Mutual effects of several fouling organisms of the White Sea (<Emphasis Type="Italic">Mytilus edulis,Styela rustica</Emphasis>, and <Emphasis Type="Italic">Hiatella arctica</Emphasis>) on their growth rate and survival

The mutual effects of several fouling species (the bivalves Mytilus edulis and Hiatella arctica and a solitary ascidian Styela rustica) on their growth rate and mortality were studied through field experiments. The interactions between S. rustica and H. arctica appeared to be the least antagonistic. In contrast, the mussel was the most “aggressive” species with regard to both competitors. It was observed that the ascidians died, because they were intensively braided and gummed up with the byssus threads of the mussels. However, in some cases the intraspecific competition was stronger than the interspecific one.     

The complete mitochondrial genomes of six heterodont bivalves (Tellinoidea and Solenoidea): variable gene arrangements and phylogenetic implications

Background

Taxonomy and phylogeny of subclass Heterodonta including Tellinoidea are long-debated issues and a complete agreement has not been reached yet. Mitochondrial (mt) genomes have been proved to be a powerful tool in resolving phylogenetic relationship. However, to date, only ten complete mitochondrial genomes of Heterodonta, which is by far the most diverse major group of Bivalvia, have been determined. In this paper, we newly sequenced the complete mt genomes of six species belonging to Heterodonta in order to resolve some problematical relationships among this subclass.

Principal Findings

The complete mt genomes of six species vary in size from 16,352 bp to 18,182. Hairpin-like secondary structures are found in the largest non-coding regions of six freshly sequenced mt genomes, five of which contain tandem repeats. It is noteworthy that two species belonging to the same genus show different gene arrangements with three translocations. The phylogenetic analysis of Heterodonta indicates that Sinonovacula constricta, distant from the Solecurtidae belonging to Tellinoidea, is as a sister group with Solen grandis of family Solenidae. Besides, all five species of Tellinoidea cluster together, while Sanguinolaria diphos has closer relationship with Solecurtus divaricatus, Moerella iridescens and Semele scaba rather than with Sanguinolaria olivacea.

Conclusions/Significance

By comparative study of gene order rearrangements and phylogenetic relationships of the five species belonging to Tellinoidea, our results support that comparisons of mt gene order rearrangements, to some extent, are a useful tool for phylogenetic studies. Based on phylogenetic analyses of multiple protein-coding genes, we prefer classifying the genus Sinonovacula within the superfamily Solenoidea and not the superfamily Tellinoidea. Besides, both gene order and sequence data agree that Sanguinolaria (Psammobiidae) is not monophyletic. Nevertheless, more studies based on more mt genomes via combination of gene order and phylogenetic analysis are needed to further understand the phylogenetic relationships in subclass Heterodonta.     

Heart rate variation patterns in some representatives of Bivalvia

The pattern of heart rate variation was studied in bivalves sublittoral (aquaculture) and littoral mussels Mytilus edulis L. and Hiatella arctica L. in a long-term experiment at constant salinity (25‰) and temperature (10°C). Periodic changes in heart rate were observed in both littoral and sublittoral mussels. Heart activity could regularly decrease up to temporary cardiac arrest. Changes in H. arctica heart rate were much less pronounced compared to mussels and no cardiac arrest was observed.     

The complete mitochondrial genome sequence of Sogatella furcifera (Horváth) and a comparative mitogenomic analysis of three predominant rice planthoppers

The white-backed planthopper (WBPH), Sogatella furcifera (Horváth), is one of the most destructive pests of rice crops in many Asian countries. Using long-PCR and shotgun library methods, we sequenced the entire mitochondrial genomes (mt-genomes) of two WBPH individuals. Total lengths of the mt-genome of the two WBPH individuals were 16,612 bp and 16,654 bp with an identical AT content of 76.19%. Among the 13 protein coding genes (PCGs), only nad5 used an atypical initiation codon GTG. Most of the tRNA genes had the typical cloverleaf secondary structure except that the dihydrouridine (DHU) arms in two trnS genes and the TΨC arm of trnG gene did not form a stable stem-loop structure. Similar to the brown planthopper (BPH), Nilaparvata lugens (Stål), and the small brown planthopper (SBPH), Laodelphax striatellus (Fallén), some extraordinary features were observed in the WBPH mt-genome. These include similar gene rearrangement pattern, unusually short length of the atp8 gene and variable numbers of tandem repeat (VNTR) structure in control region. Interestingly, the same tandem repeat unit with stable secondary structure appeared in two different planthoppers, WBPH and SBPH, which belong to two different genera of the Delphacidae. This peculiar feature provides a direct evidence for the close relationship between the two planthoppers and updates our understanding of the evolutionary characteristics of mitochondrial control region. Comparison with two other predominant rice planthoppers (BPH and SBPH) revealed that different PCGs of mitochondria exhibit different evolutionary patterns.     

