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

Yuan JB, Zhang XJ, Liu CZ, Wei JK, Li FH, Xiang JH - BMC Evol. Biol. (2013)

Bottom Line: 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.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, 7, Nanhai Road, Qingdao 266071, China.

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.

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Nine HGT genes participate in the TCA cycle and electron transport chain of the shrimp mitochondrion. The majority of the functions of these HGT genes are predicted relate to energy metabolism. The HGT genes are shown in gray oblongs and the HGT genes differentially expressed during five development stages are marked with additional red borders.
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Figure 4: Nine HGT genes participate in the TCA cycle and electron transport chain of the shrimp mitochondrion. The majority of the functions of these HGT genes are predicted relate to energy metabolism. The HGT genes are shown in gray oblongs and the HGT genes differentially expressed during five development stages are marked with additional red borders.

Mentions: Both TCA cycle and the electron-transport chain are predominant pathways of energy metabolism in the matrix of the mitochondria [39,40]. The HGT gene acsf is predicted to Acetyl-CoA synthetase, which is involved in the metabolism of carbohydrate during the first step of energy generation in the tricarboxylic acid cycle (TCA cycle) [41]. Other four HGT genes (dhfr, sdrp, deha and mopB) are predicted as genes in electron transport (Figure 4). dhfr is an HGT gene annotated to encode dihydrofolate reductase which can use NADH as an electron donor to produce tetrahydrofolate for certain amino acids synthesis in 1-carbon transfer chemistry [42], and sdrp are predicted to encode NAD(H) or NADP(H) oxidoreductases. deha, predicted to be an HGT gene from fungi, encodes a cytochrome b5 reductase-like enzyme that catalyzes the reduction of cytochrome b5 using NADH as the electron donor [43]. mopB is predicted to encode molybdopterin oxidoreductase which participates in transferring electrons to cytochrome c [44]. Furthermore, a gene encoding cytochrome c, which contains a heme-binding domain for energy production and conversion, is located upstream of mopB and was transferred along with mopB (Figure 3). And at last, the energy-transducing protein ExbB, encoded by HGT gene exbB, is a part of TonB-ExbB-ExbD complex to form an energy transduction system [45-47]. Therefore, according to the information of predicted functions, all these six HGT genes may associate with energy metabolism.


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

Yuan JB, Zhang XJ, Liu CZ, Wei JK, Li FH, Xiang JH - BMC Evol. Biol. (2013)

Nine HGT genes participate in the TCA cycle and electron transport chain of the shrimp mitochondrion. The majority of the functions of these HGT genes are predicted relate to energy metabolism. The HGT genes are shown in gray oblongs and the HGT genes differentially expressed during five development stages are marked with additional red borders.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3750580&req=5

Figure 4: Nine HGT genes participate in the TCA cycle and electron transport chain of the shrimp mitochondrion. The majority of the functions of these HGT genes are predicted relate to energy metabolism. The HGT genes are shown in gray oblongs and the HGT genes differentially expressed during five development stages are marked with additional red borders.
Mentions: Both TCA cycle and the electron-transport chain are predominant pathways of energy metabolism in the matrix of the mitochondria [39,40]. The HGT gene acsf is predicted to Acetyl-CoA synthetase, which is involved in the metabolism of carbohydrate during the first step of energy generation in the tricarboxylic acid cycle (TCA cycle) [41]. Other four HGT genes (dhfr, sdrp, deha and mopB) are predicted as genes in electron transport (Figure 4). dhfr is an HGT gene annotated to encode dihydrofolate reductase which can use NADH as an electron donor to produce tetrahydrofolate for certain amino acids synthesis in 1-carbon transfer chemistry [42], and sdrp are predicted to encode NAD(H) or NADP(H) oxidoreductases. deha, predicted to be an HGT gene from fungi, encodes a cytochrome b5 reductase-like enzyme that catalyzes the reduction of cytochrome b5 using NADH as the electron donor [43]. mopB is predicted to encode molybdopterin oxidoreductase which participates in transferring electrons to cytochrome c [44]. Furthermore, a gene encoding cytochrome c, which contains a heme-binding domain for energy production and conversion, is located upstream of mopB and was transferred along with mopB (Figure 3). And at last, the energy-transducing protein ExbB, encoded by HGT gene exbB, is a part of TonB-ExbB-ExbD complex to form an energy transduction system [45-47]. Therefore, according to the information of predicted functions, all these six HGT genes may associate with energy metabolism.

Bottom Line: 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.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, 7, Nanhai Road, Qingdao 266071, China.

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.

Show MeSH