The compositional patterns of the avian genomes and their evolutionary implications

The compositional distributions of large (main-band) DNA fragments from eight birds belonging to eight different orders (including both paleognathous and neognathous species) are very broad and extremely close to each other. These findings, which are paralleled by the compositional similarity of homologous coding sequences and their codon positions, support the idea that birds are a monophyletic group.The compositional distribution of third-codon positions of genes from chicken, the only avian species for which a relatively large number of coding sequences is known, is very broad and bimodal, the minor GC-richer peak reaching 100% GC. The very high compositional heterogeneity of avian genomes is accompanied (as in the case of mammalian genomes) by a very high speciation rate compared to cold-blooded vertebrates which are characterized by genomes that are much less heterogeneous. The higher GC levels attained by avian compared to mammalian genomes might be correlated with the higher body temperature (41–43°C) of birds compared to mammals (37°C).A comparison of GC levels of coding sequences and codon positions from man and chicken revealed very close average GC levels and standard deviations. Homologous coding sequences and codon positions from man and chicken showed a surprisingly high degree of compositional similarity which was, however, higher for GC-poor than for GC-rich sequences. This indicates that GC-poor isochores of warm-blooded vertebrates reflect the composition of the isochores of the genome of the common reptilian ancestor of mammals and birds, which underwent only a small compositional change at the transition from cold- to warm-blooded vertebrates. In contrast, the GC-rich isochores of birds and mammals are the result of large compositional changes at the same evolutionary transition, where were in part different in the two classes of warm-blooded vertebrates.Correspondence to: G. Bernaadi     

Compositional transitions in the nuclear genomes of cold-blooded vertebrates

Summary The compositional properties of DNAs from 122 species of fishes and from 18 other coldblooded vertebrates (amphibians and reptiles) were compared with those from 10 warm-blooded vertebrates (mammals and birds) and found to be substantially different. Indeed, DNAs from cold-blooded vertebrates are characterized by much lower intermolecular compositional heterogeneities and CsCl band asymmetries, by a much wider spectrum of modal buoyant densities in CsCl, by generally lower amounts of satellites, as well as by the fact that in no case do buoyant densities reach the high values found in the GC-richest components of DNAs from warm-blooded vertebrates.In the case of fish genomes, which were more extensively studied, different orders were generally characterized by modal buoyant densities that were different in average values as well as in their ranges. In contrast, different families within any given order were more often characterized by narrow ranges of modal buoyant densities, and no difference in modal buoyant density was found within any single genus (except for the genusAphyosemion, which should be split into several genera).The compositional differences that were found among species belonging to different orders and to different families within the same order are indicative of compositional transitions, which were shown to be essentially due to directional base substitutions. These transitions were found to be independent of geological time. Moreover, the rates of directional base substitutions were found to be very variable and to reach, in some cases, extremely high values, that were even higher than those of silent substitutions in primates. The taxonomic and evolutionary implications of these findings are discussed.     

Compositional compartmentalization and gene composition in the genome of vertebrates

Summary The compositional distribution of coding sequences from five vertebrates (Xenopus, chicken, mouse, rat, and human) is shifted toward higher GC values compared to that of the DNA molecules (in the 35–85-kb size range) isolated from the corresponding genomes. This shift is due to the lower GC levels of intergenic sequences compared to coding sequences. In the cold-blooded vertebrate, the two distributions are similar in that GC-poor genes and GC-poor DNA molecules are largely predominant. In contrast, in the warm-blooded vertebrates, GC-rich genes are largely predominant over GC-poor genes, whereas GC-poor DNA molecules are largely predominant over GC-rich DNA molecules. As a consequence, the genomes of warm-blooded vertebrates show a compositional gradient of gene concentration. The compositional distributions of coding sequences (as well as of DNA molecules) showed remarkable differences between chicken and mammals, and between mouse (or rat) and human. Differences were also detected in the compositional distribution of housekeeping and tissue-specific genes, the former being more abundant among GC-rich genes.     