Characterization of a mitochondrial ORF from the gender-associated mtDNAs of Mytilus spp. (Bivalvia: Mytilidae): identification of the "missing" ATPase 8 gene

Bivalve species are characterized by extraordinary variability in terms of mitochondrial (mt) genome size, gene arrangement and tRNA gene number. Many species are thought to lack the mitochondrial protein-coding gene atp8. Of these species, the Mytilidae appears to be the only known taxon with doubly uniparental inheritance of mtDNA that does not possess the atp8 gene. This raises the question as to whether mytilids have completely lost the ATP8 protein, whether the gene has been transferred to the nucleus or whether they possess a highly modified version of the gene/protein that has led to its lack of annotation. In the present study, we re-investigated all complete (or nearly complete) F and M mytilid mt genomes previously sequenced for the presence of conserved open reading frames (ORFs) that might code for ATP8 and/or have other functional importance in these bivalves. We also revised the annotations of all available complete mitochondrial genomes of bivalves and nematodes that are thought to lack atp8 in an attempt to detect it. Our results indicate that a novel mytilid ORF of significant length (i.e., the ORF is >85 amino acids in length), with complete start and stop codons, is a candidate for the atp8 gene: (1) it possesses a pattern of evolution expected for a protein-coding gene evolving under purifying selection (i.e., the 3rd>1st>2nd codon pattern of evolution), (2) it is actively transcribed in Mytilus species, (3) it has one predicted transmembrane helix (as do other metazoan ATP8 proteins), (4) it has conserved functional motifs and (5), comparisons of its amino acid sequence with ATP8 sequences of other molluscan or bivalve species reveal similar hydropathy profiles. Furthermore, our revised annotations also confirmed the mt presence of atp8 in almost all bivalve species and in one nematode species. Our results thus support recognizing the presence of ATPase 8 in most bivalves mt genomes (if not all) rather than the continued characterization of these genomes as lacking this gene.     

Resistance of larvae of common species of White Sea invertebrates to extreme changes in salinity

This study examines the effect of sharp changes in salinity on pelagic larvae of ten common species of invertebrates from the brackish White Sea (Mollusca, Polychaeta, Echinodermata, Cnidaria, Ascidia). For five species, the low salinity resistance limit was in the range of 8–12‰: for the gastropod Littorina littorea, it was below 8‰; for Dyaphana sp. and the bivalves Hiatella arctica and Heteranomia ovata, it was more than 12‰; and for the ascidian Styela rustica, it was 16‰. About 50% of larvae of four investigated species were able to withstand high salinity and survived at 36–40 and even 50‰ (Littorina). Larvae of littoral-sublittoral species proved to be more euryhaline than larvae of sublittoral species.     

Shell form,growth and life span of <Emphasis Type="Italic">Astarte arctica</Emphasis> and <Emphasis Type="Italic">A. borealis</Emphasis> (Mollusca: Bivalvia) from the subtidal zone of northeastern Sakhalin

This study investigates changes in body proportions during ontogenesis of the bivalves Astarte arctica and A. borealis from the subtidal zone of northeastern Sakhalin. Marked differences in the shell form of bivalves were found. The shell of A. arctica is convex and compact, shell length and height are comparable, and shell width is more than 50% of shell height. A. borealis has a slightly elongate and flattened shell, its width is less than 50% of its height. Shell proportions can provide a reliable criterion for differentiating the species. Mollusks grow at nearly the same rate but attain different maximum sizes. Linear growth is described by Bertalanffy’s equation: L_t = 48.2[1 ? e ^{?0.4850(t ? 0.4396)}] for A. arctica and L_t = 53.1[1 ? e^{?0.4106(t ? 0.4253)}] for A. borealis. In northeastern Sakhalin, the life span of A. arctica is 7 years and of A. borealis, 8 years. By life span, the two bivalve species from Sakhalin slightly differ from their counterparts in other regions, particularly the arctic seas.     

