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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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Structures of three large horizontally transferred DNA fragments and their locations in both the donor and receptor genome. The conserved regions between shrimp genomic contigs and corresponding donor genomes are displayed.
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Figure 3: Structures of three large horizontally transferred DNA fragments and their locations in both the donor and receptor genome. The conserved regions between shrimp genomic contigs and corresponding donor genomes are displayed.

Mentions: When comparing the donor genome with the shrimp genome contigs, three pairs of relatively large segments showed significant similarity around the position of HGT genes (Figure 3). HGT gene tnpA, which encodes a transposase, is derived from a transposon of E. coli that comprises three transposase-encoding genes (tnpX, tnpR, tnpA) and non-coding regions. In addition to the whole transposon, there was also a kch gene (encoding a voltage-gated potassium channel) downstream of the transposon, and the whole segment (6,913 bp) was completely integrated into the genome of L. vannamei. Transposons generally contribute little or nothing to the host’s phenotype, but some horizontally transferred transposons have been identified to benefit the recipient’s genomic evolution [30,31]. In addition to this large segment, there was one more gene, tonB, encoding a membrane spanning protein in the TonB-ExbB-ExbD complex [32], which was located downstream of the transposon in the donor genome. The other two genes (exbB and exbD, which encode ExbB and ExbD) were located far from tonB in the downstream. The exbB gene is one of the homologs of HGT gene exbB that was detected in this study (Table 1). It seems this horizontally transferred transposon might have served as a carrier for foreign genetic materials [31].


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)

Structures of three large horizontally transferred DNA fragments and their locations in both the donor and receptor genome. The conserved regions between shrimp genomic contigs and corresponding donor genomes are displayed.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 3: Structures of three large horizontally transferred DNA fragments and their locations in both the donor and receptor genome. The conserved regions between shrimp genomic contigs and corresponding donor genomes are displayed.
Mentions: When comparing the donor genome with the shrimp genome contigs, three pairs of relatively large segments showed significant similarity around the position of HGT genes (Figure 3). HGT gene tnpA, which encodes a transposase, is derived from a transposon of E. coli that comprises three transposase-encoding genes (tnpX, tnpR, tnpA) and non-coding regions. In addition to the whole transposon, there was also a kch gene (encoding a voltage-gated potassium channel) downstream of the transposon, and the whole segment (6,913 bp) was completely integrated into the genome of L. vannamei. Transposons generally contribute little or nothing to the host’s phenotype, but some horizontally transferred transposons have been identified to benefit the recipient’s genomic evolution [30,31]. In addition to this large segment, there was one more gene, tonB, encoding a membrane spanning protein in the TonB-ExbB-ExbD complex [32], which was located downstream of the transposon in the donor genome. The other two genes (exbB and exbD, which encode ExbB and ExbD) were located far from tonB in the downstream. The exbB gene is one of the homologs of HGT gene exbB that was detected in this study (Table 1). It seems this horizontally transferred transposon might have served as a carrier for foreign genetic materials [31].

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