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Comparative Evolution of Duplicated Ddx3 Genes in Teleosts: Insights from Japanese Flounder, Paralichthys olivaceus.

Wang Z, Liu W, Song H, Wang H, Liu J, Zhao H, Du X, Zhang Q - G3 (Bethesda) (2015)

Bottom Line: We confirmed that the two genes originated from teleost-specific genome duplication through synteny and phylogenetic analysis.Additionally, comparative analysis of genome structure, molecular evolution rate, and expression pattern of the two genes in Japanese flounder revealed evidence of subfunctionalization of the duplicated Ddx3 genes in teleosts.Thus, the results of this study reveal novel insights into the evolution of the teleost Ddx3 genes and constitute important groundwork for further research on this gene family.

View Article: PubMed Central - PubMed

Affiliation: Key Laboratory of Marine Genetics and Breeding (MGB), Ministry of Education, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China.

No MeSH data available.


Alignment of the deduced amino acid sequences of teleost Ddx3 genes. Identical amino acids are in gray background. Amino acid sequences with identical underline are encoded by the same exon. Numbers 1−10 stand for the ten exons of uniform size and position in both Ddx3a and Ddx3b genes. The 12 conserved motifs characteristic of DEAD-box proteins are boxed. Amino acid sites under positive selection are in yellow background. Asterisk stand for posterior probability > 0.95.
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fig3: Alignment of the deduced amino acid sequences of teleost Ddx3 genes. Identical amino acids are in gray background. Amino acid sequences with identical underline are encoded by the same exon. Numbers 1−10 stand for the ten exons of uniform size and position in both Ddx3a and Ddx3b genes. The 12 conserved motifs characteristic of DEAD-box proteins are boxed. Amino acid sites under positive selection are in yellow background. Asterisk stand for posterior probability > 0.95.

Mentions: Multiple sequence alignment of deduced full-length DDX3a/b proteins revealed that teleost DDX3a proteins shared higher identity with homologous genes in different species than with DDX3b within the same species (Figure 3). Figure S2 illustrates the genomic structure of Ddx3 genes in four teleost species. The teleost Ddx3 genes contained 18−19 exons. In addition, deep analysis of these exons revealed the presence of 10 exons of uniform size and position in both Ddx3a and Ddx3b genes (Figure 3). Notably, these 10 exons encoded highly identical amino acids containing all the motifs characteristic of DEAD-box proteins (Figure 3).


Comparative Evolution of Duplicated Ddx3 Genes in Teleosts: Insights from Japanese Flounder, Paralichthys olivaceus.

Wang Z, Liu W, Song H, Wang H, Liu J, Zhao H, Du X, Zhang Q - G3 (Bethesda) (2015)

Alignment of the deduced amino acid sequences of teleost Ddx3 genes. Identical amino acids are in gray background. Amino acid sequences with identical underline are encoded by the same exon. Numbers 1−10 stand for the ten exons of uniform size and position in both Ddx3a and Ddx3b genes. The 12 conserved motifs characteristic of DEAD-box proteins are boxed. Amino acid sites under positive selection are in yellow background. Asterisk stand for posterior probability > 0.95.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4528332&req=5

fig3: Alignment of the deduced amino acid sequences of teleost Ddx3 genes. Identical amino acids are in gray background. Amino acid sequences with identical underline are encoded by the same exon. Numbers 1−10 stand for the ten exons of uniform size and position in both Ddx3a and Ddx3b genes. The 12 conserved motifs characteristic of DEAD-box proteins are boxed. Amino acid sites under positive selection are in yellow background. Asterisk stand for posterior probability > 0.95.
Mentions: Multiple sequence alignment of deduced full-length DDX3a/b proteins revealed that teleost DDX3a proteins shared higher identity with homologous genes in different species than with DDX3b within the same species (Figure 3). Figure S2 illustrates the genomic structure of Ddx3 genes in four teleost species. The teleost Ddx3 genes contained 18−19 exons. In addition, deep analysis of these exons revealed the presence of 10 exons of uniform size and position in both Ddx3a and Ddx3b genes (Figure 3). Notably, these 10 exons encoded highly identical amino acids containing all the motifs characteristic of DEAD-box proteins (Figure 3).

Bottom Line: We confirmed that the two genes originated from teleost-specific genome duplication through synteny and phylogenetic analysis.Additionally, comparative analysis of genome structure, molecular evolution rate, and expression pattern of the two genes in Japanese flounder revealed evidence of subfunctionalization of the duplicated Ddx3 genes in teleosts.Thus, the results of this study reveal novel insights into the evolution of the teleost Ddx3 genes and constitute important groundwork for further research on this gene family.

View Article: PubMed Central - PubMed

Affiliation: Key Laboratory of Marine Genetics and Breeding (MGB), Ministry of Education, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China.

No MeSH data available.