Genetic diversity of introduced Manila clam Ruditapes philippinarum populations inferred by 16S rDNA

Manila clam Ruditapes philippinarum – synonym Venerupis philippinarum (Adams and Reeve, 1850) – is one of the most successful marine invaders, being introduced worldwide for aquaculture and fisheries. Genetic diversity and structure of its populations are largely unknown, especially in the invaded environments. Herein we present molecular genetic data on 12 introduced Manila clam populations in Italy, Spain, and Portugal from both Mediterranean (Adriatic) and Atlantic sampling sites. The phylogenetic information was investigated by the direct sequencing of 16S mitochondrial DNA. Results of mtDNA analyses showed the occurrence of 11 haplotypes for European introduced populations, as a consequence of multiple founder effects from different source populations. Rp hap1 was the most frequent, shared among all populations. The other 10 haplotypes were rare and distributed at local scale, in agreement with what was observed in other invasive bivalves. Biogeographic and phylogenetic analyses based on 16S rDNA of introduced Manila clam populations showed a complex scenario, dominated by multiple pools of individuals coming from different sources, as a consequence of multiple introductions.     

A comparative study of the pumping activity of some fouling animals from the White Sea

The pumping activity of the bivalve Mytulus edulus, Hiatella arctica, and solitary ascidian Styela rustica from the White Sea has been studied. The dependence of the pumping activity on the mass and size of animals has been analyzed. It was shown that the mussel is the most active filter-feeder, that the least value of the pumping activity has been registered for H. arctica, and that S. rustica occupies an intermediate position according this index. The results obtained are examined in connection with the competitive relationship of the animals in the fouling community.     

Complete mitochondrial DNA sequence of the ark shell Scapharca broughtonii: An ultra-large metazoan mitochondrial genome

The complete mitochondrial (mt) genome of the ark shell Scapharca broughtonii was determined using long PCR and a genome walking sequencing strategy with genus-specific primers. The S. broughtonii mt genome (GenBank accession number AB729113) contained 12 protein-coding genes (the atp8 gene is missing, as in most bivalves), 2 ribosomal RNA genes, and 42 transfer tRNA genes, in a length of 46,985 nucleotides for the size of mtDNA with only one copy of the heteroplasmic tandem repeat (HTR) unit. Moreover the S. broughtonii mt genome shows size variation; these genomes ranged in size from about 47 kb to about 50 kb because of variation in the number of repeat sequences in the non-coding region. The mt-genome of S. broughtonii is, to date, the longest reported metazoan mtDNA sequence. Sequence duplication in non-coding region and the formation of HTR arrays were two of the factors responsible for the ultra-large size of this mt genome. All the tRNA genes were found within the S. broughtonii mt genome, unlike the other bivalves usually lacking one or more tRNA genes. Twelve additional specimens were used to analyze the patterns of tandem repeat arrays by PCR amplification and agarose electrophoresis. Each of the 12 specimens displayed extensive heteroplasmy and had 8–10 length variants. The motifs of the HTR arrays are about 353–362 bp and the number of repeats ranges from 1 to 11.     

Late quaternary variations in oxygen and carbon isotopic compositions in Canadian Arctic marine bivalves

The oxygen and carbon isotopic composition of arctic marine bivalves Mya truncata, Hiatella arctica, and Mytilus edulis are reported on samples from raised marine deposits in Hudson Bay and eastern Baffin Island. The shells range in age from modern, through the Holocene, to “old” marine units. During the Holocene the ¹⁸O/¹⁶O ratio in shells rose to a maximum about 3,500 B.P. which coincides in time with the period of maximum growth rates of bivalves, maximum size and maximum faunal diversity. The change is interpreted to indicate that about 3,500 years ago arctic waters may have reached a salinity ≈ 1–2% greater than present. Comparison of Holocene shell-carbonate isotopic compositions with those from the “old” marine shells (that are characteristically extremely thick) suggests that during the early Wisconsin advance on eastern Baffin Island, surface and near-surface waters were more saline than at present. This may have been related to low meltwater discharge. Paradoxically, positive values of ¹⁸O/¹⁶O and ¹³O/¹²C in marine shells occurred during the Holocene marine optimum and during the early Wisconsin ice advance.     

