Phenoloxidase activity in three commercial bivalve species. Changes due to natural infestation with Perkinsus atlanticus

The phenoloxidase (PO) activity of the haemolymph and haemocytes from three clam species of commercial interest (Ruditapes philippinarum, Chamelea gallina and Tapes decussatus) has been compared. The activity was assayed spectrophotometrically by recording the formation of dopachrome from L-DOPA using sodium dodecyl sulphate, laminarin, trypsin or lipopolysaccharide as elicitors. Fewer PO units were observed in the haemolymph from T. decussatus than in the haemolymph from R. philippinarum, while the highest values were found in C. gallina. In all cases the activity was only significantly increased when sodium dodecyl sulphate was used as elicitor. PO activity in the haemocytes of all three clam species showed a very similar pattern to that found in the haemolymph from the same species. Furthermore, T. decussatus naturally parasitized by Perkinsus atlanticus (Protozoa, Apicomplexa) was used to study the influence of such infestation on PO activity, which was found to increase significantly in both haemolymph and haemocytes compared with non-infected (control) samples. PO activity in the haemocytes and in the haemolymph was higher when the level of parasitization was low or medium, respectively, and SDS was used as elicitor. No statistically significant differences were observed when the parasitization level was high. The present work constitutes the first report on the influence of this parasite on PO activity in haemolymph and haemocytes from T. decussatus.     

Molecular evolution and recombination in gender-associated mitochondrial DNAs of the Manila clam Tapes philippinarum

Doubly uniparental inheritance (DUI) provides an intriguing system for addressing aspects of molecular evolution and intermolecular recombination of mitochondrial DNA. For this reason, a large sequence analysis has been performed on Tapes philippinarum (Bivalvia, Veneridae), which has mitochondrial DNA heteroplasmy that is consistent with a DUI. The sequences of a 9.2-kb region (containing 29 genes) from 9 individuals and the sequences of a single gene from another 44 individuals are analyzed. Comparisons suggest that the two sex-related mitochondrial genomes do not experience a neutral pattern of divergence and that selection may act with varying strength on different genes. This pattern of evolution may be related to the long, separate history of M and F genomes within their tissue-specific "arenas." Moreover, our data suggest that recombinants, although occurring in soma, may seldom be transmitted to progeny in T. philippinarum.     

The mitogenome of Paphia euglypta (Bivalvia: Veneridae) and comparative mitogenomic analyses of three venerids

Extraordinary variation has been found in mitochondrial (mt) genome inheritance, gene content and arrangement among bivalves. However, only few bivalve mt genomes have been comparatively analyzed to infer their evolutionary scenarios. In this study, the complete mt genome of the venerid Paphia euglypta (Bivalvia: Veneridae) was firstly studied and, secondly, it was comparatively analyzed with other venerids (e.g., Venerupis philippinarum and Meretrix petechialis) to better understand the mt genome evolution within a family. Though several common features such as the AT content, codon usage of protein-coding genes, and AT/GC skew are shared by the three venerids, a high level of variability is observed in genome size, gene content, gene order, arrangements and primary sequence of nucleotides or amino acids. Most of the gene rearrangement can be explained by the "tandem duplication and random loss" model. From the observed rearrangement patterns, we speculate that block interchange between adjacent genes may be common in the evolution of mt genomes in venerids. Furthermore, this study presents several new findings in mt genome annotation of V. philippinarum and M. petechialis, and hence we have reannotated the genome of these two species as: (1) the ORF of the formerly annotated cox2 gene in V. philippinarum is deduced by using a truncated "T" codon and a second cox2 gene is identified; (2) the trnS-AGN gene is identified and marked in the mt genome of both venerids. Thus, this study demonstrated a high variability of mt genomes in the Veneridae, and showed the importance of comparative mt genome analysis to interpret the evolution of the bivalve mt genome.     

Ruditapes decussatus and Ruditapes philippinarum exposed to cadmium: toxicological effects and bioaccumulation patterns

Since differences in metal accumulation may exist between bivalve species, the aim of this study was to assess the impact of cadmium (Cd) on Ruditapes decussatus and Ruditapes philippinarum. For this, the Cd accumulation, mortality rates and biochemical responses were analysed in the two species after 5days of exposure, under laboratory-controlled conditions. The concentration of Cd that caused 50% of mortality on clams was two-times higher in R. decussatus than in R. philippinarum. For both species, higher percentage (84.5-98.2%) of the Cd was in the insoluble fraction, but the Cd concentration in solution was 3 to 8 times higher in R. decussatus. Nevertheless, R. philippinarum presented higher oxidative stress and higher CAT activity. The paradox observed between the two clams can be explained by the higher capacity of R. decussatus to increase the expression of MTs when exposed to Cd.     

