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.     

Unraveling the sequence dynamics of the formation of genus-specific satellite DNAs in the family solanaceae

Tandemly repeated DNAs, referred to as satellite DNAs, often occur in a genome in a genus-specific manner. However, the mechanisms for generation and evolution for these sequences are largely unknown because of the uncertain origins of the satellite DNAs. We found highly divergent genus-specific satellite DNAs that showed sequence similarity with genus-specific intergenic spacers (IGSs) in the family Solanaceae, which includes the genera Nicotiana, Solanum and Capsicum. The conserved position of the IGS between 25S and 18S rDNA facilitates comparison of IGS sequences across genera, even in the presence of very low sequence similarity. Sequence comparison of IGS may elucidate the procedure of the genesis of complex monomer units of the satellite DNAs. Within the IGS of Capsicum species, base substitutions and copy number variation of subrepeat monomers were causes of monomer divergence in IGS sequences. At the level of inter-generic IGS sequences of the family Solanaceae, however, genus-specific motif selection, motif shuffling between subrepeats and differential amplification among motifs were involved in formation of genus-specific IGS. Therefore, the genus-specific satellite DNAs in Solanaceae plants can be generated from differentially organized repeat monomers of the IGS rather than by accumulation of mutations from pre-existent satellite DNAs.     

Origin and evolution of Mytilus mussel satellite DNAs.

A phylogenetic reconstruction based on the amplification of 3 satellite DNAs (stDNAs) was carried out in 1 crustacean species and 15 bivalve species of the subclass Pteriomorphia (10, subfamily Mytilinae; 1, subfamily Litophaginae; 1, subfamily Modiolinae, all belonging to family Mytilidae; 1, family Arcidae; and 2, family Pectinidae). The sequences obtained showed motifs with high similarity to those of A and B boxes of tRNA promoter regions. Dot-blot hybridizations revealed that the 3 stDNAs are present mainly in high copy numbers for each species of the genus Mytilus, whereas for the other species they appear in low copy numbers. Maximum-parsimony trees evidenced a tendency to group Mytilus clones together, and species containing these sequences as a single copy were distributed among the different mytilids. Finally, the possible origin and evolution of these stDNAs is discussed.     

Genetic connections between some species of Mytilidae (Mollusca: Bivalvia) from the northern part of the Pacific Ocean

In 1978 and 1999, seven and eight species of Mytilidae (Mollusca: Bivalvia) were analyzed using gel electrophoresis. Mean heterozygosity per individual (Hobs and Hexp) and genetic distances (Rogers' DR, Nei's DN, and others) were estimated for 21 and 24 allozyme loci. Mytilus modiolus had the highest variation among the species examined. Genetic distances were lowest for the M. trossulus-M. galloprovincialis species pair: DR = 0.147, DN = 0.078. Overall, five species of the genera Mytilus and Crenomytilus were genetically closer to each other (DR = 0.147, DN = 0.078) than to the remaining three species of this group (DR = 0.807, DN = 2.243). The relationships among the species were examined using cluster analysis and parsimony methods. The densest clusters in the dendrograms consisted of (1) M. trossulus and M. galloprovincialis and (2) M. coruscus, M. californianus, and M. grayanus. These two clusters form a larger cluster (3), which comprises all representatives of the nominal genus Mutilus and C. grayanus. The Mytilus-Crenomytilus cluster is consecutively joined by Adula falcatoides, Mytilus modiolus, and Septifer keenae. According to Nei's genetic distances DN, the time of divergence between M. trossulus and M. galloprovincialis is 0.8-1.6 Myr; between M. californianus and C. grayanus, it is approximately 9 Myr; and between M. coruscus and the latter pair, it is 13 Myr before present. Two representatives of the Mytilus ex gr. edulis complex diverged from the Mytilus-Crenomytilus group of large-size Pacific species about 20 Myr ago. These results are in good agreement with paleontological data and indicate a relatively recent origin of the Mytilus ex gr. edulis complex. The results obtained can be used in systematics and phylogeny of modern Mytilidae.     

