Genetic diversity and population structure of the ark shell Scapharca broughtonii along the coast of China based on microsatellites

As a commercially important species in East Asia, the natural resources of Scapharca broughtonii have been suffering from severe population decline across its main habitats. In China, recovery efforts for S. broughtonii are in progress. To provide scientific bases for fisheries management and conservation program, genetic diversity and population structure of seven wild populations of S. broughtonii from the northern China coast was assessed using seven microsatellite loci in this study. High genetic diversity was present in all the seven populations, as observed in mean allelic richness per locus (11.3–12.5), and average expected heterozygosity (0.835–0.867). No significant difference in allelic richness or expected heterozygosity was observed among the seven populations. Pairwise F_ST estimates and NJ tree topologies based on D_C distances indicated that the seven populations fell into two groups, showing a clear division between the populations from the south and north of the Shandong Peninsula. Genetic differentiation was further analyzed using AMOVA and assignation tests. Genetic barrier analysis using Monmonier algorithm also confirmed that the Shandong Peninsula was the putative barrier separating the northern and southern populations. In addition, marine currents probably play an important role in high gene flow among three populations from the same marine gyre.     

Polymorphic microsatellite DNA markers for the ark shell Scapharca subcrenata (bivalve: Arcidae)

We have isolated and characterized twelve novel polymorphic microsatellite loci from Scapharca subcrenata to analyse the population structure. The number of observed alleles per locus ranged from 3 to 17. Observed heterozygosity (H _O) ranged from 0.321 to 0.929. Cross-species amplification was tested successfully in three other bivalve species. These microsatellite markers will be useful for genetic diversity studies of S. subcrenata and other Lamellibranchia species.     

Complete sequence of bovine mitochondrial DNA conserved features of the mammalian mitochondrial genome

We present here the complete 16,338 nucleotide DNA sequence of the bovine mitochondrial genome. This sequence is homologous to that of the human mitochondrial genome (Anderson et al., 1981) and the genes are organized in virtually identical fashion. The bovine mitochondrial protein genes are 63 to 79% homologous to their human counterparts, and most of the nucleotide differences occur in the third positions of codons. The minimum rate of base substitution that accounts for the nucleotide differences in the codon third positions is very high: at least 6 × 10^?9 changes per position per year. The bovine and human mitochondrial transfer RNA genes exhibit more interspecies variation than do their cytoplasmic counterparts, with the “TΨC” loop being the most variable part of the molecule. The bovine 12 S and 16 S ribosomal RNA genes, when compared with those from human mitochondrial DNA, show conserved features that are consistent with proposed secondary structure models for the ribosomal RNAs. Unlike the pattern of moderate-to-high homology between the bovine and human mitochondrial DNAs found over most of the genome, the DNA sequence in the bovine D-loop region is only slightly homologous to the corresponding region in the human mitochondrial genome. This region is also quite variable in length, and accounts for the bulk of the size difference between the human and bovine mitochondrial DNAs.     

Sibship reconstruction and effective population size estimation in mass spawning ark shell, Scapharca broughtonii based on microsatellite analysis

Five highly polymorphic microsatellite loci were utilized to reconstruct sibship during a mass spawning event of ark shell, Scapharca broughtonii and to estimate the genetic variability between the D-shaped larvae and metamorphosed juvenile stage. The allelic diversity, and observed and expected heterozygosities exhibited similarity between the two sampling stages. The sibship reconstruction results of 180 offspring in each stage demonstrated that the effective population size was 20 in the D-shaped larvae stage and decreased to 16 in the metamorphosed juvenile stage. The inferred number of parents at the metamorphosed juvenile stage decreased 16.13 % and the inbreeding rate increased 0.6 % comparing to the D-shaped larvae stage. Multiple matings were detected both in males and females, and the reproductive success of both sexes in the two stages was positively correlated to the number of individuals with which it had mated. The results lend insight to S. broughtonii cultivation in China and provide a genetic guide for the development of more effective spawning techniques in the future.     

Complete DNA sequence of the mitochondrial genome ofCepaea nemoralis (Gastropoda: Pulmonata)

The nucleotide sequence of a mitochondrial genome of the pulmonate gastropod molluscCepaea nemoralis has been determined. Contained within the 14,100 basepairs (bp) are the two ribosomal RNA genes and 13 protein coding genes typical of metazoan mitochondrial genomes. TheCepaea mtDNA does contain a gene for ATPase subunit 8, like the clausiliid pulmonate,Albinaria, and the chiton,Katharina, but unlike the bivalve mollusc,Mytilus. The mitochondrial genetic code ofCepaea is proposed to be the same as that ofMytilus, Katharina, andDrosophila. Only 14 putative tRNA genes are presented, although there is sufficient unassigned sequence to encode the remainder of the expected total of 22 tRNA genes. These 14 tRNA genes are a mixture of standard cloverleaf structures and nonstandard structures containing TV replacement loops as seen in nematode and mosquito mitochondrial genomes. If the eight unidentified tRNA genes are indeed present, very little unassigned sequence would remain to serve as a control region. Genes are transcribed from both strands of the molecule. Base composition is the least biased for any reported animal mitochondrial genome and is also very little skewed between strands using measures independent of base composition. TheCepaea mitochondrial gene order is quite unlike that of any other reported metazoan mtDNA, with the exception of the recently reported partial sequences ofAlbinaria. No gene bound-aries are shared among all the reported molluscan taxa, demonstrating a complete lack of conservation of mitochondrial gene order across the phylum Mollusca.     