First evidence of cell division in circulating haemocytes from the Manila clam Tapes philippinarum

In the present study, we report on haemocyte distribution, determined by a Coulter Counter, in the clam Tapes philippinarum. In addition, cytoskeleton components of haemocytes were examined using specific probes for F-actin and alpha-tubulin. The mean number of circulating haemocytes was 5 (x10(6))cells/ml haemolymph. Two main haemocyte populations were found in the haemolymph: small cells, 2-3microm in diameter and 10-100fl in volume; and large cells, 6-10microm in diameter and 150-400fl in volume. Analysis of the haemocyte cytoskeleton revealed bundles of actin filaments oriented according to the cell major axis, and microtubules radiating from the microtubule-organizing centre in proximity of the nucleus. Interestingly, mitotic spindles were also found radiating from the microtubule-organizing centres, located at the spindle poles (centrosomes) of undifferentiated cells. On the basis of both our previous findings regarding circulating stem cells (Cima, F., Matozzo, V., Marin, M.G., Ballarin, L., 2000. Haemocytes of the clam Tapes philippinarum (Adams & Reeve, 1850): morphofunctional characterisation. Fish Shellfish Immunol 10, 677-693) and new information from the present study, we suggest that haemoblasts are able to divide in the haemolymph of T. philippinarum. To our knowledge, this is the first report of mitotic spindles in circulating haemocytes from a bivalve species.     

Phylogeny of Veneroidea (Mollusca: Bivalvia) based on morphology and molecules

The largest Recent family of Bivalvia, the marine Veneridae with approximately 800 species, comprises one of the least understood and most poorly defined molluscan taxa, despite including some of the most economically important and abundant bivalves, for example quahog, Pismo clams, and Manila clams. A review of previous phylogenetic analyses including the superfamily Veneroidea (Veneridae, Petricolidae, Glauconomidae, Turtoniidae, Neoleptonidae) and within the Veneridae shows minimal taxon sampling leading to weak conclusions and few supported synapomorphies. New phylogenetic analyses on 114 taxa tested the monophyly of Veneroidea, Veneridae, and 17 nominal venerid subfamilies, using morphological (conchological, anatomical) data and molecular sequences from mitochondrial (16S, cytochrome oxidase I) and nuclear (28S, histone 3) genes. Morphological analyses using 45 exemplar taxa and 23 traditional characters were highly homoplastic and failed to reconstruct traditional veneroid classification. Full morphological analyses (31 characters) supported the monophyly of Veneroidea and Veneridae but only when certain taxa were excluded, revealing analytical difficulties caused by a suite of characters associated with neotenous or miniaturized morphology. Molecular analyses resulted in substantially higher clade consistency. The combined molecular data set resulted in significant support for a particular topology. The monophyly of Veneridae was supported only when Petricolidae and Turtoniidae were subsumed, and recognized as members with derived or neotenous morphologies, respectively. Morphological character mapping on molecular trees retained a high level of homoplasy, but revealed synapomorphies for major branch points and supported six subfamily groups (Dosiniinae, Gemminae, Samarangiinae, Sunettinae, Tapetinae, combined Chioninae + Venerinae). Glauconomidae and Neoleptonidae are provisionally maintained in Veneroidea pending further study; Petricolinae and Turtoniinae are placed in Veneridae. © 2006 The Linnean Society of London, Zoological Journal of the Linnean Society, 2006, 148 , 439–521.     

