A Leucine Aminopeptidase Gene of the Pacific Oyster Crassostrea gigas Exhibits an Unusually High Level of Sequence Variation, Predicted to Affect Structure, and Hence Activity, of the Enzyme

Wharam, Susan D.; Wardill, Trevor J.; Goddard, Victoria; Donald, Kirsten M.; Parry, Helen; Pascoe, P. L.; Pickerill, Paul; Smerdon, Gary R.; Hawkins, A. J. S.

doi:10.2983/0730-8000-27.5.1143

Cited by 5 publications

(6 citation statements)

References 35 publications

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“…High amino acid diversity is not restricted to a few extremely polymorphic proteins but appeared to be more a general feature of the whole collection of genes analyzed (Figure 1B). It is worth emphasizing that none of the examples of protein diversity previously reported to be extremely high (Moy et al 2008; Wharam et al 2008; Costa et al 2009; Parisi et al 2009) would appear as outliers if compared to the distribution we obtained in Figure 1B. Using the meta-analysis of Gossmann et al (2010) in plants and some published results on nuclear DNA in animals (Fay et al 2001; Bierne and Eyre-Walker 2004; Cutter 2008; Axelsson and Ellegren 2009; Halligan et al 2010; Carneiro et al 2012; Gagnaire et al 2012; Tsagkogeorga et al 2012), we computed θ s and θ n for a variety of species, shown in Figure 3.…”

Section: Discussionmentioning

confidence: 99%

“…This was true at the allozyme time, during which numerous studies questioned neutrality of these markers in marine mollusks (Koehn and Shumway 1982; Koehn 1990; Karl and Avise 1992; Mitton 1993, 1997; Riginos et al 2002). More recently this has been reiterated in some surveys of DNA sequence polymorphism of protein-coding genes (Moy et al 2008; Wharam et al 2008; Costa et al 2009; Parisi et al 2009). It is therefore crucial to build a clearer picture by evaluating the genomic average of diversity of various categories of substitutions from a large panel of genes in different species of bivalves.…”

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confidence: 93%

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A High Load of Non-neutral Amino-Acid Polymorphisms Explains High Protein Diversity Despite Moderate Effective Population Size in a Marine Bivalve With Sweepstakes Reproduction

Harrang

Lapègue

Morga

et al. 2013

G3 Genes|Genomes|Genetics

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Marine bivalves show among the greatest allozyme diversity ever reported in Eukaryotes, putting them historically at the heart of the neutralist−selectionist controversy on the maintenance of genetic variation. Although it is now acknowledged that this high diversity is most probably a simple consequence of a large population size, convincing support for this explanation would require a rigorous assessment of the silent nucleotide diversity in natural populations of marine bivalves, which has not yet been done. This study investigated DNA sequence polymorphism in a set of 37 nuclear loci in wild samples of the flat oyster Ostrea edulis. Silent diversity was found to be only moderate (0.7%), and there was no departure from demographic equilibrium under the Wright-Fisher model, suggesting that the effective population size might not be as large as might have been expected. In accordance with allozyme heterozygosity, nonsynonymous diversity was comparatively very high (0.3%), so that the nonsynonymous to silent diversity ratio reached a value rarely observed in any other organism. We estimated that one-quarter of amino acid-changing mutations behave as neutral in O. edulis, and as many as one-third are sufficiently weakly selected to segregate at low frequency in the polymorphism. Finally, we inferred that one oyster is expected to carry more than 4800 non-neutral alleles (or 4.2 cM−1). We conclude that a high load of segregating non-neutral amino-acid polymorphisms contributes to high protein diversity in O. edulis. The high fecundity of marine bivalves together with an unpredictable and highly variable success of reproduction and recruitment (sweepstakes reproduction) might produce a greater decoupling between Ne and N than in other organisms with lower fecundities, and we suggest this could explain why a higher segregating load could be maintained for a given silent mutation effective size.

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Section: Discussionmentioning

confidence: 99%

mentioning

confidence: 93%

A High Load of Non-neutral Amino-Acid Polymorphisms Explains High Protein Diversity Despite Moderate Effective Population Size in a Marine Bivalve With Sweepstakes Reproduction

Harrang

Lapègue

Morga

et al. 2013

G3 Genes|Genomes|Genetics

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“…It is apparent that high frequency of null alleles is due to extremely high level of polymorphism in the sequences likely located in the flanking regions (Pemberton et al 1995). Furthermore, evidences from genome sequencing and mass EST data analysis of oysters clearly showed a frequency of one SNP every dozens to a hundred of base pairs (Sauvage et al 2007;Wharam et al 2008). In despite of null alleles, the loci developed here would be useful for not only stock analysis but also important for genetic studies in C. hongkongensis.…”

