Conservation of genome organization in two multicapsid nuclear polyhedrosis viruses.

The genome of the multicapsid nuclear polyhedrosis virus of Orgyia pseudotsugata was mapped by examining overlapping HindIII fragments from cosmid clones which had been constructed from partial HindIII digests of viral DNA. Five OpMNPV cosmid clones containing fragments encompassing the entire OpMNPV genome were hydridized to blots of DNA from the multicapsid nuclear polyhedrosis virus of Autographa californica. The hybridization pattern indicated that the genomes of these viruses are similarly organized.     

On the tetraploid origin of the maize genome

Data from cytological and genetic mapping studies suggest that maize arose as a tetraploid. Two previous studies investigating the most likely mode of maize origin arrived at different conclusions. Gaut and Doebley [7] proposed a segmental allotetraploid origin of the maize genome and estimated that the two maize progenitors diverged at 20.5 million years ago (mya). In a similar study, using larger data set, Brendel and colleagues (quoted in [8]) suggested a single genome duplication at 16 mya. One of the key components of such analyses is to examine sequence divergence among strictly orthologous genes. In order to identify such genes, Lai and colleagues [10] sequenced five duplicated chromosomal regions from the maize genome and the orthologous counterparts from the sorghum genome. They also identified the orthologous regions in rice. Using positional information of genetic components, they identified 11 orthologous genes across the two duplicated regions of maize, and the sorghum and rice regions. Swigonova et al. [12] analyzed the 11 orthologues, and showed that all five maize chromosomal regions duplicated at the same time, supporting a tetraploid origin of maize, and that the two maize progenitors diverged from each other at about the same time as each of them diverged from sorghum, about 11.9 mya.     

On the problem of genome redundancy in viruses and prokaryotes

A specific index of nucleotide sequence redundancy, the specific restriction length of a finite frequency dictionary, was determined for a complete set of genes in some viral genomes and a genome of a bacterium, Bacillus subtilis. The distribution of the gene number over the specific restriction length was shown to be bimodal for viral genomes and unimodal for the Bac. subtilis genome. These results agree with earlier data.     

An evolutionary model for the origin of non-randomness, long-range order and fractality in the genome.

We present a model for genome evolution, comprising biologically plausible events such as transpositions inside the genome and insertions of exogenous sequences. This model attempts to formulate a minimal proposition accounting for key statistical properties of genomes, avoiding, as far as possible, unsupportable hypotheses for the remote evolutionary past. The statistical properties that are observed in genomic sequences and are reproduced by the proposed model are: (i) deviations from randomness at different length scales, measured by suitable algorithms, (ii) a special form of size distribution (power law distribution) characterising different levels of genome organisation in the non-coding, and (iii) extensive resemblance in the alternation of coding and non-coding regions at several length scales (self-similarity) in long genomic sequences of higher eukaryotes.     

Sequence and gene organization of the chicken mitochondrial genome. A novel gene order in higher vertebrates

The 16,775 base-pair mitochondrial genome of the white Leghorn chicken has been cloned and sequenced. The avian genome encodes the same set of genes (13 proteins, 2 rRNAs and 22 tRNAs) as do other vertebrate mitochondrial DNAs and is organized in a very similar economical fashion. There are very few intergenic nucleotides and several instances of overlaps between protein or tRNA genes. The protein genes are highly similar to their mammalian and amphibian counterparts and are translated according to the same variant genetic code. Despite these highly conserved features, the chicken mitochondrial genome displays two distinctive characteristics. First, it exhibits a novel gene order, the contiguous tRNA(Glu) and ND6 genes are located immediately adjacent to the displacement loop region of the molecule, just ahead of the contiguous tRNA(Pro), tRNA(Thr) and cytochrome b genes, which border the displacement loop region in other vertebrate mitochondrial genomes. This unusual gene order is conserved among the galliform birds. Second, a light-strand replication origin, equivalent to the conserved sequence found between the tRNA(Cys) and tRNA(Asn) genes in all vertebrate mitochondrial genomes sequenced thus far, is absent in the chicken genome. These observations indicate that galliform mitochondrial genomes departed from their mammalian and amphibian counterparts during the course of evolution of vertebrate species. These unexpected characteristics represent useful markers for investigating phylogenetic relationships at a higher taxonomic level.     

Sequence organization of the human genome

The organization of three sequence classes—single copy, repetitive, and inverted repeated sequences—within the human genome has been studied by renaturation techniques, hydroxylapatite binding methods, and DNA hyperchromism. Repetitive sequence classes are distributed throughout 80% or more of the genome. Slightly more than half of the genome consists of short single copy sequences, with a length of about 2 kb interspersed with repetitive sequences. The average length of the repetitive sequences is also small and approximates the length of these sequences found in other organisms. The sequence organization of the human genome therefore resembles the sequence organization found in Xenopus and sea urchin. The inverted repeats are essentially randomly positioned with respect to both sequence class and sequence arrangement, so that all three sequence classes are found to be mutually interspersed in a portion of the genome.     

