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1.
Quantification of metallothioneins (MTs) is classically associated with a cellular response to heavy metal contamination and is used in the monitoring of disturbed ecosystems. Despite the characterization of several MT genes in marine bivalves, only a few genetic studies have used MT genes as potential biomarkers of pollution. The aim of this study was to assess whether MT gene polymorphism could be used to monitor exposure of the Pacific oyster Crassostrea gigas to heavy metals and to develop specific genetic markers for population genetic studies in relation to environmental stress. The polymorphism of two exons of the C. gigas MT gene CgMT1 were studied using polymerase chain reaction single-strand conformation polymorphism (PCR-SSCP) in both field populations exposed to various metals concentrations and in experimentally exposed populations. High frequencies of two SSCP types in exons 2 and 3 of the CgMT1 gene have found to be significantly associated with tolerance to metals in experimental and field oyster populations. The use of MT1 gene polymorphism in C. gigas as in the present study should therefore be of high ecological relevance. In conclusion, the analysis of the types in these two CgMT1 gene exons, which can confer a greater tolerance to heavy metals, can constitute a good biomarker of effect of the presence of heavy metals in ecosystems. 相似文献
2.
Bindin is a major protein for species-specific recognition between sperm and congenetic egg in many free-spawning marine invertebrates.
We cloned a novel bindin gene from the oyster Crassostrea angulata by 3′ and 5′ rapid amplification of cDNA ends. The full-length bindin cDNA was 1,049 bp with a 771-bp open reading frame
encoding 257 amino acids. The deduced amino acid sequence contained a putative signal peptide of 24 amino acids. The length
of the bindin genomic DNA was 8,508 bp containing four exons and three introns. Three haplotypes of F-lectin repeat were detected
from seven sequences of F-lectin repeat of six male oysters. Both neighbor-joining and minimum-evolution phylogenetic trees
show that haplotype an1 was close to Crassostrea gigas while an2 and an3 were close to Crassostrea sikamea. Intron-4 in the middle of F-lectin repeat is highly variable in both size and sequence. We classified intron-4 into three
types according to their size and the F-lectin repeat they were located in. Intron-4 may play an important role in recombination.
We compared the number of nonsynonymous substitutions (Dn) and synonymous substitutions (Ds) per nucleotide site among 19
F-lectin haplotypes of the three species. Dn/Ds ratios suggested that positive selection occurred between C. gigas and C. sikamea and between C. gigas and C. angulata. Nine positive selected positions (p > 90%) are identified among 19 haplotypes of three species. They are located on the F-lectin binding face around the three
recognition motif residues. We assume that these nine clustered amino acids are related with species-specific recognition. 相似文献
3.
The giant garter snake, Thamnophis gigas, is a threatened species endemic to California’s Central Valley. We tested the hypothesis that current watershed boundaries
have caused genetic differentiation among populations of T. gigas. We sampled 14 populations throughout the current geographic range of T. gigas and amplified 859 bp from the mitochondrial gene ND4 and one nuclear microsatellite locus. DNA sequence variation from the
mitochondrial gene indicates there is some genetic structuring of the populations, with high FST values and unique haplotypes occurring at high frequency in several populations. We found that clustering populations by
watershed boundary results in significant between-region genetic variance for mtDNA. However, analysis of allele frequencies
at the microsatellite locus NSU3 reveals very low FST values and little between-region variation in allele frequencies. The discordance found between mitochondrial and microsatellite
data may be explained by aspects of molecular evolution and/or T. gigas life history characteristics. Differences in effective population size between mitochondrial and nuclear DNA, or male-biased
gene flow, result in a lower migration rate of mitochondrial haplotypes relative to nuclear alleles. However, we cannot exclude
homoplasy as one explanation for homogeneity found for the single microsatellite locus. The mitochondrial nucleotide sequence
data supports conservation practices that identify separate management units for T. gigas. 相似文献
4.
