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Molecular diversity of antimicrobial effectors in the oyster Crassostrea gigas.

Schmitt P, Gueguen Y, Desmarais E, Bachère E, de Lorgeril J - BMC Evol. Biol. (2010)

Bottom Line: To gain insight into the molecular diversity of antimicrobial peptides and proteins in the oyster Crassostrea gigas, we characterized and compared the sequence polymorphism of the antimicrobial peptides (AMPs), Cg-Defensins (Cg-Defs) and Cg-Proline Rich peptide (Cg-Prp), and of the bactericidal permeability increasing protein, Cg-BPI.High diversification among the three antimicrobial effectors was evidenced by this polymorphism survey.This study shows for the first time in a mollusc that antimicrobial peptides and proteins have been subject to distinct patterns of diversification and we evidence the existence of different evolutionary routes leading to such sequence variability.

View Article: PubMed Central - HTML - PubMed

Affiliation: Ifremer, CNRS, Université de Montpellier II, IRD, UMR 5119 Ecosystèmes Lagunaires, Place Eugène Bataillon, CC80, 34095 Montpellier, France. Julien.De.Lorgeril@ifremer.fr

ABSTRACT

Background: To gain insight into the molecular diversity of antimicrobial peptides and proteins in the oyster Crassostrea gigas, we characterized and compared the sequence polymorphism of the antimicrobial peptides (AMPs), Cg-Defensins (Cg-Defs) and Cg-Proline Rich peptide (Cg-Prp), and of the bactericidal permeability increasing protein, Cg-BPI. For that, we analyzed genomic and transcript sequences obtained by specific PCR amplification and in silico searches.

Results: High diversification among the three antimicrobial effectors was evidenced by this polymorphism survey. On the basis of sequence phylogenies, each AMP aggregates into clearly defined groups of variants and is the product of a multigenic family displaying a variety of gene structures. In contrast, Cg-bpi forms a single group and is encoded by a single gene copy. Moreover, we identified for both AMPs several genetic mechanisms of diversification such as recombination, parallel mutations leading to phylogenetic homoplasy and indel events. In addition, the non synonymous to synonymous substitutions ratio by codon (dN/dS) revealed several negatively and positively selected sites for both AMPs, suggesting that directional selection pressures have shaped their sequence variations.

Conclusions: This study shows for the first time in a mollusc that antimicrobial peptides and proteins have been subject to distinct patterns of diversification and we evidence the existence of different evolutionary routes leading to such sequence variability.

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Alignments of amino acids sequences of putative isoforms for Cg-defs and Cg-prp from C. gigas. a. Cg-Defm (FJ669323-FJ669336) and Cg-defhs (FJ669341- FJ669352). b. Cg-Prp (FJ669354- FJ669402). Highlighted sites showed evidence of positive (in black) or negative (in gray) selection (p < 0.05). Dots indicate identical residues and gaps (-) were introduced to obtain maximum sequence identity. The different domains are indicated in white boxes at the bottom of alignments.
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Figure 4: Alignments of amino acids sequences of putative isoforms for Cg-defs and Cg-prp from C. gigas. a. Cg-Defm (FJ669323-FJ669336) and Cg-defhs (FJ669341- FJ669352). b. Cg-Prp (FJ669354- FJ669402). Highlighted sites showed evidence of positive (in black) or negative (in gray) selection (p < 0.05). Dots indicate identical residues and gaps (-) were introduced to obtain maximum sequence identity. The different domains are indicated in white boxes at the bottom of alignments.

Mentions: From all sequences analyzed in this study, we identified 43 variants of Cg-Prp, 24 variants of Cg-BPI, 9 variants of Cg-Defm, 10 variants of Cg-Defhs and only 5 variants of Cg-Actin. Thus, we then analyzed if the sequence diversity has been shaped by directional selection pressures. The ratios of non synonymous to synonymous substitutions (dN/dS) for each codon of the four molecules indicate several sites under negative and positive selection for both AMPs (Cg-Defs and Cg-Prp), but not for Cg-BPI and Cg-Actin (Figure 4). To obtain dN/dS ratios, we first excluded all obvious recombinant sequences. Then, to assess the significance of the findings, we carried out a likelihood ratio test (LRT) and considered only codons showing significantly negative and positive selection (p < 0.05). Ten and 11 residues showing significant negative selection were identified in Cg-Defs and Cg-Prp respectively. For both AMPs, we detected a lower number of positively selected sites (3 and 6 residues in Cg-Defs and Cg-Prp respectively).