帘蛤科贝类rDNA内转录间隔区序列的研究

根据18SrDNA、5．8SrDNA和28SrDNA保守序列设计引物,应用聚合酶链式反应（PCR）扩增了文蛤（Meretrix meretrix L．）、青蛤（Cyclina sinensis G）、硬壳蛤（Mercenaria mercenaria L．）和江户布目蛤（Protothaca jedoensis L．）4种帘蛤科贝类的第一内转录间隔区（ITS1）和第二内转录间隔区（ITS2）序列,并进行了测序。结果表明,文蛤、青蛤、硬壳蛤和江户布目蛤的ITS1扩增产物大小分别为978bp、663bp、757bp和942bp,GC含量分别为61．55％、60．78％、62．48％和64．86％～64．97％,其中ITS1序列长度分别为900bp、585bp、679bp和864bp,是迄今已报道双壳贝类中变化范围最大的,GC含量分别为61．67％、61．03％、63．03％和65．51％～65．62％,江户布目蛤种内ITS1序列有个体差异;ITS2扩增产物大小分别为644bp、618～620bp、593bp和513～514bp,GC含量分别为61．18％、61．29％～61．81％、62．73％和61．48％61．60％,其中ITS2序列长度分别为412bp、386～388bp、361bp和281～282bp,GC含量分别为65．29％、65．21％～66．06％、67．87％和67．38％～67．62％,青蛤和江户布目蛤种内ITS2序列有个体差异。4种蛤ITS1和ITS2序列种间差异很大,有明显的长度多态性,ITS2种间序列相似度73．0％～89．1％,与ITS1的种间序列相似度48．7％～81．5％相比略高。此外,在4种蛤ITS1和ITS2序列中各发现2个与rRNA加工有关的保守区。通过对ITS1和ITS2序列的组装获得了4种蛤5．8SrRNA基因完整序列,序列长度都是157bp,GC含量57．96％～58．60％,4种蛤5．8SrRNA基因相对保守,种间序列差异度0-6．0％,共有10个变异位点,其中转换4处,颠换6处,硬壳蛤和江户布目蛤5．8SrRNA基因序列完全相同。以ITS2序列（包含5．8SrRNA和28SrRNA基因部分序列）为标记,调用北极蛤科的Arctica islandica相应序列数据作外群,构建了帘蛤科贝类的系统发育树,其拓扑结构显示江户布目蛤与硬壳蛤亲缘关系最近,青蛤与其他3物种的亲缘关系最远。     

Shape analysis of different populations of clams in relation to their geographical structure

Bivalves are excellent candidates for geographically based studies of the morphological variation in individuals of different populations based on the analysis of their shape profiles. In this study, we quantified the overall shell shape differences in individuals of different populations of Ruditapes decussatus and Ruditapes philippinarum in relation to their geographical and genetic distances. A total of 395 and 124 individuals of R. decussatus (nine populations) and R. philippinarum (four populations), respectively, were sampled in different Mediterranean and Atlantic coastal locations. Pictures of the left valve were taken from all individuals. Their profiles were analysed using elliptic Fourier analysis. Mean outlines were computed. In order to classify different individuals for species, the coefficients of harmonic equations were analysed by partial least square discriminant analysis and soft independent modelling of class analogy. The results showed a high percentage of correct classification (99%) between the two species in the independent test. We found that the morphological distance between R. philippinarum and R. decussatus is higher than the morphological distance among populations of the same species. The absence of correspondence between the geographical location and the pattern of morphological and genetic variation indicates the occurrence of a reaction norm in the morphological adaptation of shell shapes to different local environmental conditions.     

Gene-sized DNA molecules of the macronuclei in three species of hypotrichs: Size distributions and absence of nicks

Macronuclear DNAs from three related hypotrichous ciliated protozoans were compared by agarose gel electrophoresis. Each was shown to be composed of DNA duplexes that yielded a unique pattern of bands overlying a continuous distribution of DNA sizes ranging from 400 bp to 20,000 bp. By EM, the number average molecular sizes for doublestranded DNA were 2,200 bp for Oxytricha sp., 2,514 bp for Stylonychia pustulata and 1,836 bp for Euplotes aediculatus. Contrary to previous reports we present evidence that the macronuclear DNAs in each of these three organisms lack single-stranded interruptions.     