Mortality of vertebrates on a road crossing the Biebrza Valley (NE Poland)

Mortality of vertebrates was monitored on a local road running across Poland’s Biebrza River Valley during 2 years (August 2005–July 2006). On the basis of distance from the river and surrounding habitats, the road (of total length 2,510 m) was divided into three stretches. The road was monitored on foot by two people every month, over a few consecutive days. A total of 1,892 road kills representing at least 47 species were found. Of these, 90.7% were amphibians, 4.2% mammals, 3.1% birds and 2.0% reptiles. Most (70%) of the amphibians were anurans, with the common toad, common frog and moor frog among them together accounting for 82% of the total. Mortality among amphibians differed between months, most anurans dying in May and August, while a majority of Urodela are lost in October. The peaks in mortality were connected with the migration of adult amphibians in spring and juveniles in summer and autumn. The number of amphibians killed was greatest on the (wettest) stretch adjacent to the river and decreased with distance from it. Mortality among birds was highest in July—probably in association with the dispersal of young individuals. Among recorded mammalian road kills, there was a prevalence of small rodents (mainly voles) and insectivores (mainly shrews). Medium-sized mammals were found only accidentally. Mortality in general was conditioned by the number of anurans killed.     

Detection of DNA base sequence homology between entomopoxviruses isolated from lepidoptera and orthoptera

The extent of DNA base sequence homology between entomopoxviruses (EPVs) from Lepidoptera, Orthoptera, and the vertebrate poxvirus Vaccinia was investigated by DNA-DNA hybridization. α-³²P-Labeled DNA from Amsacta moorei EPV, Melanoplus sanguinipes EPV, and Vaccinia virus strain WR was hybridized with the DNA from six different entomopoxvirus isolates. Based on the thermal denaturation temperature of hybrid DNA molecules, approximately 54% base sequence homology was detected between Amsacta moorei and Euxoa auxiliaris EPV DNAs. Extensive DNA hybridization was detected between α-³²P-labeled Melanoplus sanguinipes EPV DNA and DNA from Arphia conspirsa and Phoetaliotes nebrascensis entomopoxviruses. No base sequence homology was detected between vaccinia DNA and DNA from any of the entomopoxvirus isolates used in this study.     

Ancient repeated sequences in the pea and mung bean genomes and implications for genome evolution

Essentially all of the sequences in the pea (Pisum sativum) genome which reassociate with single copy kinetics at standard (T_m -25°C) criterion follow repetitive kinetics at lower temperatures (about T_m-35°C). Analysis of thermal stability profiles for presumptive single copy duplexes show that they contain substantial mismatch even when formed at standard criterion. Thus most of the sequences in the pea genome which are conventionally defined as single copy are actually fossil repeats — that is, they are members of extensively diverged (mutuated) and thus presumably ancient families of repeated sequences. Coding sequences as represented by a cDNA probe prepared from poly-somal poly(A) + mRNA reassociate with single copy kinetics regardless of criterion and do not form mismatched duplexes. The coding regions thus appear to be composed of true single copy sequences but they cannot represent more than a few percent of the pea genome. Ancient diverged repeats are present, but not a prominent feature of the smaller mung bean (Vigna radiata) genome. An extension of a simple evolutionary model is proposed in which these and other differences in genome organization are considered to reflect different rates of sequence amplification or genome turnover during evolution. The model accounts for some of the differences between typical plant and animal genomes.     