Complete mitochondrial genome sequence of the Tyrolean Iceman

The Tyrolean Iceman was a witness to the Neolithic-Copper Age transition in Central Europe 5350-5100 years ago, and his mummified corpse was recovered from an Alpine glacier on the Austro-Italian border in 1991 [1]. Using a mixed sequencing procedure based on PCR amplification and 454 sequencing of pooled amplification products, we have retrieved the first complete mitochondrial-genome sequence of a prehistoric European. We have then compared it with 115 related extant lineages from mitochondrial haplogroup K. We found that the Iceman belonged to a branch of mitochondrial haplogroup K1 that has not yet been identified in modern European populations. This is the oldest complete Homo sapiens mtDNA genome generated to date. The results point to the potential significance of complete-ancient-mtDNA studies in addressing questions concerning the genetic history of human populations that the phylogeography of modern lineages is unable to tackle.     

Complete sequence of the mitochondrial genome of Tetrahymena pyriformis and comparison with Paramecium aurelia mitochondrial DNA

We report the complete nucleotide sequence of the Tetrahymena pyriformis mitochondrial genome and a comparison of its gene content and organization with that of Paramecium aurelia mtDNA. T. pyriformis mtDNA is a linear molecule of 47,172 bp (78.7 % A+T) excluding telomeric sequences (identical tandem repeats of 31 bp at each end of the genome). In addition to genes encoding the previously described bipartite small and large subunit rRNAs, the T. pyriformis mitochondrial genome contains 21 protein-coding genes that are clearly homologous to genes of defined function in other mtDNAs, including one (yejR) that specifies a component of a cytochrome c biogenesis pathway. As well, T. pyriformis mtDNA contains 22 open reading frames of unknown function larger than 60 codons, potentially specifying proteins ranging in size from 74 to 1386 amino acid residues. A total of 13 of these open reading frames ("ciliate-specific") are found in P. aurelia mtDNA, whereas the remaining nine appear to be unique to T. pyriformis; however, of the latter, five are positionally equivalent and of similar size in the two ciliate mitochondrial genomes, suggesting they may also be homologous, even though this is not evident from sequence comparisons. Only eight tRNA genes encoding seven distinct tRNAs are found in T. pyriformis mtDNA, formally confirming a long-standing proposal that most T. pyriformis mitochondrial tRNAs are nucleus-encoded species imported from the cytosol. Atypical features of mitochondrial gene organization and expression in T. pyriformis mtDNA include split and rearranged large subunit rRNA genes, as well as a split nad1 gene (encoding subunit 1 of NADH dehydrogenase of respiratory complex I) whose two segments are located on and transcribed from opposite strands, as is also the case in P. aurelia. Gene content and arrangement are very similar in T. pyriformis and P. aurelia mtDNAs, the two differing by a limited number of duplication, inversion and rearrangement events. Phylogenetic analyses using concatenated sequences of several mtDNA-encoded proteins provide high bootstrap support for the monophyly of alveolates (ciliates, dinoflagellates and apicomplexans) and slime molds.     

Complete DNA sequence of the rat cytomegalovirus genome

We have determined the complete genome sequence of the Maastricht strain of rat cytomegalovirus (RCMV). The RCMV genome has a length of 229,896 bp and is arranged as a single unique sequence flanked by 504-bp terminal direct repeats. RCMV was found to have counterparts of all but one of the open reading frames (ORFs) that are conserved between murine CMV (MCMV) and human CMV (HCMV). Like HCMV, RCMV lacks homologs of the genes belonging to the MCMV m02 glycoprotein gene family. However, RCMV contains 15 ORFs with homology to members of the MCMV m145 glycoprotein gene family. Four ORFs are predicted to encode homologs of host proteins; R33 and R78 both putatively encode G protein-coupled receptors, whereas r144 and r131 encode homologs of major histocompatibility class I heavy chains and CC chemokines, respectively. An intriguing feature of the RCMV genome is the presence of an ORF, r127, with similarity to the rep gene of parvoviruses as well as ORF U94 of human herpesvirus 6A (HHV-6A) and HHV-6B. Counterparts of these ORFs have not been found in the other sequenced herpesviruses.     