Mitochondrial and nuclear DNA phylogeography of Crassostrea angulata, the Portuguese oyster endangered in Europe 总被引:4,自引:0,他引:4
The respective status of the Portuguese oyster, Crassostrea angulata, and the Pacific oyster, Crassostrea gigas, has long been a matter of controversy. Morphological and physiological similarities, homogeneity of allozyme allelic frequencies between populations of the two taxa and the demonstration of hybridization lead most authors to suggest that they should be regrouped within the same species. The risk of introgression and the present expansion of C. gigas aquaculture in Europe raises the question of the need for preservation of C. angulata in Europe, as only a few populations remain. We studied European and Asian populations of C. gigas and C. angulata using microsatellite and mitochondrial DNA markers to estimate their genetic diversity and differentiation. The analysis of genetic distances and the distribution of allelic and haplotype frequencies revealed significant genetic differences between taxa, showing two clusters: (1) C. gigas French and Japanese populations and (2) C. angulata Portuguese and Taiwanese populations. The Asian origin of the Crassostrea angulata taxa is therefore confirmed. Unlike previous studies based on allozymes, significant nuclear genome differences were noted between C. angulata and C. gigas. Despite the presumed history of the introduction of C. angulata into Southern Europe, these populations did not show any significant reduction of variability compared to Taiwanese populations. Any conservation plans for European C. angulata populations should take its non-native origin into account. They represent a valuable genetic resources for European breeding program. 相似文献
5.
Experimental examination of reproductive isolation is the first step in understanding hybridization processes. Here, we studied
preferential fertilization between 2 cupped oyster taxa, Crassostrea angulata and Crassostrea gigas, as a potential prezygotic reproductive isolation. Early examination of sperm competition is now possible by molecular analysis
of oyster embryos. This avoids the confounding effect of differential mortality during the larval stage. Six hundred embryos
were sampled from 2 crosses. Three microsatellite loci were enough to determine without ambiguity the taxa of contributing
sires of embryos. No evidence of preferential fertilization between gametes from the same taxa was shown. A significantly
higher contribution of the C. gigas males was revealed with the C. angulata females, but not with the C. gigas females, which might suggest early heterosis or interaction differences between gametes. In the light of these results, natural
hybridization between both taxa can be expected in cases of their geographical coexistence, as in the Southern European populations
in which both taxa are in contact as a result of aquaculture development.
Received May 6, 2000; accepted March 6, 2001. 相似文献
6.
Cunningham C Hikima J Jenny MJ Chapman RW Fang GC Saski C Lundqvist ML Wing RA Cupit PM Gross PS Warr GW Tomkins JP 《Marine biotechnology (New York, N.Y.)》2006,8(5):521-533
Large-insert genomic bacterial artificial chromosome (BAC) libraries of two culturally and economically important oyster species,
Crassostrea virginica and C. gigas, have been developed as part of an international effort to develop tools and reagents that will advance our ability to conduct
genetic and genomic research. A total of 73,728 C. gigas clones with an average insert size of 152 kb were picked and arrayed representing an 11.8-fold genome coverage. A total of
55,296 clones with an average insert size of 150 kb were picked and arrayed for C. virginica, also representing an 11.8-fold genome coverage. The C. gigas and C. virginica libraries were screened with probes derived from selected oyster genes using high-density BAC colony filter arrays. The probes
identified 4 to 25 clones per gene for C. virginica and 5 to 50 clones per gene for C. gigas. We conducted a preliminary analysis of genetic polymorphism represented in the C. gigas library. The results suggest that the degree of divergence among similar sequences is highly variable and concentrated in
intronic regions. Evidence supporting allelic polymorphism is reported for two genes and allelic and/or locus specific polymorphism
for several others. Classical inheritance studies are needed to confirm the nature of these polymorphisms. The oyster BAC
libraries are publicly available to the research community on a cost-recovery basis at 相似文献
7.
