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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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Flowchart for identification of HGT genes in L. vannamei. The eliminated and remaining numbers of gene segments in each step are listed on the figure.
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Figure 1: Flowchart for identification of HGT genes in L. vannamei. The eliminated and remaining numbers of gene segments in each step are listed on the figure.

Mentions: In this study, an exhaustive detection method was used to identify HGT genes in L. vannamei (see Methods). Homologous BLAST analysis was used initially to detect HGT genes with a view for identifying homologous genes of non-mating species from shrimp (Figure 1). Initially, 65,582 gene segments were filtered out because there were no homologs detected among them. These sequences probably represent shrimp unique gene segments or non-coding DNA. In the second stage of homologous searching, more than 92% of the gene segments, which were most similar to other arthropod sequence, were excluded. Then, only 965 HGT candidates were left. During this procedure, two classes of sequences were filtered out: gene segments that only showed homology to arthropods and those having higher BLAST similarity scores with arthropods than any other species. However, several potential HGT events may be missed by this procedure, in that some truly HGT of Arthropoda may be considered as vertical inheritance. In the third homologous searching procedure, BLAST searches against the GenBank non-redundant protein database (nr) were implemented to extract sequences from an even larger spectrum of species. As small numbers of homologs are not sufficient for phylogenetic analysis and tree construction, we selected HGT candidates with more than 10 homologs in the nr database. Thus, after filtering genes in above procedures, only 722 HGT candidates remained for phylogenetic analysis (Figure 1).


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)

Flowchart for identification of HGT genes in L. vannamei. The eliminated and remaining numbers of gene segments in each step are listed on the figure.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 1: Flowchart for identification of HGT genes in L. vannamei. The eliminated and remaining numbers of gene segments in each step are listed on the figure.
Mentions: In this study, an exhaustive detection method was used to identify HGT genes in L. vannamei (see Methods). Homologous BLAST analysis was used initially to detect HGT genes with a view for identifying homologous genes of non-mating species from shrimp (Figure 1). Initially, 65,582 gene segments were filtered out because there were no homologs detected among them. These sequences probably represent shrimp unique gene segments or non-coding DNA. In the second stage of homologous searching, more than 92% of the gene segments, which were most similar to other arthropod sequence, were excluded. Then, only 965 HGT candidates were left. During this procedure, two classes of sequences were filtered out: gene segments that only showed homology to arthropods and those having higher BLAST similarity scores with arthropods than any other species. However, several potential HGT events may be missed by this procedure, in that some truly HGT of Arthropoda may be considered as vertical inheritance. In the third homologous searching procedure, BLAST searches against the GenBank non-redundant protein database (nr) were implemented to extract sequences from an even larger spectrum of species. As small numbers of homologs are not sufficient for phylogenetic analysis and tree construction, we selected HGT candidates with more than 10 homologs in the nr database. Thus, after filtering genes in above procedures, only 722 HGT candidates remained for phylogenetic analysis (Figure 1).

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