Characterization of the genome ofOryctes baculovirus,a viral biocide of the insect pestOryctes rhinoceros

Oryctes baculovirus is a viral biocide exploited for the control of the insect pestOryctes rhinoceros. We have recently established a physical map of the genome of the Indian isolate ofOryctes baculovirus (OBV-KI). Here we examine the genomic relatedness between OBV-KI and OBV-PV505, the type isolate (originally from the Philippines), by DNA reassociation kinetics and by the use of restriction endonucleases. On the basis of differences in restriction-enzyme profiles between the two genomes, and previously reported differences in protein profiles and antigenic makeup, we propose the taxonomic status of a variant ofOryctes baculovirus for the Indian isolate     

Distribution of Alu repeats along the human genome: formation of clusters and features of insertion regions

The contextual analysis of nucleotide sequences of 22 Alu repeats arrangement regions in the human genome has been carried out and some of their peculiarities have been revealed. In particular, the occurrence of marked and statistical non-random homology between the repeats and the regions of their integration has been shown. A mechanism of choosing the Alu repeats insertion regions in the genome has been suggested taking into account these peculiarities. Using a sample of the 80 human Alu repeats sequences peculiarities of these repeats location within the genome has been investigated. A tendency to the formation of Alu repeats clusters in various regions of the genome was revealed. A range of possible mechanisms on such Alu clusters emergence is considered. On the basis of the data obtained an "attraction" mechanism, according to which integration of Alu repeats into the definite region of the genome increases the insertion probability of other Alu repeats into the same region, are proposed.     

Comparative fluorescence in situ hybridization mapping of a 431-kb Arabidopsis thaliana bacterial artificial chromosome contig reveals the role of chromosomal duplications in the expansion of the Brassica rapa genome

Comparative genome studies are important contributors to our understanding of genome evolution. Most comparative genome studies in plants have been based on genetic mapping of homologous DNA loci in different genomes. Large-scale comparative physical mapping has been hindered by the lack of efficient and affordable techniques. We report here the adaptation of fluorescence in situ hybridization (FISH) techniques for comparative physical mapping between Arabidopsis thaliana and Brassica rapa. A set of six bacterial artificial chromosomes (BACs) representing a 431-kb contiguous region of chromosome 2 of A. thaliana was mapped on both chromosomes and DNA fibers of B. rapa. This DNA fragment has a single location in the A. thaliana genome, but hybridized to four to six B. rapa chromosomes, indicating multiple duplications in the B. rapa genome. The sizes of the fiber-FISH signals from the same BACs were not longer in B. rapa than those in A. thaliana, suggesting that this genomic region is duplicated but not expanded in the B. rapa genome. The comparative fiber-FISH mapping results support that chromosomal duplications, rather than regional expansion due to accumulation of repetitive sequences in the intergenic regions, played the major role in the evolution of the B. rapa genome.     

The filarial genome project: analysis of the nuclear, mitochondrial and endosymbiont genomes of Brugia malayi

The Filarial Genome Project (FGP) was initiated in 1994 under the auspices of the World Health Organisation. Brugia malayi was chosen as the model organism due to the availability of all life cycle stages for the construction of cDNA libraries. To date, over 20000 cDNA clones have been partially sequenced and submitted to the EST database (dbEST). These ESTs define approximately 7000 new Brugia genes. Analysis of the EST dataset provides useful information on the expression pattern of the most abundantly expressed Brugia genes. Some highly expressed genes have been identified that are expressed in all stages of the parasite's life cycle, while other highly expressed genes appear to be stage-specific. To elucidate the structure of the Brugia genome and to provide a basis for comparison to the Caenorhabditis elegans genome, the FGP is also constructing a physical map of the Brugia chromosomes and is sequencing genomic BAC clones. In addition to the nuclear genome, B. malayi possesses two other genomes: the mitochondrial genome and the genome of a bacterial endosymbiont. Eighty percent of the mitochondrial genome of B. malayi has been sequenced and is being compared to mitochondrial sequences of other nematodes. The bacterial endosymbiont genome found in B. malayi is closely related to the Wolbachia group of rickettsia-like bacteria that infects many insect species. A set of overlapping BAC clones is being assembled to cover the entire bacterial genome. Currently, half of the bacterial genome has been assembled into four contigs. A consortium has been established to sequence the entire genome of the Brugia endosymbiont. The sequence and mapping data provided by the FGP is being utilised by the nematode research community to develop a better understanding of the biology of filarial parasites and to identify new vaccine candidates and drug targets to aid the elimination of human filariasis.     