蓝狐-卫星DNA的克隆及序列分析

利用限制性内切酶酶切蓝狐基因组, 经琼脂糖凝胶电泳, 对特异性亮带进行克隆、测序及序列分析。结果获得42个卫星DNA序列, 该卫星DNA单体大小为737 bp, G+C含量为51.9%, 单体之间同源性为91%~97%; 每个单体由3个约245 bp的亚重复串联构成, 亚重复之间的同源性为49%~55%; 在物种进化过程中, 该卫星DNA有G+C含量逐渐降低而A+T含量逐渐上升的趋势; 该卫星DNA为犬科动物种属所特有, 与犬着丝粒相关卫星DNA为同类卫星DNA, 同源性为74%, 命名为α-卫星DNA。     

Detection of satellite DNA in Palorus ratzeburgii: analysis of curvature profiles and comparison with Tenebrio molitor satellite DNA.

Very abundant and homogenous satellite DNA has been found in the flour beetle Palorus ratzeburgii, representing 40% of its genome. Sequencing of 14 randomly cloned satellite monomers revealed a conserved monomer length of 142 bp and an average A+T content of 68%. Sequence variation analysis showed that base substitutions, appearing with a frequency of 2.3%, are predominant differences among satellite monomers. The satellite sequence is unique without significant direct repeats and with only two potentially stable inverted repeats. After electrophoresis of satellite monomers on native polyacrylamide gel retarded mobilities characteristic for curved DNA molecules are observed. The curvature profiles and DNA helix axis trajectory are calculated on the basis of three different algorithms. These calculations predict that P ratzeburgii satellite DNA forms a left-handed solenoid superstructure. Comparison of described features with other satellite DNAs reveals some striking similarities with satellite DNA from related species Tenebrio molitor, which belongs to the same family of Tenebrionidae. Both satellites are very abundant and homogenous with the same, highly conserved monomer length, although there is no homology at the nucleotide level. Their monomers, as well as multimers, exhibit very similar retarded electrophoretic mobilities. The calculated curvature profiles predict two bend centers in monomers of each satellite, resulting in a model of left-handed solenoid superstructures of similar appearance.     

Detection of satellite DNA in Palorus ratzeburgii: Analysis of curvature profiles and comparison with Tenebrio molitor satellite DNA

Very abundant and homogenous satellite DNA has been found in the flour beetle Palorus ratzeburgii, representing 40% of its genome. Sequencing of 14 randomly cloned satelite monomers revealed a conserved monomer length of 142 bp and an average A+T content of 68%. Sequence variation analysis showed that base substitutions, appearing with a frequency of 2.3%, are predominant differences among satellite monomers. The satellite sequence is unique without significant direct repeats and with only two potentially stable inverted repeats. After electrophoresis of satellite monomers on native polyacrylamide gel retarded mobilities characteristic for curved DNA molecules are observed. The curvature profiles and DNA helix axis trajectory are calculated on the basis of three different algorithms. These calculations predict that P ratzeburgii satellite DNA forms a left-handed solenoid superstructure. Comparison of described features with other satellite DNAs reveals some striking similarities with satellite DNA from related species Tenebrio molitor, which belongs to the same family of Tenebrionidae. Both satellites are very abundant and homogenous with the same, highly conserved monomer length, although there is no homology at the nucleotide level. Their monomers, as well as multimers, exhibit very similar retarded electrophoretic mobilities. The calculated curvature profiles predict two bend centers in monomers of each satellite, resulting in a model of left-handed solenoid superstructures of similar appearance.     

DNA content, karyotypes, and chromosomal location of 18S-5.8S-28S ribosomal loci in some species of bivalve molluscs from the Pacific Canadian coast.

The DNA content of 10 species of bivalve molluscs from British Columbia coast was determined by image analysis, and the karyotypes of the horse clam Tressus capax, the bent-nose macoma Macoma nasuta, and the nuttall's mahogany clam Nuttallia nuttallii are described here for the first time. We also have analyzed the location of rDNA loci using a 28S-5.8S-18S probe in four of these species: Mytilus californianus, M. trossulus, Macoma nasuta and N. nuttallii. Results obtained report new data about cytogenetic characteristics of bivalve molluscs.     

Satellite DNA in the ant Messor structor (Hymenoptera, Formicidae).