We analyzed precursor messenger RNAs (pre-mRNAs) of 12 eukaryotic species. In each species, three groups of highly expressed
genes, ribosomal proteins, heat shock proteins, and amino-acyl tRNA synthetases, were compared with a control group (randomly
selected genes). The purine-pyrimidine (R-Y) composition of pre-mRNAs of the three targeted gene groups proved to differ significantly
from the control. The exons of the three groups tested have higher purine contents and R-tract abundance and lower abundance
of Y-tracts compared to the control (R-tract—tract of sequential purines with R
n
≥ 5; Y-tract—tract of sequential pyrimidines with Y
n
≥ 5). In species widely employing “intron definition” in the splicing process, the Y content of introns of the three targeted
groups appeared to be higher compared to the control group. Furthermore, in all examined species, the introns of the targeted
genes have a lower abundance of R-tracts compared to the control. We hypothesized that the R-Y composition of the targeted
gene groups contributes to high rate and efficiency of both splicing and translation, in addition to the mRNA coding role.
This is presumably achieved by (1) reducing the possibility of the formation of secondary structures in the mRNA, (2) using
the R-tracts and R-biased sequences as exonic splicing enhancers, (3) lowering the amount of targets for pyrimidine tract
binding protein in the exons, and (4) reducing the amount of target sequences for binding of serine/arginine-rich (SR) proteins
in the introns, thereby allowing SR proteins to bind to proper (exonic) targets.
(Reviewing
Editor: Dr. Axel Meyer) 相似文献
8.
9.
《FEBS letters》1987,224(2):297-305
Analysis of the structure of the 3′-end of the human α2(IV) gene demonstrated that the α1(IV) and α2(IV) genes have diverged extensively in spite of the apparent homology of the respective gene products. The NC-1 domain and the 3′-untranslated region are encoded by three exons in the α2(IV) gene but five exons in the α1(IV) gene. The two introns present in the NC- 1 domain coding part of the α2(IV) gene had the same location as two of the introns of the α1(IV) gene. The junction exon in the α2(IV) gene contains 53 bp coding for Gly-X-Y sequences whereas there are 71 bp in the α1(IV) gene. Three other Gly-X-Y coding exons studied from the human ⇌2(IV) gene have sizes that differ from corresponding exons in the α1(IV) gene and only one intron location matches here between the two genes. None of the exons studied has 54 bp or multiples thereof. 相似文献
10.
The Pacific oyster (Crassostrea gigas) is globally distributed and is one of the most commercially and ecologically important marine organisms. However, little is known about the genome of this species. In this study, a C. gigas fosmid library was constructed that contains 459,936 clones with an average insert size of approximately 40 kb, representing 22.34-fold haploid genome equivalents. End sequencing generated 90,240 fosmid end sequences (FESs) with an average length of 384.27 base pairs (bp), covering approximately 2.58% of the Pacific oyster genome. The FESs were subsequently assembled and annotated, resulting in 6332 sequences with predicted open reading frames≥300 and 1,189,100 bp repeats. Furthermore, a total of 3200 microsatellite repeats were identified, and dinucleotide repeats were found to occur most abundantly, with AG and AAT being the most abundant repeat class of dinucleotides and trinucleotides. We also found that the repeat number was generally negatively proportional to the repeat element length. Microsatellites composition between the transcribed sequences and genomic sequences was shown to be different. Point mutations of microsatellite were non-random and underwent strong selection stress. Overall, a comprehensive sequence resource for the Pacific oyster was created, including annotated transposable elements, tandem repeats, protein coding sequences and microsatellites. These initial findings will serve as resources for further in-depth studies of physical mapping, gene discovery, microsatellite marker developing and evolution studies. 相似文献
11.
We analyzed occurrences of bases in 20,352 introns, exons of 25,574 protein-coding genes, and among the three codon positions in the protein-coding sequences. The nucleotide sequences originated from the whole spectrum of organisms from bacteria to primates. The analysis revealed the following: (1) In most exons, adenine dominates over thymine. In other words, adenine and thymine are distributed in an asymmetric way between the exon and the complementary strand, and the coding sequence is mostly located in the adenine-rich strand. (2) Thymine dominates over adenine not only in the strand complementary to the exon but also in introns. (3) A general bias is further revealed in the distribution of adenine and thymine among the three codon positions in the exons, where adenine dominates over thymine in the second and mainly the first codon position while the reverse holds in the third codon position. The product (A1/T1) × (A2/T2) × (T3/A3) is smaller than one in only a few analyzed genes.
