Development of a Rapid and Efficient Method for Non-Lethal DNA Sampling and Genotyping in Scallops

Non-lethal DNA sampling has long appealed to researchers studying population and conservation genetics, as it does not necessitate removing individuals permanently from their natural environment or destroying valuable samples. However, such an approach has not yet been well established in bivalves. In this study, we demonstrate that the gill represents a good source of tissue for non-lethal sampling in scallops. Removal of a few gill filaments caused no noticeable behavioral abnormalities or increased mortality rates in Zhikong scallop (Chlamys farreri) during a three-month period of observation. To facilitate rapid gill-based DNA extraction, six methods (MA-MF) were designed and evaluated, each requiring less than one hour of processing time. The optimal method was identified as MF, in terms of maintaining DNA integrity and genotyping accuracy. Further optimization of MF method by orthogonal experimental design suggested that the utilization of gills could be limited to 2 mg of sample, which is sufficient for performing up to 20,000 PCR reactions. We also demonstrate the excellent cross-species utility of MF in two additional scallop species, Yesso scallop (Patinopecten yessoensis) and bay scallop (Argopecten irradians). Taken together, our study provides a rapid and efficient approach for applying non-lethal DNA sampling in bivalve species, which would serve as a valuable tool for maintaining bivalve populations and conservation genetics, as well as in breeding studies.     

Neuroactive substances specifically modulate rhythmic body contractions in the nerveless metazoon Tethya wilhelma (Demospongiae, Porifera)

Background

Mitochondrial (mt) gene arrangement is highly variable among molluscs and especially among bivalves. Of the 30 complete molluscan mt-genomes published to date, only one is of a heterodont bivalve, although this is the most diverse taxon in terms of species numbers. We determined the complete sequence of the mitochondrial genomes of Acanthocardia tuberculata and Hiatella arctica, (Mollusca, Bivalvia, Heterodonta) and describe their gene contents and genome organisations to assess the variability of these features among the Bivalvia and their value for phylogenetic inference.

Results

The size of the mt-genome in Acanthocardia tuberculata is 16.104 basepairs (bp), and in Hiatella arctica 18.244 bp. The Acanthocardia mt-genome contains 12 of the typical protein coding genes, lacking the Atpase subunit 8 (atp8) gene, as all published marine bivalves. In contrast, a complete atp8 gene is present in Hiatella arctica. In addition, we found a putative truncated atp8 gene when re-annotating the mt-genome of Venerupis philippinarum. Both mt-genomes reported here encode all genes on the same strand and have an additional trnM. In Acanthocardia several large non-coding regions are present. One of these contains 3.5 nearly identical copies of a 167 bp motive. In Hiatella, the 3' end of the NADH dehydrogenase subunit (nad)6 gene is duplicated together with the adjacent non-coding region. The gene arrangement of Hiatella is markedly different from all other known molluscan mt-genomes, that of Acanthocardia shows few identities with the Venerupis philippinarum. Phylogenetic analyses on amino acid and nucleotide levels robustly support the Heterodonta and the sister group relationship of Acanthocardia and Venerupis. Monophyletic Bivalvia are resolved only by a Bayesian inference of the nucleotide data set. In all other analyses the two unionid species, being to only ones with genes located on both strands, do not group with the remaining bivalves.

Conclusion

The two mt-genomes reported here add to and underline the high variability of gene order and presence of duplications in bivalve and molluscan taxa. Some genomic traits like the loss of the atp8 gene or the encoding of all genes on the same strand are homoplastic among the Bivalvia. These characters, gene order, and the nucleotide sequence data show considerable potential of resolving phylogenetic patterns at lower taxonomic levels.     

Application of monoclonal antibody against granulocytes of scallop Chlamys farreri on granulocytes occurrence at different developmental stages and antigenic cross-reactivity of granulocytes in five other bivalve species