Discrimination of the closely related A and B genomes in AABB tetraploid species of Avena

Fluorescent in situ (FISH) and Southern hybridization procedures were used to investigate the chromosomal distribution and genomic organization of the satellite DNA sequence As120a (specific to the A-genome chromosomes of hexaploid oats) in two tetraploid species, Avena barbata and Avena vaviloviana. These species have AB genomes. In situ hybridization of pAs120a to tetraploid oat species revealed elements of this repeated family to be distributed over both arms of 14 of the 28 chromosomes of these species. Genomes A and B were subsequently distinguished, indicating an allopolyploid origin for A. barbata. This was confirmed by assigning the satellited chromosomes to individual genomes, using the satellite itself and two ribosomal probes in simultaneous and sequential in situ hybridization analyses. Differences between A. barbata and A. vaviloviana genomes were also revealed by both FISH and Southern techniques using pAs120a probes. Whereas two B-genome chromosome pairs were found to be involved in intergenomic translocations in A. vaviloviana, FISH detected no intergenomic rearrangements in A. barbata. When using pAs120a as a probe, Southern hybridization also revealed differences in the hybridization patterns of the two genomes. A 1300-bp EcoRV fragment was present in A. barbata but absent in A. vaviloviana. This fragment was also detected in Southern analyses of A-genome diploid and hexaploid oat species. Received: 27 November 2000 / Accepted: 28 February 2001     

Tempo and mode of mitochondrial DNA evolution in vertebrates at the amino acid sequence level: Rapid evolution in warm-blooded vertebrates

Summary By using complete sequence data of mitochondrial DNAs, three Markov models (Day-hoff, Proportional, and Poisson models) for amino acid substitutions during evolution were applied in maximum likelihood analyses of mitochondrially encoded proteins to estimate a phylogenetic tree depicting human, cow, whale, and murids (mouse and rat), with chicken, frog, and carp as outgroups. A cow/whale clade was confirmed with a more than 99.8% confidence level by any of the three models, but the branching order among human, murids, and the cow/whale clade remained uncertain. It turned out that the Dayhoff model is by far the most appropriate model among the alternatives in approximating the amino acid substitutions of mitochondrially encoded proteins, which is consistent with a previous analysis of a more limited data set. It was shown that the substitution rate of mitochondrially encoded proteins has increased in the order of fishes, amphibians, birds, and mammals and that the rate in mammals is at least six times, probably an order of magnitude, higher than that in fishes. The higher evolutionary rate in birds and mammals than in amphibians and fishes was attributed to relaxation of selective constraints operating on proteins in warm-blooded vertebrates and to high mutation rate of bird and mammalian mitochondrial DNAs.Offprint requests to: M. Hasegawa     

The protein sequence homology of gamma-crystallins among major vertebrate classes and their DNA sequence homology to heat-shock protein genes

A systematic characterization of lens crystallins from five major classes of vertebrates was carried out by exclusion gel filtration, cation-exchange chromatography and N-terminal sequence determination. All crystallin fractions except that of -crystallin were found to be N-terminally blocked. -Crystallin is present in major classes of vertebrates except the bird, showing none, or decreased amounts, of this protein in chicken and duck lenses, respectively. N-Terminal sequence analysis of the purified -crystallin polypeptides showed extensive homology between different classes of vertebrates, supporting the close relatedness of this family of crystallin even from the evolutionarily distant species. Comparison of nucleotide sequences and their predicted amino acid sequences between -crystallins of carp and rat lenses and heat-shock proteins demonstrated partial sequence homology of the encoded polypeptides and striking homology at the gene level. The unexpected strong homology of complementary DNA (cDNA) lies in the regions coding for 40 N-terminal residues of carp -II, rat 2-1, and the middle segments of 23,000- and 70,000-M _r heat-shock proteins. The optimal alignment of DNA sequences along these two segments shows about 50% homology. The percentage of protein sequence identity for the corresponding aligned segments is only 20%. The weak sequence homology at the protein level is also found between the invertebrate squid crystallin and rat -crystallin polypeptides. These results pointed to the possibility of unifying three major classes of vertebrate crystallins into one // superfamily and corroborated the previous supposition that the existing crystallins in the animal kingdom are probably mutually interrelated, sharing a common ancestry.     