中国石蒜属种间亲缘关系ITS序列分析

本文利用核糖体DNA内转录间隔区(ITS)序列对石蒜属13个种(含变种)的亲缘关系进行分析。结果表明,各样品的ITS1长度为259~260 bp,ITS2为230 bp,分别有多个特异性信息位点。以ITS序列为依据对石蒜属植物亲缘关系进行分析,表明石蒜属13个种可分为三大类,其中类Ⅰ包括中国石蒜、地笑、安徽石蒜和长筒石蒜,核型为M+T型;类Ⅱ包括矮小石蒜、换锦花、玫瑰石蒜和红蓝石蒜,核型为ST型;类Ⅲ包括稻草石蒜、乳白石蒜、短蕊石蒜和两种人工杂交种,核型为ST+M+T。系统进化树与核型分析结果相似,第Ⅲ类可能为自然杂交种。     

Phylogenetic analysis of Veneridae (Bivalvia): Comparison of molecular and palaeontological data

An approximately 400-by-long portion of the 16s rRNA gene sequence has been determined for the venerid clamsChamelea gallina (Chioninae),Dosinia lupinus (Dosiniinae),Pitar rudis,Callista chione (Pitarinae),Tapes decussatus,T. philippinarum,Venerupis (=Paphia)aurea (Tapetinae), andVenus verrucosa (Venerinae). Neighbor-joining and maximum parsimony trees support the results of traditional classification methods at the subfamily level but do not support the concept of a genusTapes. The transversion divergence rate estimated on the basis of the palaeontological record for theC. gallina/V. verrucosa separation and for the Pitarinae is very close (0.14–0.16% per Myr, respectively) to that of ungulates and cetaceans, while the Tapetinae exhibit a much higher (0.36% per Myr) rate. Correspondence to: E. Olmo     

Observations on trichodinid ectoparasites (Ciliophora: Peritricha) from the gills of maricultured molluscs in China, with descriptions of three new species of Trichodina Ehrenberg, 1838

During surveys of the trichodinid parasites in mariculture beds off the coast of Shandong Province, China, four species of the genus Trichodina from the gills of marine molluscs were investigated and morphologically studied. Of these, three are described as new: T. ruditapicis n. sp. from Ruditapes philippinarum (Veneridae), T. scapharcae n. sp. from Scapharca subcrenata (Arcidae) and T. mactrae n. sp. from Mactra veneriformis (Mactridae). One little-known species, T. macomarum Raabe & Raabe, 1959, is redescribed from M. veneriformis. Taxonomic and morphometric data for these trichodinids based on wet silver nitrate and protargol-impregnated specimens are presented. For each of the new species, comparisons with closely related species are provided.     

Study on Sequences of Ribosomal DNA Internal Transcribed Spacers of Clams Belonging to the Veneridae Family (Mollusca: Bivalvia)

The first and second internal transcribed spacer (ITS1 and ITS2) regions of the ribosomal DNA from four species, Meretrix meretrix L., Cyclina sinensis G., Mercenaria mercenaria L., and Protothaca jedoensis L., belonging to the family Veneridae were amplified by PCR and sequenced. The size of the ITS1 PCR amplification product ranged from 663 bp to 978 bp, with GC contents ranging from 60.78% to 64.97%. The size of the ITS1 sequence ranged from 585 bp to 900 bp, which is the largest range reported thus far in bivalve species, with GC contents ranging from 61.03% to 65.62%. The size of the ITS2 PCR amplification product ranged from 513 bp to 644 bp, with GC contents ranging from 61.29% to 62.73%. The size of the ITS2 sequence ranged from 281 bp to 412 bp, with GC contents ranging from 65.21% to 67.87%. Extensive sequence variation and obvious length polymorphisms were noted for both regions in these species, and sequence similarity of ITS2 was higher than that of ITS1 across species. The complete sequences of 5.8S ribosomal RNA gene were obtained by assembling ITS1 and ITS2 sequences, and the sequence length in all species was 157 bp. The phylogenetic tree of Veneridae clams was reconstructed using ITS2-containing partial sequences of both 5.8S and 28S ribosomal DNA as markers and the corresponding sequence information in Arctica islandica as the outgroup. Tree topologies indicated that P. jedoensis shared a close relationship with M. mercenaria and C. sinensis, a distant relationship with other species.     

