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Deep-sea fishes provide a unique opportunity to study the physiology and evolutionary adaptation to extreme environments. We carried out a high throughput sequencing analysis on a 454 GS-FLX titanium plate using unnormalized cDNA libraries from six tissues of A. carbo. Assemblage and annotationswere performed byNewbler and InterPro/Pfamanalyses, respectively. The assembly of 544,491 high quality reads provided 8,319 contigs, 55.6% of which retrieved blast hits against theNCBI nonredundant database or were annotated with ESTscan. Comparison of functional genes at both the protein sequences and protein stability levels, associated with adaptations to depth, revealed similarities between A. carbo and other bathypelagic fishes. A selection of putative genes was standardized to evaluate the correlation between number of contigs and their normalized expression, as determined by qPCR amplification. The screening of the libraries contributed to the identification of new EST simple-sequence repeats (SSRs) and to the design of primer pairs suitable for population genetic studies as well as for tagging and mapping of genes. The characterization of the deep-sea fish A. carbo first transcriptome is expected to provide abundant resources for genetic, evolutionary, and ecological studies of this species and the basis for further investigation of depth-related adaptation processes in fishes. [ABSTRACT FROM AUTHOR]

The marine environment presents particular challenges for our understanding of the factors that determine gene flow and consequent population structure. For marine fish, various aspects of life history have been considered important in an environment with few physical barriers, but dominated by current patterns, often varying with depth. These factors include the abundance and longevity of larval stages, typically more susceptible to movement along current paths. It also includes adult body size, fecundity and longevity with ‘ r-selected’ species typically thought capable of greater gene flow and consequent panmixia. Here we investigate the population genetics of the orange roughy ( Hoplostethus atlanticus), a clearly ‘ K-selected’ species with habitat dependence on sea mounts for spawning, relatively large body size, a brief larval stage and relatively low fecundity. We used 14 polymorphic microsatellite loci to test the hypothesis that these characteristics will result in philopatry and genetic structure in the Atlantic Ocean. We discuss possible evolutionary mechanisms that could explain the results, which show the opposite pattern, with effective panmixia across thousands of kilometres in the North Atlantic. [ABSTRACT FROM AUTHOR]

Paucity of data on population structure and connectivity in deep sea species remains a major obstacle to their sustainable management and conservation in the face of ever increasing fisheries pressure and other forms of impacts on deep sea ecosystems. The roughhead grenadier Macrourus berglax presents all the classical characteristics of a deep sea species, such as slow growth and low fecundity, which make them particularly vulnerable to anthropogenic impact, due to their low resilience to change. In this study, the population structure of the roughhead grenadier is investigated throughout its geographic distribution using two sets of molecular markers: a partial sequence of the Control Region of mitochondrial DNA and species-specific microsatellites. No evidence of significant structure was found throughout the North Atlantic, with both sets of molecular markers yielding the same results of overall homogeneity. We posit two non-mutually exclusive scenarios that can explain such outcome: i) substantial high gene flow among locations, possibly maintained by larval stages, ii) very large effective size of post-glacially expanded populations. The results can inform management strategies in this by-caught species, and contribute to the broader issue of biological connectivity in the deep ocean. [ABSTRACT FROM AUTHOR]