Spatial and temporal expression of the two sucrose synthase genes in maize: immunohistological evidence

Summary The DNAs of two diploid species of Gossypium, G. herbaceum var. africanum (A₁ genome) and G. raimondii (D₅ genome), and the allotetraploid species, G. hirsutum (A_h and D_h genomes), were characterized by kinetic analyses of single copy and repetitive sequences. Estimated haploid genome sizes of A₁ and D₅ were 1.04 pg and 0.68 pg, respectively, in approximate agreement with cytological observations that A genome chromosomes are about twice the size of D genome chromosomes. This differences in genome size was accounted for entirely by differences in the major repetitive fraction (0.56 pg versus 0.20 pg), as single copy fractions of the two genomes were essentially identical (0.41 pg for A₁ and 0.43 pg for D₅). Kinetic analyses and thermal denaturation measurements of single copy duplexes from reciprocal intergenomic hybridizations showed considerable sequence similarity between A₁ and D₅ genomes (77% duplex formation with an average thermal depression of 6 °C). Moreover, little sequence divergence was detectable between diploid single copy sequences and their corresponding genomes in the allotetraploid, consistent with previous chromosome pairing observations in interspecific F₁ hybrids.Journal paper No. 4461 of the Arizona Agricultural Experiment Station     

Prediction of atomic structure from sequence for double helical DNA oligomers

DNA can adopt different conformations depending on the base sequence, solvent, electrolyte composition and concentration, pH, temperature, and interaction with proteins. Here we present a model for calculating the three-dimensional atomic structure of double-stranded DNA oligomers. A theoretical energy function is used for calculating the interactions within the base steps and an empirical backbone function is used to restrict the conformational space accessible to the bases and to account for the conformational coupling of neighboring steps in a sequence. Conformational searching on large structures or a large number of structures is possible, because each base step can be described by just two primary degrees of freedom (slide and shift). A genetic algorithm is used to search for low-energy structures in slide-shift space, and this allows very rapid optimization of DNA oligomers. The other base step parameters have been previously optimized for all possible slide-shift sequence combinations, and a heuristic algorithm is used to add the atomic details of the backbone conformation in the final step of the calculation. The structures obtained by this method are very similar to the corresponding X-ray crystal structures observed experimentally. The average RMSD is 2.24 Angstroms for a set of 20 oligomer structures. For 15 of these sequences, the X-ray crystal structure is the global energy minimum. The other 5 are bistable sequences that have B-form global energy minima but crystallize as A-DNA.     

Genome analysis: A new approach for visualization of sequence organization in genomes

In this article we describe and demonstrate the versatility of a computer program, GENOME MAPPING, that uses interactive graphics and runs on an IRIS workstation. The program helps to visualize as well as analyse global and local patterns of genomic DNA sequences. It was developed keeping in mind the requirements of the human genome sequencing programme, which requires rapid analysis of the data. Using GENOME MAPPING one can discern signature patterns of different kinds of sequences and analyse such patterns for repetitive as well as rare sequence strings. Further, one can visualize the extent of global homology between different genomic sequences. An application of our method to the published yeast mitochondrial genome data shows similar sequence organizations in the entire sequence and in smaller subsequences     

Calculation of sequence divergence from the thermal stability of DNA heteroduplexes

Summary Measurements are reported of the thermal stability of DNA heteroduplexes between clones of the eta-globin pseudogene from a variety of primates. The known sequences of this 7.1-kb region differ from each over a range from 1.6% for human versus chimp to nearly 12% for human versus spider monkey. Thermal stability was determined by standard hydroxyapatite thermal elution, and the results show a precisely linear decrease in thermal stability with divergence. The slope of the regression line is 1.18% sequence divergence per degree centigrade reduction in thermal stability.     