魁蚶幼贝对筒柱藻滤食效应的初步研究

采用实验生态学方法和"捕食者-猎物"的捕食模型,研究了黑暗条件下魁蚶(Anadara broughtonii)幼贝对筒柱藻(Cylindrotheca fusiformis)的滤食效应,测定了5种藻液浓度(30×107~150×107cells/L)及4个温度梯度(10℃、15℃、20℃和25℃)下魁蚶对饵料生物的滤食能力、功能反应类型和滤藻效应特征,并分别建立Holling圆盘方程。同时研究了水温20℃时魁蚶个体间的滤食干扰反应,建立了藻液浓度和魁蚶自身密度的联合反应方程。实验发现,水温20℃条件下,魁蚶幼贝对筒柱藻的平均滤食速率随着藻液浓度的增加而显著增大(P0.05),且0~4 h时段内的滤食速率显著高于其他时段。魁蚶滤食筒柱藻的功能反应属Holling-Ⅱ型,拟合圆盘方程为Na=1.0195N_0/1+0.002039N_0滤食功能系数为1.019 5,极限法推出壳长30~35 mm的魁蚶对筒柱藻的日均最大滤食量约为500×107 cells/L;10~25℃条件下,魁蚶的平均滤食速率和滤食功能反应系数随温度升高呈现先升高后下降的变化趋势,并于20℃时达到最大值,推测20℃是其最佳摄食温度。魁蚶的滤食效应存在较强的个体间干扰反应,平均滤食量和滤食作用率均随幼贝密度的增加而下降,且魁蚶滤食筒柱藻的功能反应与幼贝密度的关系可用幂函数方程E=0.730 8P﹣1.068表示,由此建立了魁蚶幼贝密度与筒柱藻藻液浓度之间的联合反应方程N_a=0.7451P~(-0.0684)N_0/1+0.0020N0。结果表明,水温20℃时,魁蚶幼贝具有较强的潜在滤食能力,其平均滤食量和滤食作用率与幼贝密度间存在明显的"负密度效应"特征。     

Activity of antioxidant enzymes and physiological responses in ark shell,Scapharca broughtonii,exposed to thermal and osmotic stress: Effects on hemolymph and biochemical parameters

Changes in water temperature and salinity are responsible for a variety of physiological stress responses in aquatic organisms. Stress induced by these factors was recently associated with enhanced reactive oxygen species (ROS) generation, which caused oxidative damage. In the present study, we investigated the time-related effects of changes in water temperature and salinity on mRNA expression and the activities of antioxidant enzymes (SOD and CAT) and lipid peroxidation (LPO) in the gills and digestive glands of the ark shell, Scapharca broughtonii. To investigate physiological responses, hydrogen peroxide (H₂O₂), lysozyme activity, aspartate aminotransferase (AspAT), and alanine aminotransferase (AlaAT) were measured in the hemolymph. Water temperature and salinity changes significantly increased antioxidant enzyme mRNA expression and activity in the digestive glands and gills in a time-dependent manner. H₂O₂ concentrations increased significantly in the high-temperature and hyposalinity treatments. LPO, AspAT and AlaAT levels also increased significantly in a time-dependent manner, while lysozyme activity decreased. These results suggest that antioxidant enzymes play important roles in reducing oxidative stress in ark shells exposed to changes in water temperature and salinity.     

Complete DNA sequence of the mitochondrial genome of the ascidian Halocynthia roretzi (Chordata, Urochordata)

The complete nucleotide sequence of the 14,771-bp-long mitochondrial (mt) DNA of a urochordate (Chordata)-the ascidian Halocynthia roretzi-was determined. All the Halocynthia mt-genes were found to be located on a single strand, which is rich in T and G rather than in A and C. Like nematode and Mytilus edulis mtDNAs, that of Halocynthia encodes no ATP synthetase subunit 8 gene. However, it does encode an additional tRNA gene for glycine (anticodon TCT) that enables Halocynthia mitochondria to use AGA and AGG codons for glycine. The mtDNA carries an unusual tRNA(Met) gene with a TAT anticodon instead of the usual tRNA(Met)(CAT) gene. As in other metazoan mtDNAs, there is not any long noncoding region. The gene order of Halocynthia mtDNA is completely different from that of vertebrate mtDNAs except for tRNA(His)-tRNA(Ser)(GCU), suggesting that evolutionary change in the mt-gene structure is much accelerated in the urochordate line compared with that in vertebrates. The amino acid sequences of Halocynthia mt-proteins deduced from their gene sequences are quite different from those in other metazoans, indicating that the substitution rate in Halocynthia mt-protein genes is also accelerated.     