Investigations on the artificial synthesis of amphidiploids of Brassica tournefortii Gouan with the other elementary species of Brassica. I. Genomic relationships

With the object of studying the genomic relationships of Brassica tournefortii Gouan with the other elementary species of Brassica viz. B. campestris (2n=20, A genome), B. oleracea (2n=18, C genome) and B. nigra (2n=16, B genome), it has been hybridized with them. The percentage of F₁ hybrids formed, their morphology and meiotic behaviour have been described. Based upon crossability relationships and meiotic pairing in the F₁ hybrids, it is inferred that the D genome of B. tournefortii is more closely related to the A genome than to the B and C genomes. It may have been derived from the A genome which likewise shows a strong genetic isolation from B and C. The species has developed a strong genetic barrier in the course of its evolution and shows little crossability, high hybrid sterility and no gene flow with any of the other elementary species. The fact that it has not formed any natural amphidiploids with the elementary species which otherwise are formed in all combinations, is more evidence that it originated more recently than the A genome. It is presumed that B. tournefortii, being more distantly related to B. nigra than to other elementary species, may form stable artificial aphid resistant amphidiploids with the former.     

Journey through the past: 150 million years of plant genome evolution

The genome sequence of the plant model organism Arabidopsis thaliana was presented in December of the year 2000. Since then, the 125 Mb sequence has revealed many of its evolutionary secrets. Through comparative analyses with other plant genomes, we know that the genome of A. thaliana, or better that of its ancestors, has undergone at least three whole genome duplications during the last 120 or so million years. The first duplication seems to have occurred at the dawn of dicot evolution, while the later duplications probably occurred <70 million years ago (Ma). One of those younger genome-wide duplications might be linked to the K-T extinction. Following these duplication events, the ancestral A. thaliana genome was hugely rearranged and gene copies have been massively lost. During the last 10 million years of its evolution, almost half of its genome was lost due to hundreds of thousands of small deletions. Here, we reconstruct plant genome evolution from the early angiosperm ancestor to the current A. thaliana genome, covering about 150 million years of evolution characterized by gene and genome duplications, genome rearrangements and genome reduction.     

Sample sequencing of a Salmonella typhimurium LT2 lambda library: comparison to the Escherichia coli K12 genome

As part of the ongoing sequencing of the complete Salmonella typhimurium LT2 genome, a partly ordered set of 416 lambda clones has been developed, representing over 90% of the genome. The average insert size is 17 kb. Sequences were obtained from both ends of each clone in this set. A total of over 600 kb of sequence has been deposited in the genome survey sequence section of GenBank. This resource of clones is available from the Salmonella Genome Stock Center. A preliminary comparison with the Escherichia coli K12 genome indicates that there are likely to be many hundred insertion deletion events, encompassing more than one gene, that distinguish these genomes. Fully 30% of the S. typhimurium sequences have no close homologs in the GenBank database.     

Epstein-Barr virus DNA recombines via latent origin of replication with the human genome in the lymphoblastoid cell line RGN1.

We show here that in a lymphoblastoid cell line Epstein-Barr virus DNA recombines with the human genome. The genetic exchange involves the oriP region of the virus. A junction between viral and human DNA from this line has been cloned and sequenced. The results indicate that the integration of Epstein-Barr virus DNA involves a region of the human genome which contains internal short repetition. An 800-bp probe has been isolated from the human part of the junction. This probe has been used to show that the human region exists as a duplication in normal cells.     

Coelichelin, a new peptide siderophore encoded by the Streptomyces coelicolor genome: structure prediction from the sequence of its non-ribosomal peptide synthetase

A gene cluster for the non-ribosomal synthesis of a peptide of unknown structure has been identified in the partial genome sequence of Streptomyces coelicolor. Using molecular and computational analyses, the total structure of a tripeptide siderophore synthesized by the non-ribosomal peptide synthetase within the cluster has been deduced from the translated sequence of its encoding gene. This represents a novel method for the structural assignment of natural products from genome sequence data.     