A Comparative Analysis of the <Emphasis Type="Italic">atp8</Emphasis> Gene Between a Cytoplasmic Male Sterile Line and Its Maintainer and Further Development of a Molecular Marker Specific to Male Sterile Cytoplasm in Kenaf (<Emphasis Type="Italic">Hibiscus cannabinus</Emphasis> L.)

In this study, the atp8 gene was cloned from the cytoplasmic male sterile (CMS) line UG93A and its maintainer line UG93B in kenaf. Its DNA sequence analysis showed that atp8 containing 480-bp, encoding 159 amino acid residues, and a 9-bp insertion was found at the 3′flanking sequence in UG93A compared with UG93B. The cDNA sequence of atp8 analyzed by RT-PCR indicated that there were five loci edited, but six loci edited in UG93B. The editing frequencies were higher in sterile cytoplasm than in fertile cytoplasm. The relative expression of atp8 analyzed by real-time PCR showed that the expressed level of atp8 in UG93A was lower than that of its maitainer UG93B and its F₁ hybrid UG93A/992 (a restore line). Furthermore, based on the difference of the 9-bp differences at the 3′flanking sequence of atp8 between UG93A and UG93B, a molecular marker specific to male sterile cytoplasm was developed, which can be used for indentifying whether any germplasm of kenaf is male sterile cytoplasm or male fertile cytoplasm.     

Molecular cloning and expression of a C-type lectin gene from Venerupis philippinarum

C-type lectins have been demonstrated to play important roles in invertebrate innate immunity by mediating the recognition of pathogens and clearing the micro-invaders. In the present study, a C-type lectin gene (denoted as VpCTL) was identified from Venerupis philippinarum by expressed sequence tag and rapid amplification of cDNA ends approaches. The full-length cDNA of VpCTL consists of 904 nucleotides with an open-reading frame of 456 bp encoding a peptide of 151 amino acids. The deduced amino acid sequence of VpCTL shared high similarity with C-type lectins from other species. The C-type lectin domain and the characteristic EPN and WND motifs were found in VpCTL. The VpCTL mRNA was dominantly expressed in the haemocytes of the V. philippinarum. After Listonella anguillarum challenge, the temporal expression of VpCTL mRNA in haemocytes was increased by 97- and 84-fold at 48 and 96 h, respectively. With high expression level in haemocytes and hepatopancreas, and the up-regulated expression in haemocytes indicted that VpCTL was perhaps involved in the immune responses to L. anguillarum challenge.     

Byssus production rate of the White Sea blue mussel <Emphasis Type="Italic">Mytilus edulis</Emphasis> (Linnaeus, 1758) in the presence of metabolites of some hydrobionts

The byssus production of the blue mussel Mytilus edulis L. was studied in the laboratory in the presence of the metabolites of the following animals: a predator (a starfish Asterias rubens L.) and several species competing with the mussel in White Sea fouling communities (a bivalve Hiatella arctica L. and a solitary ascidian Styela rustica L.). The byssus threads and attachment plaques produced by each mussel per day were counted. The number of byssus threads and plaques was smallest in pure sea water and in the presence of metabolites produced by conspecific individuals.     

The complete mitochondrial genome of the grand jackknife clam, Solen grandis (Bivalvia: Solenidae): a novel gene order and unusual non-coding region

Molluscs in general, and bivalves in particular, exhibit an extraordinary degree of mitochondrial gene order variation when compared with other metazoans. The complete mitochondrial genome of Solen grandis (Bivalvia: Solenidae) was determined using long-PCR and genome walking techniques. The entire mitochondrial genome sequence of S. grandis is 16,784 bp in length, and contains 36 genes including 12 protein-coding genes (atp8 is absent), 2 ribosomal RNAs, and 22 tRNAs. All genes are encoded on the same strand. Compared with other species, it bears a novel gene order. Besides these, we find a peculiar non-coding region of 435 bp with a microsatellite-like (TA)₁₂ element, poly-structures and many hairpin structures. In contrast to the available heterodont mitochondrial genomes from GenBank, the complete mtDNA of S. grandis has the shortest cox3 gene, and the longest atp6, nad4, nad5 genes.     