Molecular phylogeny of venus clams (Mollusca,Bivalvia, Veneridae) with emphasis on the systematic position of taxa along the coast of mainland China

Chen, J., Li, Q., Kong, L. & Zheng, X. (2011). Molecular phylogeny of venus clams (Mollusca, Bivalvia, Veneridae) with emphasis on the systematic position of taxa along the coast of mainland China. —Zoologica Scripta, 40, 260–271. Veneridae is the most richly speciose family of heterodont bivalves with high ecological and economic value. Attention to the Veneridae systematics has been raised since traditional conchology‐based ideas on relationships among the venerids were challenged by recent studies using molecular makers and other new approaches and methods. Herein, DNA sequence information from fragments of two mitochondrial genes (COI and 16S) and one nuclear protein‐coding gene (H3) for 135 taxa (128 venerids, five nonvenerid veneroids and two other outgroups) are used to reconstruct the phylogenetic relationships of venus clams under maximum parsimony, maximum likelihood and Bayesian inference approaches. According to our molecular results, the traditional Veneridae is not recovered as monophyletic and most of the nominal subfamilies and genera formed para‐polyphyletic clades. The findings indicate that the current venerid classification cannot validly reflect a natural subdivision. In the present study, the classification of taxa along the coast of mainland China within this family are also revised based on their phylogenetic position and morphological characters. The synonymization of chionine genus Placamen with Clausinella is rejected. Chionine subgenera Anomalodiscus and Cryptonema are given full generic rank again and incorporated into Venerinae and Tapetinae, respectively. Tapetine Marcia hiantina, M. japonica and M. marmorata were distantly related to Katelysia spp., so assigning those three species into the genus Katelysia by some malacologists is rejected herein. Our results also evidence that the synonymization of the genus Tigammona and Periglypta might be inappropriate.     

Glycoconjugate histochemistry and nNOS immunolocalization in the mantle and foot epithelia of Tapes philippinarum (bivalve mollusc)

Glycosaminoglycans and NO synthase probably regulate mucous cell secretion in the skin of Tapes philippinarum. We have demonstrated the presence of "protein" cells, "glycogen" cells, "phenol" cells and five types of mucous cells, with different chemical composition of the mucus in the mantle epithelium of T. philippinarum. The foot epithelium contained "protein" cells and two types of mucous cells. Using biotinylated lectins, in the mantle and foot epithelia we have shown specific sites for the following oligosaccharides: alpha-D-glucose, alpha-D-mannose, alpha-L-fucose, alpha-D-1,3-N-acetyl-galactosamine and alpha-N-acetyl-glucosamine. nNOS immunoreactivity in the intraepithelial and intradermal cells and in the mucocytes suggested a regulatory role of NO in mucus secretion, as demonstrated also in other invertebrates.     

Strict sex-specific mtDNA segregation in the germ line of the DUI species Venerupis philippinarum (Bivalvia: Veneridae)

Doubly Uniparental Inheritance (DUI) is one of the most striking exceptions to the common rule of standard maternal inheritance of metazoan mitochondria. In DUI, two mitochondrial genomes are present, showing different transmission routes, one through eggs (F-type) and the other through sperm (M-type). In this paper, we report results from a multiplex real-time quantitative polymerase chain reaction analysis on the Manila clam Venerupis philippinarum (formerly Tapes philippinarum). We quantified M- and F-types in somatic tissues, gonads, and gametes. Nuclear and external reference sequences were used, and the whole experimental process was designed to avoid any possible cross-contamination. In most male somatic tissues, the M-type is largely predominant: This suggests that the processes separating sex-linked mitochondrial DNAs (mtDNAs) in somatic tissues are less precise than in other DUI species. In the germ line, we evidenced a strict sex-specific mtDNA segregation because both sperm and eggs do carry exclusively M- and F-types, respectively, an observation that is in contrast with a previous analysis on Mytilus galloprovincialis. More precisely, whereas two mtDNAs are present in the whole gonad, only the sex-specific one is detected in gametes. Because of this, we propose that the mtDNA transmission is achieved through a three-checkpoint process in V. philippinarum. The cytological mechanisms of male mitochondria segregation in males and degradation in females during the embryo development (here named Checkpoint #1 and Checkpoint #2) are already well known for DUI species; a Checkpoint #3 would act when primordial germ cells (PGCs) are first formed and would work in both males and females. We believe that Checkpoint #3 is a mere variation of the "mitochondrial bottleneck" in species with standard maternal inheritance, established when their PGCs separate during embryo cleavage.     