Correspondence to: J. Kypr 相似文献
12.
Introns are widespread and variable in eukaryotic genomes. Although their histories and functions, or even whether all of them have any function, remain largely unknown, analysis of intron sequences and genomic contexts may shed light on the evolutionary history of genes and organisms. The number and frequency of introns vary widely in the small number of published genomes of protists and algae suggesting that the same is true of the vast diversity of protists and algae that remain uncultivated. The objective of this study were to investigate introns in sequences of functional genes of phytoplankton, both in published genomes and in sequences obtained from environmental clone libraries. We examined the introns of the genes involved in nitrogen uptake and assimilation pathways in the genome sequences of cultivated phytoplankton as well as in environmental clone libraries of nitrate reductases (NR), nitrite reductase (NiR), nitrate transporter (Nrt2) and ammonium transporter (AMT) genes constructed from pelagic phytoplankton communities in Monterey Bay (CA, USA) and Onslow Bay (NC, USA). Here we describe the most extensive set to date of intron sequences from uncultivated marine algae and report important differences for diatom vs. non-diatom sequences. The majority of the introns in NR, NiR, Nrt2 and AMT from cultured phytoplankton and environmental libraries showed canonical splice patterns. Introns found in diatom-like NR environmental libraries had lower GC content than the respective exons. The green algal-like NR and Nrt2 environmental sequences had introns and exons of much more similar GC content, and both higher than in diatoms. These patterns suggest a different evolutionary history and recent acquisition of diatom introns compared to other algae. 相似文献
13.
A new gene,msta, was found in region 2E of theDrosophila melanogaster X-chromosome. The gene is expressed in the head of adults, consists of two exons, and codes for a protein containing the
SET domain, as characteristic of several proteins modulating chromatin structure and gene activity. Its shortened copy,msts, was found in the vicinity of,msta. Since the divergence between their coding regions was lower than between the introns,msts was assumed to have functioned for some time after duplication. The genes proved to be separated by the 1.688-2E complex
microsatellite. 相似文献
14.
15.
Jenny MJ Chapman RW Mancia A Chen YA McKillen DJ Trent H Lang P Escoubas JM Bachere E Boulo V Liu ZJ Gross PS Cunningham C Cupit PM Tanguy A Guo X Moraga D Boutet I Huvet A De Guise S Almeida JS Warr GW 《Marine biotechnology (New York, N.Y.)》2007,9(5):577-591
The eastern oyster, Crassostrea virginica, and the Pacific oyster, C. gigas, are species of global economic significance as well as important components of estuarine ecosystems and models for genetic
and environmental studies. To enhance the molecular tools available for oyster research, an international group of collaborators
has constructed a 27,496-feature cDNA microarray containing 4460 sequences derived from C. virginica, 2320 from C. gigas, and 16 non-oyster DNAs serving as positive and negative controls. The performance of the array was assessed by gene expression
profiling using gill and digestive gland RNA derived from both C. gigas and C. virginica, and digestive gland RNA from C. ariakensis. The utility of the microarray for detection of homologous genes by cross-hybridization between species was also assessed
and the correlation between hybridization intensity and sequence homology for selected genes determined. The oyster cDNA microarray
is publicly available to the research community on a cost-recovery basis. 相似文献
16.