A monoclonal antibody (MAb) 6H7 raised specifically against granulocytes of scallop (Chlamys farreri) was employed to observe granulocyte occurrence successively in blastulae, gastrulae, trochophore larvae, D-shape larvae, umbo-veliger larvae and creeping larvae of C. farreri by immunohistochemistry assay contrasted with H&E stain using semi-thin sections. Moreover, the reactivity of the MAb with granulocytes of C. farreri, Bay scallop Argopecten irradians, Japanese scallop Patinopecten yessoensis, Blue mussel Mytilus edulis, Pacific oyster Crassostrea gigas and Manila clam Ruditapes philippinarum, was detected by immunofluorescence assay (IFA) with differential interference contrast and fluorescent microscopy and flow cytometric immunofluorescence assay (FCIFA). The results showed that positive signals were first observed at D-shape larval stage, about 28 h post fertilization, after that, umbo-veliger larvae exhibited the positive cells with a diameter of 3–5 μm distributed in velum, digestive gland and esophagus. Then in creeping larvae, the number of positive cells increased with average diameter of 5–7 μm, and widely distributed in foot, digestive gland, gills and adductor muscles. No positive signal was found in blastulae, gastrulae and trochophore larvae. The results of IFA and FCIFA showed MAb 6H7 reacted to granulocytes of C. farreri, A. irradians, P. yessoensis and C. gigas, and the positive percentage reactivity were 53 ± 2.5%, 15 ± 2.5%, 12 ± 2.1% and 19 ± 2.1%, respectively, however, no cross-reaction was detected in hemocytes of R. philippinarum and M. edulis.     

Complete mitochondrial DNA sequence and phylogenetic analysis of Zhikong scallop <Emphasis Type="Italic">Chlamys farreri</Emphasis> (Bivalvia: Pectinidae)

The complete mitochondrial genome of Zhikong scallop Chlamys farreri is 21,695 bp in length and contains 12 protein-coding genes (the atp8 gene is absent, as in most bivalves), 2 ribosomal RNA genes, and 22 transfer RNA genes. The heavy strand has an overall A+T content of 58.7%. GC and AT skews for the mt genome of C. farreri are 0.337 and ?0.184, respectively, indicating the nucleotide bias against C and A. The mitochondrial gene order of C. farreri differs drastically from the scallops Argopecten irradians, Mimachlamys nobilis and Placopecten magellanicus, which belong to the same family Pectinidae. 6623 bp non-coding nucleotides exist intergenically in the mitogenome of C. farreri, with a large continuous sequence (4763 bp) between tRNA ^Val and tRNA ^Asn . Two repeat families are found in the large continuous sequence, which seems to be a common feature of scallops. Phylogenetic analysis based on 12 concatenated amino acid sequences of protein-coding genes supports the monophyly of Pectinidae and paraphyletic Pteriomorphia with respect to Heteroconchia.     

The Mitochondrial Genomes of Two Scallops, Argopecten irradians and Chlamys farreri (Mollusca: Bivalvia): The Most Highly Rearranged Gene Order in the Family Pectinidae

Molluscs in general and bivalves in particular, exhibit an extraordinary degree of mitochondrial gene order variation when compared with other metazoans. Here, we determined the mitochondrial genomes of two scallops Argopecten irradians and Chlamys farreri. The complete mitochondrial genome of A. irradians is 16,211 nts in length and the nearly complete mitochondrial genome of C. farreri is 20,789 nts in length. Both of the genomes contain 35 genes including 12 protein-coding genes, 2 ribosomal RNAs, and 21 transfer RNAs. In contrast to the typical animal mitochondrial genome, both of them lack one protein-coding gene atp8 and two trnSs, but show an additional copy of trnF in A. irradians and of trnM in C. farreri, respectively. Gene order and genome content were compared among the four sequenced scallops. Gene arrangement of C. farreri closely resembles that of Mizuhopecten yessoensis. However, two genomes of C. farreri and A. irradians show only three small identical gene blocks and two genomes of A. irradians and Placopecten magellanicus share only one gene block. Comparison of the gene arrangement demonstrated that the four scallops share few identical gene blocks although they belong to the same family. This feature is seldom observed in Metazoa, even in other molluscan classes. The dramatic gene rearrangement often occurs in bivalves, especially in marine bivalves. In addition, comparisons of genomic character among bivalves are also presented.     

Comparison of fungal complexes of Japanese scallop Mizuhopecten yessoensis (Jay, 1856) from different areas in the Peter the Great Bay of the Sea of Japan

Mycological investigation of the Japanese scallop Mizuhopecten yessoensis (Jay) (Bivalvia) from different areas of the Peter the Great Bay (Sea of Japan) was conducted. Isolates from internal organs of M. yessoensis scallop comprise 72 species of filamentous fungi from 30 genera of ascomycetes, anamorphic fungi, and zygomycetes. Species richness of filamentous fungi—fungi of the genera Aspergillus, Penicillium, Cladosporium, and Chaetomium—in the internal organs of bivalve mollusks increases in polluted coastal waters.     

Filamentous fungi in the epibiosis of the scallop Mizuhopecten yessoensis (Bivalvia) in Peter the Great Bay, Sea of Japan

This study considers the taxonomic composition of filamentous fungi in the epibiosis on the shell of the Yesso scallop Mizuhopecten yessoensis (Jay, 1856) (Bivalvia), which were collected in open waters of Peter the Great Bay, Sea of Japan. The taxonomic composition was found to include ten species of filamentous fungi, nine of which were identified. The revealed species belong to six genera, viz., Aspergillus, Aphanocladium, Cladosporium, Penicillium, Phialophorophoma, and Eurotium.     