Alignments of mitochondrial genome arrangements: applications to metazoan phylogeny

Mitochondrial genomes provide a valuable dataset for phylogenetic studies, in particular of metazoan phylogeny because of the extensive taxon sample that is available. Beyond the traditional sequence-based analysis it is possible to extract phylogenetic information from the gene order. Here we present a novel approach utilizing these data based on cyclic list alignments of the gene orders. A progressive alignment approach is used to combine pairwise list alignments into a multiple alignment of gene orders. Parsimony methods are used to reconstruct phylogenetic trees, ancestral gene orders, and consensus patterns in a straightforward approach. We apply this method to study the phylogeny of protostomes based exclusively on mitochondrial genome arrangements. We, furthermore, demonstrate that our approach is also applicable to the much larger genomes of chloroplasts.     

Complete DNA sequence of the mitochondrial genome of the sea-slug, Aplysia californica: conservation of the gene order in Euthyneura

We have sequenced and characterized the complete mitochondrial genome of the sea slug, Aplysia californica, an important model organism in experimental biology and a representative of Anaspidea (Opisthobranchia, Gastropoda). The mitochondrial genome of Aplysia is in the small end of the observed sizes of animal mitochondrial genomes (14,117 bp, NCBI Accession No. NC_005827). The Aplysia genome, like most other mitochondrial genomes, encodes genes for 2 ribosomal subunit RNAs (small and large rRNAs), 22 tRNAs, and 13 protein subunits (cytochrome c oxidase subunits 1-3, cytochrome b apoenzyme, ATP synthase subunits 6 and 8, and NADH dehydrogenase subunits 1-6 and 4L). The gene order is virtually identical between opisthobranchs and pulmonates, with the majority of differences arising from tRNA translocations. In contrast, the gene order from representatives of basal gastropods and other molluscan classes is significantly different from opisthobranchs and pulmonates. The Aplysia genome was compared to all other published molluscan mitochondrial genomes and phylogenetic analyses were carried out using a concatenated protein alignment. Phylogenetic analyses using maximum likelihood based analyses of the well aligned regions of the protein sequences support both monophyly of Euthyneura (a group including both the pulmonates and opisthobranchs) and Opisthobranchia (as a more derived group). The Aplysia mitochondrial genome sequenced here will serve as an important platform in both comparative and neurobiological studies using this model organism.     

A bayesian analysis of metazoan mitochondrial genome arrangements

Genome arrangements are a potentially powerful source of information to infer evolutionary relationships among distantly related taxa. Mitochondrial genome arrangements may be especially informative about metazoan evolutionary relationships because (1) nearly all animals have the same set of definitively homologous mitochondrial genes, (2) mitochondrial genome rearrangement events are rare relative to changes in sequences, and (3) the number of possible mitochondrial genome arrangements is huge, making convergent evolution of genome arrangements appear highly unlikely. In previous studies, phylogenetic evidence in genome arrangement data is nearly always used in a qualitative fashion-the support in favor of clades with similar or identical genome arrangements is considered to be quite strong, but is not quantified. The purpose of this article is to quantify the uncertainty among the relationships of metazoan phyla on the basis of mitochondrial genome arrangements while incorporating prior knowledge of the monophyly of various groups from other sources. The work we present here differs from our previous work in the statistics literature in that (1) we incorporate prior information on classifications of metazoans at the phylum level, (2) we describe several advances in our computational approach, and (3) we analyze a much larger data set (87 taxa) that consists of each unique, complete mitochondrial genome arrangement with a full complement of 37 genes that were present in the NCBI (National Center for Biotechnology Information) database at a recent date. In addition, we analyze a subset of 28 of these 87 taxa for which the non-tRNA mitochondrial genomes are unique where the assumption of our inversion-only model of rearrangement is more plausible. We present summaries of Bayesian posterior distributions of tree topology on the basis of these two data sets.     

Complete mitochondrial genome sequence of Catla catla and its phylogenetic consideration

Complete nucleotide sequence of mitochondrial genome (mitogenome) of the Catla catla (Ostariophysi: Cypriniformes: Cyprinidae) was determined in the present study. Its length is 16,594 bp and contains 13 protein coding genes, 22 transfer RNAs, two ribosomal RNAs and one non-coding control region. Most of the genes were encoded on the H-strand, while the ND6 and eight tRNA (Gln, Ala, Asn, Cys, Tyr, Ser (UCN), Glu and Pro) genes were encoded on the L-strand. The reading frames of two pair of genes overlapped: ATPase 8 with 6 and ND4L with ND4 by seven nucleotides each. The main non-coding region was 929 bp, with three conserved sequence blocks (CSB-I, CSB-II, and CSB-III) and an unusual simple sequence repeat, (TA)₇. Phylogenetic analyses based on complete mitochondrial genome sequences were in favor of the traditional taxonomy of family Cyprinidae. In conclusion present mitogenome of Catla catla adds more information to our understanding of diversity and evolution of mitogenome in fishes.