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confidence: 85%

Development of 20 novel microsatellite markers in the Hong Kong oyster, Crassostrea hongkongensis

Xiao

Zhou

2010

Conservation Genet Resour

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Twenty microsatellite markers were developed for the Hong Kong oyster, Crassostrea hongkongensis, and their polymorphisms were examined in a population. Allele numbers varied from 4 to 19 with an average of 9.35 per locus; observed heterozygosities fluctuated from 0.125 to 0.833 averaging 0.520, and the expected values ranged from 0.233 to 0.938 with an average of 0.664. Fifteen loci accorded statistically with Hardy-Weinberg equilibrium, while others showed a significant departure from the equilibrium, apparently due to heterozygote deficiency. Additionally, two pairs of loci showed significant linkage disequilibrium. Possible causes for null alleles were also discussed. In despite of null alleles, this set of microsatellite loci would be useful for genetic studies in C. hongkongensis.

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“…LAP3 plays crucial roles in cell maintenance, growth and development, and defense [13]. In marine mollusks, LAPs are believed to be of selective importance during adaptation to changes in salinity as a result of tides and varying freshwater input, which is the main function in marine organisms [11,35].…”

Section: Quantitative Expression Analysis Of Tg-lap3mentioning

confidence: 99%

“…Three SNPs associated with high milk production in cow and two SNPs associated with high birth weight in sheep were investigated and could be used in marker-assisted selective breeding [9,10]. In marine mollusks, LAPs are also known to play an important role in growth and development, stress responses, and adaptation to changing environmental conditions [11,12], and SNPs associated with growth traits have been found in several aquatic species [13,14]. For example, 23 SNPs of the LAP gene were found to be linked to growth rates in the Pacific oyster, Crassostrea gigas, and three SNPs of the LAP3 gene were identified in the razor clam, Sinonovacula constricta; these SNPs could be used for genetic breeding markers in aquaculture.…”

Section: Introductionmentioning

confidence: 99%

Molecular Characterization and Expression of the LAP3 Gene and Its Association with Growth Traits in the Blood Clam Tegillarca granosa

Yao

Ren

Bao

et al. 2021

Fishes

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Leucine aminopeptidase 3 (LAP3) is a metallopeptidase that cleaves N-terminal residues and is involved in protein maturation and degradation. In this study, we characterized the leucine aminopeptidase 3 (LAP3) gene from Tegillarca granosa (Tg-LAP3 for short), which appeared to consist of 15,731 nucleotides encoding 530 amino acids. We identified 12 introns and 13 exons in the Tg-LAP3 gene, suggesting a highly conserved genomic structure. The proximal promoter sequence consists of 1922 bps with a typical TATA box structure, which is the general structural characteristic of core promoters in eukaryotes. We found two functional domains in the Tg-LAP3 protein, including an N-terminal domain (41–174aa) and a peptidase_M17 catalytic domain (209–522aa). Multiple alignment showed that Tg-LAP3 shares 73.4% identity with LAP3 of Mizuhopecten yessoensis and 55.2–70.7% identity with LAP3 of other species. Quantitative analysis of Tg-LAP3 in embryos/larvae and adult tissues indicated that the highest expression occurred in eyebot larva, with limited expression in other stages; among tissues, the highest expression was found in the liver (p < 0.05). Association analysis found that three single-nucleotide polymorphisms (SNPs) (g.-488A > G, g.-1123C > T, and g.-1304C > A) in the proximal promoter were successfully typed, but there was no significant difference in growth traits (body weight, shell length, shell width, and shell height) among these genotypes. The results of our study demonstrate the functional roles of the Tg-LAP3 gene and provide valuable information for molecular marker-assisted selection (MAS) of the blood clam.

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A Leucine Aminopeptidase Gene of the Pacific Oyster Crassostrea gigas Exhibits an Unusually High Level of Sequence Variation, Predicted to Affect Structure, and Hence Activity, of the Enzyme

Cited by 5 publications

References 35 publications

A High Load of Non-neutral Amino-Acid Polymorphisms Explains High Protein Diversity Despite Moderate Effective Population Size in a Marine Bivalve With Sweepstakes Reproduction

A High Load of Non-neutral Amino-Acid Polymorphisms Explains High Protein Diversity Despite Moderate Effective Population Size in a Marine Bivalve With Sweepstakes Reproduction

Development of 20 novel microsatellite markers in the Hong Kong oyster, Crassostrea hongkongensis

Molecular Characterization and Expression of the LAP3 Gene and Its Association with Growth Traits in the Blood Clam Tegillarca granosa

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