Molecular diversity of antimicrobial effectors in the oyster Crassostrea gigas.

Schmitt P, Gueguen Y, Desmarais E, Bachère E, de Lorgeril J - BMC Evol. Biol. (2010)

Alignments of amino acids sequences of putative isoforms for Cg-defs and Cg-prp from C. gigas. a. Cg-Defm (FJ669323-FJ669336) and Cg-defhs (FJ669341- FJ669352). b. Cg-Prp (FJ669354- FJ669402). Highlighted sites showed evidence of positive (in black) or negative (in gray) selection (p < 0.05). Dots indicate identical residues and gaps (-) were introduced to obtain maximum sequence identity. The different domains are indicated in white boxes at the bottom of alignments.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2823732&req=5

Figure 4: Alignments of amino acids sequences of putative isoforms for Cg-defs and Cg-prp from C. gigas. a. Cg-Defm (FJ669323-FJ669336) and Cg-defhs (FJ669341- FJ669352). b. Cg-Prp (FJ669354- FJ669402). Highlighted sites showed evidence of positive (in black) or negative (in gray) selection (p < 0.05). Dots indicate identical residues and gaps (-) were introduced to obtain maximum sequence identity. The different domains are indicated in white boxes at the bottom of alignments.
Mentions: From all sequences analyzed in this study, we identified 43 variants of Cg-Prp, 24 variants of Cg-BPI, 9 variants of Cg-Defm, 10 variants of Cg-Defhs and only 5 variants of Cg-Actin. Thus, we then analyzed if the sequence diversity has been shaped by directional selection pressures. The ratios of non synonymous to synonymous substitutions (dN/dS) for each codon of the four molecules indicate several sites under negative and positive selection for both AMPs (Cg-Defs and Cg-Prp), but not for Cg-BPI and Cg-Actin (Figure 4). To obtain dN/dS ratios, we first excluded all obvious recombinant sequences. Then, to assess the significance of the findings, we carried out a likelihood ratio test (LRT) and considered only codons showing significantly negative and positive selection (p < 0.05). Ten and 11 residues showing significant negative selection were identified in Cg-Defs and Cg-Prp respectively. For both AMPs, we detected a lower number of positively selected sites (3 and 6 residues in Cg-Defs and Cg-Prp respectively).

Bottom Line: To gain insight into the molecular diversity of antimicrobial peptides and proteins in the oyster Crassostrea gigas, we characterized and compared the sequence polymorphism of the antimicrobial peptides (AMPs), Cg-Defensins (Cg-Defs) and Cg-Proline Rich peptide (Cg-Prp), and of the bactericidal permeability increasing protein, Cg-BPI.High diversification among the three antimicrobial effectors was evidenced by this polymorphism survey.This study shows for the first time in a mollusc that antimicrobial peptides and proteins have been subject to distinct patterns of diversification and we evidence the existence of different evolutionary routes leading to such sequence variability.

View Article: PubMed Central - HTML - PubMed

Affiliation: Ifremer, CNRS, Université de Montpellier II, IRD, UMR 5119 Ecosystèmes Lagunaires, Place Eugène Bataillon, CC80, 34095 Montpellier, France. Julien.De.Lorgeril@ifremer.fr

ABSTRACT

Background: To gain insight into the molecular diversity of antimicrobial peptides and proteins in the oyster Crassostrea gigas, we characterized and compared the sequence polymorphism of the antimicrobial peptides (AMPs), Cg-Defensins (Cg-Defs) and Cg-Proline Rich peptide (Cg-Prp), and of the bactericidal permeability increasing protein, Cg-BPI. For that, we analyzed genomic and transcript sequences obtained by specific PCR amplification and in silico searches.

Results: High diversification among the three antimicrobial effectors was evidenced by this polymorphism survey. On the basis of sequence phylogenies, each AMP aggregates into clearly defined groups of variants and is the product of a multigenic family displaying a variety of gene structures. In contrast, Cg-bpi forms a single group and is encoded by a single gene copy. Moreover, we identified for both AMPs several genetic mechanisms of diversification such as recombination, parallel mutations leading to phylogenetic homoplasy and indel events. In addition, the non synonymous to synonymous substitutions ratio by codon (dN/dS) revealed several negatively and positively selected sites for both AMPs, suggesting that directional selection pressures have shaped their sequence variations.

Conclusions: This study shows for the first time in a mollusc that antimicrobial peptides and proteins have been subject to distinct patterns of diversification and we evidence the existence of different evolutionary routes leading to such sequence variability.

Show MeSH