This paper is the first record of the satellite DNA of Formicidae. The satellite DNA of the ant Messor structor is organized in a tandem repeat of monomers of 79 bp. Like satellite DNAs of other insects, it is AT rich and presents direct and inverted internal repeats. Restriction analysis of the total DNA with methylation-sensitive enzymes strongly suggests that this DNA is undermethylated. The presence of this repetitive DNA in other species of the genus Messor is also tested.     

Identical satellite DNA sequences in sibling species of Drosophila

The evolution of simple satellite DNAs was examined by DNA-DNA hybridization of ten Drosophila melanogaster satellite sequences to DNAs of the sibling species, Drosophila simulans and Drosophila erecta. Seven of these repeat types are present in tandem arrays in D. simulans and each of the ten sequences is repeated in D. erecta. In thermal melts, six of the seven satellite sequences in D. simulans and seven of the ten sequences in D. erecta melted within 1 deg.C of the corresponding values in D. melanogaster. The remaining sequences melted within 3 deg.C of the homologous hybrids. Therefore, there is little or no alteration in those satellite sequences held in common, despite a period of about ten million years since the divergence of D. melanogaster and D. simulans from a common ancestor. Simple satellite sequences appear to be more highly conserved than coding regions of the genome, on a per nucleotide basis. Since multiple copies of three satellite sequences could not be detected in D. simulans yet are present in D. erecta, a species more distantly related to D. melanogaster than is D. simulans, these sequences show discontinuities in evolution. There were major quantitative variations between species, showing that satellite DNAs are prone to massive amplification or diminution events over timespans as short as those separating sibling species. In D. melanogaster, these sequences amount to 21% of the genome but only 5% in D. simulans and 0.4% in D. erecta. There was a general trend of lower abundance with evolutionary distance for most satellites, suggesting that the amounts of different satellite sequences do not vary independently during evolution.     

Detection and location of three simple sequence DNAs in polytene chromosomes from virilis group species of Drosophila

In vitro synthesized RNAs complementary to the three satellite DNAs of Drosophila virilis have been used in a series of in situ hybridization experiments with polytene chromosomes from virilis group species. Gall and Atherton (1974) demonstrated that each of the satellites of D. virilis is comprised of many repeats of a distinct, seven base pair long, simple sequence. With few exceptions, copies of each of these simple sequences are detected in the chromocenters of all virilis group species. This is true even in species which do not possess satellite DNAs at buoyant densities corresponding to those of the satellite DNAs of D. virilis. Small quantities of the three simple sequences are also detected in euchromatic arms of several different species. The same euchromatic location may contain detectable copies of one, two, or all three simple sequence DNAs. The amounts of simple sequences at each location in the euchromatin may vary between species, between different stocks of the same species, and even between individuals of the same stock. The simple sequences located in the euchromatin appear to undergo DNA replication during formation of polytene chromosomes unlike those in heterochromatin. The locations of the euchromatic sequences are not the results of single chromosomal inversion events involving heterochromatic and euchromatic breakpoints.     

Interactions of organic pollutants with gills of the bivalve molluscs Anodonta californiensis and Mytilus californianus: uptake and effect on membrane fluxes. II

1. The uptakes of 2,4,5-T, glyphosate, parathion, paranitrophenol, naphthalene, glycine, and inulin by gills of the bivalve molluscs Anodonta californiensis (freshwater) and Mytilus californianus (marine) show non-polar compounds are taken up to a greater extent than polar compounds except where active transport occurs. 2. The uptake of glycine by M. californianus is reduced by pollutants containing complexing functional groups but not by non-polar compounds. 3. The uptake of parathion alters the polyphosphate-inorganic phosphate balance in M. californianus. 4. The uptakes of pollutants parallel their toxicities toward rats.     

