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Horizontally transferred genes in the genome of Pacific white shrimp, Litopenaeus vannamei.

ABSTRACT: BACKGROUND: In recent years, as the development of next-generation sequencing technology, a growing number of genes have been reported as being horizontally transferred from prokaryotes to eukaryotes, most of them involving arthropods. As a member of the phylum Arthropoda, the Pacific white shrimp Litopenaeus vannamei has to adapt to the complex water environments with various symbiotic or parasitic microorganisms, which provide a platform for horizontal gene transfer (HGT). RESULTS: In this study, we analyzed the genome-wide HGT events in L. vannamei. Through homology search and phylogenetic analysis, followed by experimental PCR confirmation, 14 genes with HGT event were identified: 12 of them were transferred from bacteria and two from fungi. Structure analysis of these genes showed that the introns of the two fungi-originated genes were substituted by shrimp DNA fragment, two genes transferred from bacteria had shrimp specific introns inserted in them. Furthermore, around other three bacteria-originated genes, there were three large DNA segments inserted into the shrimp genome. One segment was a transposon that fully transferred, and the other two segments contained only coding regions of bacteria. Functional prediction of these 14 genes showed that 6 of them might be related to energy metabolism, and 4 others related to defense of the organism. CONCLUSIONS: HGT events from bacteria or fungi were happened in the genome of L. vannamei, and these horizontally transferred genes can be transcribed in shrimp. This is the first time to report the existence of horizontally transferred genes in shrimp. Importantly, most of these genes are exposed to a negative selection pressure and appeared to be functional.

SUBMITTER: Yuan JB

PROVIDER: S-EPMC3750580 | biostudies-literature | 2013

REPOSITORIES: biostudies-literature

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Horizontally transferred genes in the genome of Pacific white shrimp, Litopenaeus vannamei.

Yuan Jian-Bo JB Zhang Xiao-Jun XJ Liu Cheng-Zhang CZ Wei Jian-Kai JK Li Fu-Hua FH Xiang Jian-Hai JH

BMC evolutionary biology 20130806

<h4>Background</h4>In recent years, as the development of next-generation sequencing technology, a growing number of genes have been reported as being horizontally transferred from prokaryotes to eukaryotes, most of them involving arthropods. As a member of the phylum Arthropoda, the Pacific white shrimp Litopenaeus vannamei has to adapt to the complex water environments with various symbiotic or parasitic microorganisms, which provide a platform for horizontal gene transfer (HGT).<h4>Results</h ...[more]

PMID: 23914989

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Project description:A simple bioassay that quantifies feed intake as an estimation of relative attractability of feeds containing different ingredients in the Pacific white shrimp Litopenaeus vannamei is described. Fish meal (FM), fish protein hydrolysate (FPH), squid meal (SqM) and casein (CN) were assessed at the same dietary level for their relative influence on feed intake rates of Litopenaeus vannamei. A bland diet containing 92% whole wheat grain meal, 6% diatomaceous earth and 2% alginate with a known low attractability was used as the standard control or base diet. Ingredients were added to the bland base control diet at a level of 3% as fed. Shrimp were stocked into 80 L glass tanks (n= 20 per tank) in a recirculating aquaculture system. Tanks were randomly assigned to one of five diet treatments (3tanks/treatment). Experiments measuring the attractability of each feed were conducted twice daily at 0900 hours and 1330 hours over a five day period. For each experiment, 40 feed pellets (ca. 1 g) corresponding to the assigned treatment were provided to each tank. To calculate the rate of feed intake, pellets remaining in each tank were counted at six minute intervals for a seventy-two minute period. Differences in rate of feed intake among diets were evaluated using Cox Regression Analysis. This attractability assay required only small amounts of ingredients and incorporated ingredients into a bland feed, which significantly reduces the influence from other ingredients or compound in the pellets. All of the test protein ingredients, especially SqM, in the feeds significantly increased the feed consumption rate. The diet containing SqM was consumed at a significantly higher rate than those containing casein and FM but not FPH. FPH and CN containing diets were not significantly different but consumed at a higher rate than the diet containing FM. Results of these trials indicate that the presence of certain ingredients can increase feed intake, thereby increasing nutrient availability of the diets. This reported method to determine consumption of diets containing certain ingredients can be considered as a valid method to estimate attractability.

Project description:BackgroundEugenol is the most commonly used plant anesthetic to relieve the stressors during various aquaculture procedures. This study aims to investigate the pharmacokinetics of eugenol in Pacific white shrimp by immersion baths in a simulated transportation.ResultsThe pharmacokinetics of eugenol were firstly investigated in Pacific white shrimp by immersion baths of 300 mg L- 1 eugenol over 5 min (Treatment 1), 10 mg L- 1 eugenol during 24 h (Treatment 2) and a sequential immersion administration (Treatment 3). Concentrations of eugenol in hemolymph, hepatopancreas, and muscle were determined using Gas chromatography-tandem mass spectrometry (GC-MS/MS). After immersion bath of Treatment 1, the elimination half-life (t1/2z) values are 1.3 h and 11 h for hepatopancreas and muscles, indicating the rapid absorption and elimination of eugenol in shrimp. Under the Treatment 2 administration, the eugenol peak concentration is 6527.9 μg/kg in muscle, followed by 402.8 μg/kg in hepatopancreas, with the lowest concentration of 37.9 μg/L in hemolymph. Area under the curve (AUC0-∞) values lie in the order of muscle > hepatopancreas > hemolymph, suggesting that eugenol tends to accumulate in muscle by the immersion administration. Moreover, the average residence time (MRT0-∞) values of 38.6, 23.0 and 115.3 h for hemolymph, hepatopancreas and muscle are achieved, which may indicate that hepatopancreas is the main organ for elimination of eugenol. After combining the conditions in a sequential bath immersion of eugenol (Treatment 3), the maximum concentration (Cmax) values of eugenol are higher than those achieved in Treatment 2, indicating that accumulation of eugenol happened in haemolymph, hepatopancreas and muscle. In addition, the corresponding t1/2z values are 4.7, 14.9 and 47.6 h, respectively, suggesting the faster elimination from the tissues following sequential administration. After the immersion bath, eugenol concentrations in muscle of Pacific white shrimp are lower than 2.5 mg/kg at 2 h, 48 h and 24.5 h in Treatment 1 ~ 3.ConclusionsA withdrawal period of 2 h, 48 h and 24.5 h following a 300 mg L- 1 of eugenol over a 5-min, 10 mg L- 1 eugenol concentration during a 24-h and combined conditions in a sequential immersion bath were suggested.

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Horizontally transferred genes in the genome of Pacific white shrimp, Litopenaeus vannamei.

Publications

Horizontally transferred genes in the genome of Pacific white shrimp, Litopenaeus vannamei.

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