Basement membrane (type IV) collagen, a subfamily of the collagen protein family, is encoded by six distinct genes in mammals. Three of those,COL4A3, COL4A4,andCOL4A5,are linked with Alport syndrome (hereditary nephritis). Patients with leimoyomatosis associated with Alport syndrome have been shown to have deletions in the 5′ end of theCOL4A6gene, in addition to having deletions inCOL4A5(Zhouet al., Science261: 1167–1169, 1993). The humanCOL4A6gene is reported to be 425 kb as determined by mapping of overlapping YAC clones by probes for its 5′ and 3′ ends. In the present study we describe the complete exon/intron size pattern of the humanCOL4A6gene. The 12 λ phage clones characterized in the study spanned a total of 110 kb, including 85 kb of the actual gene and 25 kb of flanking sequences. The overlapping clones contained all 46 exons of the gene and all introns, except for intron 2. Since the total size of the exons and all introns except for intron 2 is about 85 kb, intron 2 must be about 340 kb. All exons of the gene were assigned toEcoRI restriction fragments to facilitate analysis of the gene in patients with leiomyomatosis associated with Alport syndrome. The exon size pattern ofCOL4A6is highly homologous with that of the human and mouseCOL4A2genes, with 27 of the 46 exons ofCOL4A6being identical in size between the genes. 相似文献
17.
Matsumoto T Nakamura AM Takahashi KG 《Comparative biochemistry and physiology. Part B, Biochemistry & molecular biology》2006,145(3-4):325-330
In bivalve molluscs including oysters, lysozymes play an important role in the host defense mechanisms against invading microbes. However, it remains unclear in which sites/cells the lysozyme genes are expressed and which subsequently produced the enzyme. This study cloned lysozyme cDNAs from the digestive organs of Pacific oyster Crassostrea gigas and European flat oyster Ostrea edulis. Both complete sequences of two oysters' lysozymes were composed of 137 amino acids. Two translated proteins present a high content in cysteine residues. Phylogenetic analyses showed that these oysters' lysozymes clustered with the invertebrate-type lysozymes of other bivalve species. In the Pacific oyster, lysozyme mRNA was expressed in all tissues except for those of the adductor muscle. In situ hybridization analyses revealed that lysozyme mRNA was expressed strongly in basophil cells in the digestive gland tubule of C. gigas, but not in digestive cells. Results indicated that the basophil cells of the oyster digestive gland are the sites of lysozyme synthesis. 相似文献
18.
The protein-coding sequences of the major histocompatibility complex (MHC) genes are characterized by extraordinarily high
polymorphism, apparently maintained by balancing selection, which favors diversity in the peptide-binding domains of the MHC
glycoproteins. Here we report that the introns flanking the polymorphic exons of the human MHC class I loci HLA-A, -B, and -C genes have been relatively conserved and have become locus-specific apparently as a result of recombination and subsequent
genetic drift, leading to homogenization within loci over evolutionary time. Thus, HLA class I genes have been shaped by contrasting evolutionary forces maintaining polymorphism in the exons and leading to conservation
in the introns. This study provides the first extensive analysis of the introns of a highly polymorphic gene family.
Received: 10 April 1997 / Revised: 15 July 1997 相似文献
19.
20.
K. Schmidt-Bleek V. Heiser O. Thieck A. Brennicke L. Grohmann 《Molecular & general genetics : MGG》1997,253(4):448-454
The intrinsic 28.5-kDa iron-sulfur protein of complex I in the mitochondrial respiratory chain is encoded in the nucleus
in animals and fungi, but specified by a mitochondrial gene in trypanosomes. In plants, the homologous protein is now found
to be encoded by a single-copy nuclear gene in Arabidopsis thaliana and by two nuclear genes in potato. The cysteine motifs involved in binding two iron-sulfur clusters are conserved in the
plant protein sequences. The locations of the seven introns, with sizes between 60 and 1700 nucleotides, are identical in
the A. thaliana and the two potato genes, while their primary sequences diverge considerably. The A+T contents of the intron sequences range
between 61% and 73%, as is characteristic for dicot plants, but are in some instances not higher than in the adjacent exons.
Here, differences in T content may instead serve to discriminate exons and introns. In potato, both genes are expressed, with
the highest levels found in flowers. Sequence similarities between the homologous nuclear and mitochondrial genes indicate
that the nuclear forms in animals and plants originate from the endosymbiont genome.
Received: 28 May 1996 / Accepted: 22 August 1996 相似文献