Phosphorylation events catalyzed by major cell signaling proteins differ in response to thermal and osmotic stress among native (Mytilus californianus and Mytilus trossulus) and invasive (Mytilus galloprovincialis) species of mussels

Sharp environmental gradients encountered within the intertidal zone have driven the evolution of physiological adaptations that allow its inhabitants to maintain cellular function in the presence of fluctuating abiotic factors. These adaptations are mediated by gene-regulatory networks that, despite their inherent complexity, must remain evolvable and capable of responding to different selection pressures associated with specific ecological niches. Phosphorylation events catalyzed by cell-signaling enzymes represent a parsimonious mechanism to integrate new functional or regulatory properties into these gene-regulatory networks. In this study, proteins phosphorylated on consensus sequences for protein kinases A, B, and C; cyclin-dependent kinases; and mitogen-activated protein kinases, as well as the abundance of phosphorylated stress-activated protein kinase (phospho-SAPK/JNK), were quantified in order to ascertain whether phosphorylation events are divergent among native (Mytilus californianus and Mytilus trossulus) and invasive (Mytilus galloprovincialis) species of mussels that differ in their tolerance toward environmental stress. Abundances of phosphorylated substrate proteins for each of the major signaling proteins that were investigated, as well as the abundance of phospho-SAPK/JNK, differed both within and between species during thermal and osmotic stress. These data suggest that modulating protein function via phosphorylation may be an important mechanism to integrate novel properties into stress-regulatory networks. In turn, differential phosphorylation during environmental stress may contribute to species-specific tolerances toward abiotic stress, interspecies dynamics, and biogeographic patterns in Mytilus congeners.     

Preliminary Observations on the Uptake of Poliovirus by West Coast Shore Crabs

West Coast shore crabs (Pachygrapsus sp. and Hemigrapsus sp.), when in seawater contaminated with poliovirus or allowed to feed on virus-contaminated mussels (Mytilus californianus), were found to accumulate high titers of virus.     

Protein gradients in byssal threads of some marine bivalve molluscs

Many marine bivalve molluscs produce byssal threads for attachment to solid substrata. Small (less than 10 mm) consecutive sections of the byssal threads of Mytilus edulis, M. californianus, Geukensia demissa, Atrina vexillum, and A. rigida were analyzed by amino acid analysis to determine if chemical composition remains constant as a function of location in thread segments. Nonlinear longitudinal protein gradients, probably involving collagen and an elastic protein, were found in the Mytilus species. In these, collagen peaks in the distal third of the thread. In Geukensia and the Atrina species, although the two differed greatly in composition, there is a clear nonvariability in composition of the thread within each species as a function of location in the thread. The adhesive plaque at the tip of the thread of all species examined differs substantially in composition from the remainder of the thread. Protein gradients in the threads of some bivalves may reflect specific adaptations evolved to respond to exposed habitats in high-energy environments.     

Fluorescent heterochromatin staining in primate chromosomes

Recently, in addition to quinacrine staining, fluorochrome techniques have been developed which brilliantly stain other heterochromatic regions. Two of these staining techniques are Distamycin/DAPI (DA/DAPI) and D287/170. We stained the chromosomes of all species of great apes and 14 species of primates (48 individuals) using these three fluorochrome techniques. Only african apes and man show brilliant quinacrine staining while, man and all the great apes show brilliant DA/DAPI staining and only species belonging to the hominoidea (including the siamang) showed bright D287/170 staining. In the lower primates a medium level of DA/DAPI fluorescence was found in some species with large amount of pericentromeric heterochromatin. Brilliant DA/DAPI staining could represent a derived trait linking all great apes and humans, while D287/170 may link all hominoidea. Fluorochrome staining is believed to be correlated with some satellite DNA sequences. However, data available on the chromosome location of satellite DNAs in non-human primates were derived from buoyant density fractions resulting in cross hybridization and now are not considered reliable. Before making any correlation between fluorochrome staining and satellite DNAs in non human primates there is need of data onin situ hybridization with cloned DNA sequences on primate chromosomes. These data would help clarify the evolution and relationship of satellite DNAs and heterochromatin in primates.     