An SfiI restriction map of the Bacillus subtilis 168 genome

A restriction map of 24 SfiI (GGCCN4/NGGCC) restriction fragments has been constructed for the Bacillus subtilis genome. The combined sizes of the fragments indicate a genome size of approx. 4.2 Mb. The SfiI fragments range in size from 7-730 kb. Genetic markers have been located on 19 of the SfiI fragments, and 69 genetic markers have been assigned to the SfiI restriction map.     

Evolution of MIR-repeats in coding regions of the human genome]

A search for new members of the mammalian interspersed repeat (MIR) family has been done over the coding regions of human genome from GenBank-116. Only 254 nucleotide sequences contained MIRs in coding regions, of which 45 MIR copies were unknown before, including 17 that occurred in translated gene regions. The program developed by the authors has been demonstrated to surpass the CENSOR program in the search power. The evolution of the MIR copies located in translated regions of human genome is discussed.     

Evolution of MIR Elements Located in the Coding Regions of Human Genome

A search for new members of the mammalian interspersed repeat (MIR) family has been done over the coding regions of human genome from GenBank-116. Only 254 nucleotide sequences contained MIRs in coding regions, of which 45 MIR copies were unknown before, including 17 that occurred in translated gene regions. The program developed by the authors has been demonstrated to surpass the CENSOR program in the search power. The evolution of the MIR copies located in translated regions of human genome is discussed.     

Molecular-genetic organization of plasmid R89S of the incompatibility group Q

A new IncQ plasmid R89S has been analysed by molecular-genetic methods. A restriction map of this plasmid has been constructed and regions of homology with the plasmid RSF1010 have been identified. A genetic map of the plasmid R89S has been prepared based on the deletion and insertion plasmid derivatives. The phenotypic analysis of the derivatives has identified the location of genes coding for replication, incompatibility, mobilization for genetic transfer and resistance to streptomycin in the genome of R89S.     

Construction of a contig of BAC clones spanning the region of the apple scab avirulence gene AvrVg

The ascomycete Venturia inaequalis, causal pathogen of apple scab, underlies a gene-for-gene relationship with its host plant apple (Malus spp.). 'Golden Delicious', one of the most common cultivated apples in the world, carries the ephemeral resistance gene Vg. Avirulence gene AvrVg, matching resistance gene Vg has recently been mapped on the V. inaequalis genome. In this paper, we present the construction of a BAC library from a V. inaequalis AvrVg isolate. The library is composed of 7680 clones, with an average insert size of 80kb. By hybridization, it has been estimated that the library contains six haploid genome equivalents. Thus the V. inaequalis genome can be predicted to be approximately 100Mb in size. A chromosome walk, starting from the marker VirQ5 co-segregating with AvrVg, has been performed using the BAC library. Twelve BAC clones were identified during four steps of the chromosome walking. The size of the resulting contig is approximately 330kb.     

Study of the fine structure of adeno-associated virus DNA with bacterial restriction endonucleases.

A physical map of the adeno-associated virus type 2 genome has been constructed on the basis of the five fragments produced by the restriction endonucleases HindII + III from Hemophilus influenzae. There are three endo R-HindII cleavage sites and one endo R-HindIII site. Evidence has been obtained to support the existence of two nucleotide sequence permutations in adeno-associated virus DNA, the start points of which have been estimated to be separated by 1% of the genome. The three cleavage fragments produced by endo R-Eco RI have been ordered and oriented with respect to the endo R-HindII + III cleavage map.     

A phylogenetic analysis of indel dynamics in the cotton genus

Genome size evolution is a dynamic process involving counterbalancing mechanisms whose actions vary across lineages and over time. Whereas the primary mechanism of expansion, transposable element (TE) amplification, has been widely documented, the evolutionary dynamics of genome contraction have been less thoroughly explored. To evaluate the relative impact and evolutionary stability of the mechanisms that affect genome size, we conducted a phylogenetic analysis of indel rates for 2 genomic regions in 4 Gossypium genomes: the 2 coresident genomes (A(T) and D(T)) of tetraploid cotton and its model diploid progenitors, Gossypium arboreum (A) and Gossypium raimondii (D). We determined the rates of sequence gain or loss along each branch, partitioned by mechanism, and how these changed during species divergence. In general, there has been a propensity toward growth of the diploid genomes and contraction in the polyploid. Most of the size difference between the diploid species occurred prior to polyploid divergence and was largely attributable to TE amplification in the A/A(T) genome. After separating from the true parents of the polyploid genomes, both diploid genomes experienced slower sequence gain than in the ancestor, due to fewer TE insertions in the A genome and a combination of increased deletions and decreased TE insertions in the D genome. Both genomes of the polyploid displayed increased rates of deletion and decreased rates of insertion, leading to a rate of near stasis in D(T) and overall contraction in A(T) resulting in polyploid genome contraction. As expected, TE insertions contributed significantly to the genome size differences; however, intrastrand homologous recombination, although rare, had the most significant impact on the rate of deletion. Small indel data for the diploids suggest the possibility of a bias as the smaller genomes add less or delete more sequence through small indels than do the larger genomes, whereas data for the polyploid suggest increased sequence turnover in general (both as small deletions and small insertions). Illegitimate recombination, although not demonstrated to be a dominant mechanism of genome size change, was biased in the polyploid toward deletions, which may provide a partial explanation of polyploid genomic downsizing.     

