury in above ground biomass, the export of mercury by macro-detritus following the "outwelling hypothesis" is not significant for the mercury balance in the studied ecosystem. The mercury accumulated in the below ground part of the plant is quite mobile, being able to return to the sediment pool throughout the mineralisation process.http://www.sciencedirect.com/science/article/B6V74-4SRM83C-1/1/afd89d1885b88e6149c4ae0e1e4adb5

Assessment of methylmercury production in a temperate salt marsh (Ria de Aveiro Lagoon, Portugal)

http://www.sciencedirect.com/science/article/B6V6N-4R718RP-2/1/3b5a21889355817d215071a3a8033fb