Evolution of ancient satellite DNAs in sturgeon genomes

This study characterizes a repetitive DNA family of sequences in sturgeon, the PstI satellite DNA. We have found a high degree of preservation for these sequences, which are present in all 13 species analyzed, including within the genera Acipenser, Huso, and Scaphirhynchus of the family Acipenseridae. This is one of the most ancient satellite DNAs found to date, because it has been estimated to be more than 100 million years old. Alternatively, to the current view that most satellite DNAs are species-specific or preserved in a few closely related species, the PstI family and other previously characterized sturgeon satellite DNA, the HindIII, represent the most fascinating exceptions to the rapid sequence change usually undergone by satellite DNAs. Here, we compare the evolutionary pattern of these two satellite DNA families, PstI and HindIII, which differ markedly in length, sequence, and nucleotide composition. We have found that, in contrast to the situation in most other living beings, a high degree of preservation, a slow sequence change rate and slowed concerted evolution, appears to be a general rule for sturgeon satellite DNAs. The possible causes for all these features are discussed in the light of the evolutionary specifics found within these ancient organisms.     

Heterochromatin condensation and evolution of unique satellite-DNA families in two parasitic wasp species: Diadromus pulchellus and Eupelmus vuilleti (Hymenoptera)

Large quantities of satellite DNA families (15%-25% of the genome) were found in the DNA of two species of parasitic wasps, Diadromus pulchellus and Eupelmus vuilleti. In both species the satellite DNA was found to consist wholly or largely of a single family unique to that species. Several clones of each family were obtained and sequenced. Palindromes in each consensus sequence suggest the formation in vivo of hairpin structures that may play a role in the mode of heterochromatin condensation in these insects. The ancestral repeating motifs were determined from the consensus sequences. Plausible scenarios are presented for the evolution of the two satellite DNAs. The occurrence of only one family of satellite DNAs in both species may indicate that, in male haploids, such families have shorter persistence times than necessary for the origins of new duplicated sequences.     

Comparative study of satellite sequences and phylogeny of five species from the genus Palorus (Insecta, Coleoptera).

Major satellite sequences are analysed in the three tenebrionid beetles Palorus cerylonoides, P. genalis, and P. ficicola, and compared with the ones from P. ratzeburgii and P. subdepressus reported elsewhere. All of them are A+T rich, pericentromerically located, and with lengths of about 150 bp, either in the form of monomers or formed by more complex repeating units. A preliminary phylogenetic analysis of Palorus species using the 3' end of the mitochondrial Cytochrome Oxidase I gene shows that the five Palorus species have been diverging for a considerable amount of evolutionary time, with the pair P. ratzeburgii and P. genalis being the most closely related. Only these two taxa showed some similarity between their respective high-copy-number satellite sequences, while other satellites are mutually unrelated and might have originated independently. However, all the satellites have in common tertiary structure induced by intrinsic DNA curvature, a characteristic which is conserved within the genus. Palorus major satellites were previously detected in the genomes of congeneric species as low-copy-number clusters (Mestrovi? et al., Mol. Biol. Evol. 15: 1062-1068. 1998). Given the divergences between the analysed species, the substitution rate deduced from high- and low-copy-number repeats is unexpectedly low. The presence of sequence-induced DNA curvature in all Palorus satellites and similar satellite DNAs in the species pair P. ratzeburgii and P. genalis suggest (i) that constraints are at the tertiary structure; and (ii) that the satellite DNA evolutionary turnover can be dependent on the history of the taxa under study, resulting in retention of similar satellites in related taxa.     

Analysis of DNA from related and diverse species of Barley

DNAs of three closely related diploid species Hordeum vulgare, H. agriocrithon and H. spontaneum were compared among themselves and with a group of three species related to each other H. californicum (2x), H. jubatum (4x), and H. arizonicum (6x) having one genome in common.Buoyant densities of the DNAs from these species fall within a narrow range (1.700–1.701 g cm⁻³). Melting temperatures (T_m) of the DNAs are also similar (85.2–86.2°C). None of the DNAs showed any satellite band in neutral Cesium chloride gradients. In silver-cesium sulphate gradients, however, DNAs of all the species formed satellites on both the light and heavy sides of the main. band The diploid series have similar but not identical satellite patterns. The members of the polyploid series showed similar satellite patterns among themselves but distinct from those of the diploid series. In the polyploid group the amount of satellite showed a progressive decrease with the increase in the ploidy.The amount of repeated DNA (reassociating up to Cot 100) in H. vulgare was 69% and in H. arizonicum 65% of the total. The two species differed in their Cot curves. The low Cot fractions of H. arizonicum contained components of low buoyant densities which were absent in the corresponding Cot fractions of H. vulgare DNA.