Molecular genome organization in ciliates

The review summarizes modern views on to the structure and differentiation of the nuclear apparatus in ciliates. The genetic system of ciliates (type Ciliophora) includes two types of nuclei: germinal micronucleus (MIC) and somatic macronucleus (MAC). The MAC development is associated with the rearrangement of the MIC genome, which includes chromosome fragmentation and chromatin diminution. The loss of DNA constitutes from 10–15% (Tetrahymena termophila) to 95–98% of the genome in spirotrichs (Stylonychia, Oxytricha, and Euplotes). Analysis of molecular mechanisms underlying nuclear dualism in ciliates promoted radical revision of the concept on the interactions and roles of MAC and MIC. The micronucleus, as an inactive element, is an ideal field for the invasion and further expansion of mobile genetic elements. Chromatin diminution plays the purifying role, restoring the native genome structure. The process of recognition of “genetic garbage” to be eliminated has many features in common with the siRNA-mediated heterochromatization. The presence of this mechanism in very early radiated eukaryotic lineages (Opistokonta and Chromalveolata), indicates that it arose at the earliest stages of the eukaryotic evolution, probably, as a mechanism promoting genome integrity and stability.     

Rice genome organization: the centromere and genome interactions

Over the last decade, many varied resources have become available for genome studies in rice. These resources include over 4000 DNA markers, several bacterial artificial chromosome (BAC) libraries, P-1 derived artificial chromosome (PAC) libraries and yeast artificial chromosome (YAC) libraries (genomic DNA clones, filters and end-sequences), retrotransposon tagged lines, and many chemical and irradiated mutant lines. Based on these, high-density genetic maps, cereal comparative maps, YAC and BAC physical maps, and quantitative trait loci (QTL) maps have been constructed, and 93 % of the genome has also been sequenced. These data have revealed key features of the genetic and physical structure of the rice genome and of the evolution of cereal chromosomes. This Botanical Briefing examines aspects of how the rice genome is organized structurally, functionally and evolutionarily. Emphasis is placed on the rice centromere, which is composed of long arrays of centromere-specific repetitive sequences. Differences and similarities amongst various cereal centromeres are detailed. These indicate essential features of centromere function. Another view of various kinds of interactive relationships within and between genomes, which could play crucial roles in genome organization and evolution, is also introduced. Constructed genetic and physical maps indicate duplication of chromosomal segments and spatial association between specific chromosome regions. A genome-wide survey of interactive genetic loci has identified various reproductive barriers that may drive speciation of the rice genome. The significance of these findings in genome organization and evolution is discussed.     

Sequence organization of the soybean genome

The total complexity of one constituent soybean (Glycine max) genome is estimated to be 1.29 . 10(9) nucleotide pairs, as determined by analysis of the reassociation kinetics of sheared (0.47 kilobase) DNA. Single copy sequences are estimated to represent from 53 to 64% of the genome by analysis of hydroxyapatite binding of repetitive DNA as a function of fragment length. From 65 to 70% of these single copy sequences have a short period interspersion with 1.11--1.36 kilobase lengths alternating with 0.3--0.4 kilobase repetitive sequence elements. The repetitive sequences of soybean DNA are interspersed both among themselves and among single copy regions of the genome.     

Genome analysis of Amphioxus and speculation as to the origin of contrasting vertebrate genome organization patterns.

1. The genome of Amphioxus was investigated by DNA reassociation techniques for the amount of repetitive and non-repetitive sequences and its pattern of organization. 2. A comparison of the amount of non-repetitive DNA between Amphioxus and the tunicate Ciona intestinalis does not support the hypothesis that the Cephalochordates have arisen from the Tunicates by polyploidy. 3. In the Amphioxus genome repetitive and non-repetitive elements are predominantly arranged in a short period interspersion pattern. Conclusions are presented as to the evolution of contrasting genome organization patterns among vertebrates.     

Structural organization of DNA in chlorella viruses

Chlorella viruses have icosahedral capsids with an internal membrane enclosing their large dsDNA genomes and associated proteins. Their genomes are packaged in the particles with a predicted DNA density of ca. 0.2 bp nm(-3). Occasionally infection of an algal cell by an individual particle fails and the viral DNA is dynamically ejected from the capsid. This shows that the release of the DNA generates a force, which can aid in the transfer of the genome into the host in a successful infection. Imaging of ejected viral DNA indicates that it is intimately associated with proteins in a periodic fashion. The bulk of the protein particles detected by atomic force microscopy have a size of ～60 kDa and two proteins (A278L and A282L) of about this size are among 6 basic putative DNA binding proteins found in a proteomic analysis of DNA binding proteins packaged in the virion. A combination of fluorescence images of ejected DNA and a bioinformatics analysis of the DNA reveal periodic patterns in the viral DNA. The periodic distribution of GC rich regions in the genome provides potential binding sites for basic proteins. This DNA/protein aggregation could be responsible for the periodic concentration of fluorescently labeled DNA observed in ejected viral DNA. Collectively the data indicate that the large chlorella viruses have a DNA packaging strategy that differs from bacteriophages; it involves proteins and share similarities to that of chromatin structure in eukaryotes.     

Structural organization of the genome of paramyxoviruses

The review summarizes the recent papers on the studies of primary structure of genome of a number of paramyxoviruses from the three genera of a family. The cited data demonstrate that despite the common principles of the genetic material arrangement shared by paramyxoviruses, they are variable in the genome, the primary structure of intragenic region, as well as the strategy of coding for some proteins. The data on the arrangement of the genetic material is discussed as useful as a criterion for classification of single stranded viruses with unsegmented genome.