C-type lectin in Chlamys farreri (CfLec-1) mediating immune recognition and opsonization

Background

C-type lectins are a superfamily of Ca²⁺ dependent carbohydrate-recognition proteins that play significant diverse roles in nonself-recognition and clearance of invaders. Though they are well characterized in vertebrates, the study of the potential function and mechanism of C-type lectins in invertebrate immunity is still in its infancy.

Methodology

A C-type lectin (CfLec-1) from scallop Chlamys farreri, a dominant cultured mollusk species in China, was selected to investigate its mRNA expression, localization and the possible functions in innate immunity in the present study. After scallop was stimulated by three typical PAMPs, the mRNA expression of CfLec-1 in hemocytes was poles apart. It was significantly up-regulated (p<0.01) after scallops were stimulated by LPS or β-glucan, but significantly down-regulated (p<0.01) after PGN stimulation. The binding ability of recombinant CfLec-1 (designated as rCfLec-1) towards eight PAMPs was investigated subsequently by PAMPs microarray, which revealed rCfLec-1 could bind LPS, PGN and mannan in vitro, indicating CfLec-1 served as a PRR involved in the pathogen recognition. Immunofluorescence assay with polyclonal antibody specific for CfLec-1 revealed that CfLec-1 was mainly located in the mantle and gill of the scallop. CfLec-1 could bind to the surface of scallop hemocytes and recruited hemocytes to enhance their encapsulation in vitro, and this process could be specifically blocked by anti-rCfLec-1 antibody. Meanwhile, rCfLec-1 could also enhance the phagocytic activity of scallop hemocytes against Escherichia coli.

Conclusions

The results clearly suggested that CfLec-1 in C. farreri not only served as a PRR involved in the PAMPs recognition, but also functioned as an opsonin participating in the clearance of invaders. It is therefore suspected that CfLec-1 could be an attachment-molecule to nonself-agents acting as an alternative to immunoglobulin in vertebrates.     

Postingestive sorting of living and heat-killed Chlorella within the sea scallop, Placopecten magellanicus (Gmelin)

Suspension-feeding bivalves may enhance the energy value of their food supply by sorting particles both before and after ingestion. Previous research has indicated that the sea scallop (Placopecten magellanicus (Gmelin) (Mollusca: Bivalvia)) is capable of sorting particles within the gut both on the basis of physical properties (particle size and density) as well as chemical properties. In this study, the ability of the sea scallop to sort living from dead material solely on the basis of chemical properties was tested. The microalga Chlorella (Chlorophyta: Chlorophyceae) was chosen as the test particle because its thick cell wall remains physically intact following heat treatment, while its carbon, nitrogen, and chlorophyll a content declines. Scallops were fed a mixture of radiolabelled live and heat-killed Chlorella. We demonstrate that P. magellanicus can distinguish between living and dead algae, retaining live Chlorella cells longer than heat-killed cells. This ability to detect the subtle chemical differences between living algal material and detrital material would enhance the digestive efficiency of this species by reducing the amount of energy expended, digesting poor-quality materials. This paper presents the first study of the ability of a bivalve to distinguish between two physically identical but nutritionally different forms of the same species of microalgae.     

A novel role for dpp in the shaping of bivalve shells revealed in a conserved molluscan developmental program

During the molluscan evolution leading to the bivalves, the single dorsal shell was doubled. To elucidate the molecular developmental basis underlying this prominent morphological transition, we described the cell cleavage and expression patterns of three genes, brachyury, engrailed, and dpp in the Japanese spiny oyster Saccostrea kegaki, and examined the function of dpp in this species. The cleavage pattern of the S. kegaki embryo was nearly the same as the previously described pattern of other bivalve species, suggesting that the pattern itself is highly important for the establishment or the maintenance of the bivalve body plan. The expression pattern of a brachyury homolog in S. kegaki (SkBra) was similar to the pattern in gastopods even at the single cell level despite the deep divergence of gastropods and bivalves. Engrailed and dpp were previously found to be expressed around the shell anlagen in gastropods. Like that of gastropods, an engrailed homolog in S. kegaki (SkEn) was found to be expressed around the shell anlagen. However, the dpp homolog in S. kegaki (SkDpp) was expressed only in the cells along the dorsal midline. ZfBMP4 treatment experiments revealed the importance of dpp in establishing the characteristic shape of the bivalve shell anlagen.