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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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Differential expression of eight HGT genes at five developmental stages of shrimp. Gene expression level was evaluated by FPKM value. * indicates the HGT genes were significantly differentially expressed when compared with the lowest expressed development stage.
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Figure 5: Differential expression of eight HGT genes at five developmental stages of shrimp. Gene expression level was evaluated by FPKM value. * indicates the HGT genes were significantly differentially expressed when compared with the lowest expressed development stage.

Mentions: To detect whether HGT genes have effects on shrimp growth and development, we performed differential gene expression (DGE) analysis on these HGT genes, based on the transcriptomes of five developmental stages of shrimp larvae (see Methods). The number of reads aligned to the transcripts were calculated (Additional file 1: Table S4), and the expression level of each transcript was measured by FPKM values (fragments per kilobase of exon per million fragments mapped). High coverage of reads successfully supported for the following DGE analysis. Nine HGT genes showed differential expression among five stages (Figure 5, Additional file 1: Table S5). stat displayed the highest expression level (FPKM values ranged from 1018.57 to 2910.86) at all five stages, while rpsF was expressed at the lowest (FPKM values ranged from 0 to 1.43). rpsF seems only expressed at the stage of zoea and mysis. Similar to rpsF, the other two fundamental DNA and protein synthesis related HGT genes (dhfr and ankp) displayed an expression pattern that gene expression level at the stage of zoea and mysis was generously higher than the other stages (Figure 5, Additional file 1: Table S4). In addition to providing fundamental nucleic acid precursors and certain amino acids, dhfr also participates in energy metabolism. Three other energy metabolism-related HGT genes showed DGE, and two of them (acsf and sdrp) displayed similar expression pattern with dhfr. deha showed the reverse expression pattern, in that it showed lower expression at stages of zoea and mysis than at other stages (Figure 5). In addition, three defense-related HGT genes (rpc2, omtp and stat) were universally more highly expressed than other HGT genes (Figure 5, Additional file 1: Table S5), indicating that they may play an important role in early shrimp development.


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)

Differential expression of eight HGT genes at five developmental stages of shrimp. Gene expression level was evaluated by FPKM value. * indicates the HGT genes were significantly differentially expressed when compared with the lowest expressed development stage.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 5: Differential expression of eight HGT genes at five developmental stages of shrimp. Gene expression level was evaluated by FPKM value. * indicates the HGT genes were significantly differentially expressed when compared with the lowest expressed development stage.
Mentions: To detect whether HGT genes have effects on shrimp growth and development, we performed differential gene expression (DGE) analysis on these HGT genes, based on the transcriptomes of five developmental stages of shrimp larvae (see Methods). The number of reads aligned to the transcripts were calculated (Additional file 1: Table S4), and the expression level of each transcript was measured by FPKM values (fragments per kilobase of exon per million fragments mapped). High coverage of reads successfully supported for the following DGE analysis. Nine HGT genes showed differential expression among five stages (Figure 5, Additional file 1: Table S5). stat displayed the highest expression level (FPKM values ranged from 1018.57 to 2910.86) at all five stages, while rpsF was expressed at the lowest (FPKM values ranged from 0 to 1.43). rpsF seems only expressed at the stage of zoea and mysis. Similar to rpsF, the other two fundamental DNA and protein synthesis related HGT genes (dhfr and ankp) displayed an expression pattern that gene expression level at the stage of zoea and mysis was generously higher than the other stages (Figure 5, Additional file 1: Table S4). In addition to providing fundamental nucleic acid precursors and certain amino acids, dhfr also participates in energy metabolism. Three other energy metabolism-related HGT genes showed DGE, and two of them (acsf and sdrp) displayed similar expression pattern with dhfr. deha showed the reverse expression pattern, in that it showed lower expression at stages of zoea and mysis than at other stages (Figure 5). In addition, three defense-related HGT genes (rpc2, omtp and stat) were universally more highly expressed than other HGT genes (Figure 5, Additional file 1: Table S5), indicating that they may play an important role in early shrimp development.

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