RAPD polymorphisms detected among the flax genotrophs

The occurrence of environmentally induced heritable changes in certain flax varieties has been shown to be accompanied by changes in the genomic DNA. A large difference in nuclear DNA contents has been characterized between the extreme types, termed genotrophs. The genomic variation between a series of genotrophs has been studied by the polymerase chain reaction using random arbitrary oligonucleotide primers. A total of 320 primers were used in the reactions and 253 polymorphic bands observed. The polymorphic bands were derived from all parts of the genome, namely the highly repetitive, middle-repetitive and low-copy-number sequences. They were also shown to be distributed thoughout the genome. In one group of genotrophs, all of which were induced by temperature treatment, there was a clustering of the polymorphisms with a high degree of shared polymorphisms. These results are in agreement with earlier studies showing that a dispersed fraction of the genome is susceptible to variation when environmentally induced heritable changes occur.     

Physical and gene maps of the unicellular cyanobacterium Synechococcus sp. strain PCC6301 genome

A physical map of the unicellular cyanobacterium Synechococcus sp. strain PCC6301 genome has been constructed with restriction endonucleases PmeI, SwaI, and an intron-encoded endonuclease I-CeuI. The estimated size of the genome is 2.7 Mb. On the genome 49 genes or operons have been mapped. Two rRNA operons are separated by 600 kb and transcribed oppositely.     

Mitochondrial genome organization of the maize cytoplasmic male sterile type T

Summary A complete SmaI, XhoI, BamHI restriction map of the maize mitochondrial genome from the T male sterile cytoplasm (cmsT) of maize has been established. The genome exists in the form of a complex multicircular structure as found for the maize normal (N) type (Lonsdale et al. 1984) where the entire sequence complexity with a content of 540 kb can be arranged on a single circular master chromosome. However, most of the repeats (inverted or direct) present in the maize cmsT genome are different from those found in the maize N genome. Recombinational events between these repeats generate a population of circular molecules rather different from the multipartite organization of the N genome. The mitochondrial genes are dispersed throughout the genome. The open reading frame coding for a 13 kDa polypeptide associated with cytoplasmic male sterility (Dewey et al. 1986, 1987) has also been located on the map.     

The loss of CpG dinucleotides from DNA. I. Methylated and non-methylated genome compartments in eukaryotes with different levels of 5-methylcytosine in DNA

The methylation of cytosine residues in CpG significantly increases the frequency of m5CpG----TpG transitions in DNA and CpG dinucleotides are eliminated from the genome (CpG-suppression). In the millions of years of vertebrates evolution about 3 mol% of 5-methylcytosine have disappeared from their genome, i.e., 2-3-fold more than the amount persisting in the DNA of the now extant species. A computer analysis has been carried out of neighboring b.p. frequencies in more than 2500 sequenced genes of different species in the EMBL bank with an overall extension of over 3000 kb. It has been found that CpG methylated sites exhibit a highly irregular distribution pattern in the genome of eucaryotes. The majority of the vertebrate sequences (92%) bears the impress of a significant lack of CpG and an excess of TpG+CpA; therefore they may be referred to the genome methylated compartment. A group of genes has been discovered (about 8%) where CpG must have never been subjected to methylation. In invertebrates, such a nonmethylated compartment makes up 59% of the genome and in eubacteria--85%. A brief list of genes, belonging to the methylated and the non-methylated compartments of the invertebrate and yeast genome, is given. It has been established that the mean value of CpG-suppression in genes is directly proportional to the methylation level of total DNA in different species.