Marine microbial diversity studied via 16S rRNA sequences: cloning results from coastal waters and counting of native archaea with fluorescent single cell probes

New molecular approaches relying on 16S rRNA sequences allow qualitative and quantitative analysis of marine microbial diversity. Here we report on (1) continued development of lists of taxa present in marine environments, in temperate coastal waters, and (2) new fluorescent in situ hybridization (FISH) approaches to quantify taxonomic compositions, with an initial focus on archaea. Our cloning results come from Long Island Sound on the Atlantic coast (February and August), and Malibu (April) and offshore Monterey Bay (September), California. The clones were dominated (39 of 45 total clones) by proteobacteria, with the subdivision (33 clones), and the SAR11 cluster (17) in particular, being quite abundant. There were also clones from the (2) and (4) subdivisions, the cyanobacteria (4, from Monterey Bay only) and the Cytophaga group (2). Some clones were very similar to those previously reported from open ocean or deep sea environments, but others were not close relatives of any of those previously reported. The FISH results used doubly-labeled probes that were universal, bacterial, and archaeal (single and multiple), in combination with chloramphenicol treatment and probe detection by intensified video microscopy. Universal probes detected ca. 75–95% of total DAPI counts. Of 2 depth profiles from mesotrophic-oligotrophic California waters, a September one, to 300 m, indicated a low but detectable presence of archaea (about 10% above control values) as measured with single probes. A second profile in May with 4 archaeal probes showed <5% at 100 m depth, but the percentage relative to total DAPI counts increased to about 40% at 600 m depth. Samples from the French Mediterranean coast showed few detectable archaea (analyzed with single probes) in surface waters of Villefranche-sur-Mer Bay, but about 60% archaea at 200 m depth outside the bay. These results point in general to the suitability of this single cell FISH method to quantify taxonomic composition of marine samples, and the specific results indicate the high abundance of archaea in at least some midwater locations.     

Phylogenetic relationships among annual and perennial species of the genus <Emphasis Type="Italic">Cicer</Emphasis> as inferred from ITS sequences of nuclear ribosomal DNA

The cladistic analysis of the DNA sequences of the internal transcribed spacers of ribosomal cistrons (ITS1 and ITS2) for 20 species of Cicer L. (among which all the annuals), shows that various sections of the genus are not monophyletic. Annual species do not form a clade: C. arietinum, in fact, is closely related to both C. echinospermum and C. reticulatum, whereas C. bijugum, C. judaicum, and C. pinnatifidum form a separate clade. The annual C. cuneatum is sister group to the perennial C. canariense and both are archaic species within the genus. C. yamashitae is, on the contrary, the only annual species belonging to a group of perennials, within which close relationships are evident between C. graecum and C. montbretii as well as among a group of mainly Asian species.     

A sequence from drosophila DNA cross-hybridizing with a mouse class I H-2 Gene: absence of relevant nucleic acid or amino acid sequence homology

Following serological data (1) showing cross-reactivity of drosophila surface antigens with anti-H-2 and mouse beta 2-microglobulin (beta 2-m) antisera, we have looked for homologous sequences in the drosophila genome by low stringency hybridization with mouse H-2 and beta 2-m probes. A 240 bp drosophila DNA segment cross-hybridizing with a H-2 probe, was isolated and sequenced. No homology at the nucleotide or amino acid levels was found with the mouse probe which was used, except for a perfectly matching 16-mer containing 11 G-C, which might be responsible for the cross-hybridization. Therefore, our present data do not support the existence of class I H-2 and/or beta 2-m related gene sequences in the drosophila genome.     

Isolation of 24 novel cDNA fragments from microdis—sected human chromosome band

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Lessons from the genomes of bifidobacteria

The gut microbiota is a complex ecosystem composed of hundreds of different bacterial species that altogether play an important role in the physiology of their host. In the past few years the complete genome sequence of a number of bacterial strains isolated from the human gastrointestinal tract has been established including that of Bifidobacterium longum NCC2705 isolated from the feces of a healthy infant. Bifidobacteria are among the first species to colonise the human gastrointestinal tract and as such are believed to play an important role in gut homeostasis and normal development. The genome sequence of NCC2705 has revealed a number of features that suggest how this bacterium has adapted to its environment and that could help understanding how it interacts with its host. Here, we review general features of bifidobacteria and illustrate how genome-based approaches can help us better understand the biology of these organisms.