Fosmid library end sequencing reveals a rarely known genome structure of marine shrimp Penaeus monodon

<p>Abstract</p> <p>Background</p> <p>The black tiger shrimp (<it>Penaeus monodon</it>) is one of the most important aquaculture species in the world, representing the crustacean lineage which possesses the greatest species diversity among marine invertebrates. Yet, we barely know anything about their genomic structure. To understand the organization and evolution of the <it>P. monodon </it>genome, a fosmid library consisting of 288,000 colonies and was constructed, equivalent to 5.3-fold coverage of the 2.17 Gb genome. Approximately 11.1 Mb of fosmid end sequences (FESs) from 20,926 non-redundant reads representing 0.45% of the <it>P. monodon </it>genome were obtained for repetitive and protein-coding sequence analyses.</p> <p>Results</p> <p>We found that microsatellite sequences were highly abundant in the <it>P. monodon </it>genome, comprising 8.3% of the total length. The density and the average length of microsatellites were evidently higher in comparison to those of other taxa. AT-rich microsatellite motifs, especially poly (AT) and poly (AAT), were the most abundant. High abundance of microsatellite sequences were also found in the transcribed regions. Furthermore, <it>via </it>self-BlastN analysis we identified 103 novel repetitive element families which were categorized into four groups, <it>i.e</it>., 33 WSSV-like repeats, 14 retrotransposons, 5 gene-like repeats, and 51 unannotated repeats. Overall, various types of repeats comprise 51.18% of the <it>P. monodon </it>genome in length. Approximately 7.4% of the FESs contained protein-coding sequences, and the Inhibitor of Apoptosis Protein (IAP) gene and the Innexin 3 gene homologues appear to be present in high abundance in the <it>P. monodon </it>genome.</p> <p>Conclusions</p> <p>The redundancy of various repeat types in the <it>P. monodon </it>genome illustrates its highly repetitive nature. In particular, long and dense microsatellite sequences as well as abundant WSSV-like sequences highlight the uniqueness of genome organization of penaeid shrimp from those of other taxa. These results provide substantial improvement to our current knowledge not only for shrimp but also for marine crustaceans of large genome size.</p

Temperature dependency of element incorporation into European eel (Anguilla anguilla) otoliths

The present study experimentally tested the influence of water temperature on the inclusion of 15 elements into juvenile European eel (Anguilla anguilla) otoliths in freshwater. It should be investigated (1) if temperature effects on otolith Sr/Ca might impair the interpretation of migration studies and (2) if the elemental composition of otoliths can be used to reconstruct experienced temperature histories of eels. Therefore, eels were kept under full experimental conditions at three different water temperatures (14 °C, 19 °C and 24 °C) for 105 days. Thereafter, laser ablation inductively coupled mass spectrometry (LA-ICPMS) was conducted on the outer edge of their otoliths. Our analyses revealed significant temperature effects on otolith Na/Ca, Sr/Ca, Mg/Ca, Mn/Ca, Ba/Ca, Zr/Ca and Y/Ca ratios. Variations of Sr/Ca caused by temperature were far below those used to detect eel movements between waters of different salinities and will therefore not affect the interpretation of migration studies. Elemental fingerprints of Sr/Ca, Mg/Ca, Mn/Ca and Ba/Ca ratios resulted in clearly separated groups according to temperature treatments, indicating that changes in water temperature might lead to characteristic changes in otolith element composition. However, the successful application of elemental fingerprints to reconstruct moderate changes of water temperature seems doubtful because the influence of somatic growth on otolith microchemistry still remains unclear, and temperature-induced variations could be overlaid by changes of water element concentrations during growth periods. Nevertheless, our results contribute to the completion of knowledge about factors influencing element incorporation and help to explain variations in element composition of fish otoliths