Molecular fingerprinting of Vibrio tapetis strains using three PCR-based methods: ERIC-PCR, REP-PCR and RAPD

Brown Ring Disease (BRD) is a bacterial disease caused by Vibrio tapetis which affects cultured clams and causes heavy economic losses. In this study, 28 V. tapetis strains isolated from 5 different hosts were intraspecifically characterized by 3 different polymerase chain reaction- (PCR-) based typing methods: enterobacteria repetitive intergenic consensus (ERIC)-PCR, repetitive extragenic palindromic (REP)-PCR and randomly amplified polymorphic DNA (RAPD)-PCR. Cluster analysis of genetic profiles obtained from these molecular techniques clearly showed the existence of 3 genetic groups strongly correlated to the host origin. The first group was formed by 23 V. tapetis strains isolated from Manila clam Ruditapes philippinarum, 1 isolated from venus clam Venerupis aurea, and 1 isolated from common cockle Cerastoderma edule, all collected from France and Spain. The second group was formed by 2 strains isolated from carpet-shell clam R. decussatus cultured in the northwest of Spain. The third group was composed of 1 strain isolated from Atlantic halibut Hippoglossus hippoglossus from the UK. We concluded that the 3 typing methods based on PCR were useful for the intraspecific typing of V. tapetis strains, and that they can potentially be used as a fast and reliable tool for epidemiological studies in the future.     

Phylogeny of Veneridae (Bivalvia) based on mitochondrial genomes

Veneridae is one of the most diverse families of bivalve molluscs. However, their phylogenetic relationships among subfamilies have been debated for years. To explore phylogenetic relationships of Veneridae, we sequenced 13 complete mitochondrial genome sequences from eight subfamilies and compared with available complete mitochondrial genome of other Veneridae taxa (18 previously reported sequences). Phylogenetic analyses using probabilistic methods recovered two highly supported clades. In addition, the protein‐coding gene order revealed a highly conserved pattern among the same subclade lineages. According to our molecular analyses, Tapetinae should be recognized as a valid subfamily, but the genera formed para‐polyphyletic clades. Chioninae was recovered not monophyletic that differs from a previously molecular phylogeny. Furthermore, the reconstructed chronogram calibrated with fossils recovered the Veneridae have originated during the early Permian (about 290 million years ago). Noticeably, programmed frameshift was found in the nad4 gene of Leukoma jedoensis, Anomalodiscus squamosus and Antigona lamellaris and cob gene of L. jedoensis. This is the first time that the presence of the programmed frameshift has been found in the protein‐coding genes of Heterodonta species. Our results improved the phylogenetic resolution within Veneridae, and a more taxonomic sampling analysis of the subfamily Chioninae is supposed to construct.     

中国沿海帘蛤科贝类主要经济种育苗与养殖技术研究进展

系统地对我国帘蛤科中的主要养殖种类如菲律宾蛤仔、青蛤、文蛤等的繁殖生物学、发育生物学、苗种培育技术和养殖技术进行了综述,以期为解决制约我国蛤类养殖进一步发展的瓶颈因子(足够的优质健康苗种和相应的养殖技术)提供参考。     

Genetic variability in a family of satellite DNAs from tilapia (Pisces: Cichlidae).

We have cloned and sequenced members of a family of satellite DNAs from three genera of the tilapiine tribe of fishes: Oreochromis, Sarotherodon, and Tilapia. The satellite DNAs, visualized as intensely staining bands following electrophoretic separation of EcoRI-digested genomic DNA, consist of three size variants differentially distributed in the various tilapiine species. The sizes of the monomers are approximately 237 bp (type I), 230 bp (type II), and 209 bp (type III). Several cloned monomers were sequenced from Oreochromis niloticus (type III), Oreochromis placidus (types I and II), Sarotherodon galilaeus (type I), Tilapia zillii (type I), and Tilapia rendalli (type I). Comparison of derived consensus sequences for the monomer units of the satellite DNAs revealed sequence identities within and between species that ranged from 89 to 96%. The type II and type III size variants appear to have arisen by deletions of 9 and 29 bp, respectively, within different regions of the type I satellite. Hybridization of a cloned monomer satellite from O. niloticus (type III) to PalI digests of genomic DNA from all three genera detected polymorphic, high molecular weight restriction fragments that produced fingerprint-like patterns. The complexity of these DNA fingerprints varied from one species to another, suggesting a markedly different genomic organization for these polymorphic satellite DNAs.