The Rho GTPase Family Genes in Bivalvia Genomes: Sequence,Evolution and Expression Analysis

Background

Rho GTPases are important members of the Ras superfamily, which represents the largest signaling protein family in eukaryotes, and function as key molecular switches in converting and amplifying external signals into cellular responses. Although numerous analyses of Rho family genes have been reported, including their functions and evolution, a systematic analysis of this family has not been performed in Mollusca or in Bivalvia, one of the most important classes of Mollusca.

Results

In this study, we systematically identified and characterized a total set (Rho, Rac, Mig, Cdc42, Tc10, Rnd, RhoU, RhoBTB and Miro) of thirty Rho GTPase genes in three bivalve species, including nine in the Yesso scallop Patinopecten yessoensis, nine in the Zhikong scallop Chlamys farreri, and twelve in the Pacific oyster Crassostrea gigas. Phylogenetic analysis and interspecies comparison indicated that bivalves might possess the most complete types of Rho genes in invertebrates. A multiple RNA-seq dataset was used to investigate the expression profiles of bivalve Rho genes, revealing that the examined scallops share more similar Rho expression patterns than the oyster, whereas more Rho mRNAs are expressed in C. farreri and C. gigas than in P. yessoensis. Additionally, Rho, Rac and Cdc42 were found to be duplicated in the oyster but not in the scallops. Among the expanded Rho genes of C. gigas, duplication pairs with high synonymous substitution rates (Ks) displayed greater differences in expression.

Conclusion

A comprehensive analysis of bivalve Rho GTPase family genes was performed in scallop and oyster species, and Rho genes in bivalves exhibit greater conservation than those in any other invertebrate. This is the first study focusing on a genome-wide characterization of Rho GTPase genes in bivalves, and the findings will provide a valuable resource for a better understanding of Rho evolution and Rho GTPase function in Bivalvia.     

Effect of the excretory-secretory products of some marine invertebrates on byssus production of the blue mussel <Emphasis Type="Italic">Mytilus edulis</Emphasis> (Bivalvia: Mytilidae)

Under laboratory conditions, we investigated byssus production in the blue mussel Mytilus edulis, as affected by the excretory-secretory products (ESPs) of the mussel itself and some marine invertebrates: the predatory starfish Asterias rubens, and organisms competing with mussels in White Sea fouling communities—a bivalve Hiatella arctica, the solitary ascidians Styela rustica and Molgula citrine, and a sponge Halichondria panicea. The number of attachment disks produced by a mussel per day and the thickness of byssal threads were estimated. Excretory-secretory products of H. arctica and M. citrine had no effect on the number of attachment disks, while ESPs of S. rustica, H. panacea and A. rubens stimulated mussels to produce attachment plaques. The activity of the mussel was slightly increased at low levels of its own ESPs in seawater. The thickness of byssal threads decreased with an increase in the ESPs of mussels in seawater, but it increased in experiments with the ESPs of any other species tested.     

The complete mitochondrial genome of the hard clam <Emphasis Type="Italic">Meretrix meretrix</Emphasis>

Veneridae is a diverse, commercially important, and cosmopolitan family. Here we present the complete mitochondrial genome of the hard clam Meretrix meretrix (Bivalvia: Veneridae). The entire mitochondrial genome (mitogenome) sequence of M. meretrix is 19,826 bp in length, and contains 37 genes including 12 protein-coding genes, 2 ribosomal RNAs, and 23 tRNAs. All genes are encoded on the heavy strand. In contrast to the typical animal mitochondrial genome, it lacks the protein-coding gene ATP8, and has only one copy of the tRNA^Ser gene, but three duplications of the tRNA^Gln, which is the first report among the present molluscan mtDNAs. We observed that the gene arrangement between M. meretrix and M. petechialis is same except one more tRNAGln gene in M. meretrix., and the sequence similarity is as high as 99%, indicating that M. petechialis and M. meretrix could be treated as a junior synonym of M. meretrix. Maximum Likelihood and Bayeslan analysis of 12 concatenated protein-coding amino acid sequences place the Unionidae as a sister group to other bivalves, which reflects the general opinion that the Unionidae deverged very early in Bivalvia evolution.