Showing papers on "Genome published in 1992"

The Genome of Drosophila Melanogaster

Abstract: Genes. Chromosomes: Deficiencies. Duplications. Inversions. Rings. Translocations. Transpositions. External Anatomy (figure). Normal Chromosome Complement. Special Chromosomes: Balancers. Compound Chromosomes. X-Y Combinations. Y Derivatives. Autosynaptic Chromosomes. Transposable Elements. Departures from Diploidy. Satellite Sequences. Nonchromosomal Inheritance. Cytogenetic Map.

High density molecular linkage maps of the tomato and potato genomes.

Abstract: High density molecular linkage maps, comprised of more than 1000 markers with an average spacing between markers of approximately 1.2 cM (ca. 900 kb), have been constructed for the tomato and potato genomes. As the two maps are based on a common set of probes, it was possible to determine, with a high degree of precision, the breakpoints corresponding to 5 chromosomal inversions that differentiate the tomato and potato genomes. All of the inversions appear to have resulted from single breakpoints at or near the centromeres of the affected chromosomes, the result being the inversion of entire chromosome arms. While the crossing over rate among chromosomes appears to be uniformly distributed with respect to chromosome size, there is tremendous heterogeneity of crossing over within chromosomes. Regions of the map corresponding to centromeres and centromeric heterochromatin, and in some instances telomeres, experience up to 10-fold less recombination than other areas of the genome. Overall, 28% of the mapped loci reside in areas of putatively suppressed recombination. This includes loci corresponding to both random, single copy genomic clones and transcribed genes (detected with cDNA probes). The extreme heterogeneity of crossing over within chromosomes has both practical and evolutionary implications. Currently tomato and potato are among the most thoroughly mapped eukaryotic species and the availability of high density molecular linkage maps should facilitate chromosome walking, quantitative trait mapping, marker-assisted breeding and evolutionary studies in these two important and well studied crop species.

Animal mitochondrial DNA: structure and evolution.

Abstract: Publisher Summary This chapter describes structural features and evolution of metazoan mitochondrial DNA (mtDNA) molecules. Throughout the evolution of metazoa, gene content of mitochondria-genomes is highly conserved, as has the close packing of genes. Most of the occasional sequence expansions that have occurred, by way of either repeated or noncoding unique sequences, are found in the control or putative control region, rather than being dispersed between genes. Of the 13 open reading frames recognized in the human mtDNA molecules, four (COI, COII, COIII, and Cyt b) are originally identified in regard to the proteins they encode, from similarities of their predicted amino acid sequences to known amino acid sequences of bovine proteins, and predicted amino acid sequences of yeast mt-protein genes. Among mtDNAs of vertebrates and higher invertebrates, there are genes that overlap. Some overlaps are among the 3′ ends of two genes that are encoded in opposite strands of the molecule. The extent of size reduction within metazoan mitochondrial-transfer RNA (mt-tRNA) gene sets strongly correlates with the degree to which the more variable secondary structure element-forming regions of mt-rRNA genes are lost.

Whole genome amplification from a single cell: implications for genetic analysis

Abstract: We have developed an in vitro method for amplifying a large fraction of the DNA sequences present in a single haploid cell by repeated primer extensions using a mixture of 15-base random oligonucleotides. We studied 12 genetic loci and estimate that the probability of amplifying any sequence in the genome to a minimum of 30 copies is not less than 0.78 (95% confidence). Whole genome amplification beginning with a single cell, or other samples with very small amounts of DNA, has significant implications for multipoint mapping by sperm or oocyte typing and possibly for genetic disease diagnosis, forensics, and the analysis of ancient DNA samples.

Hepatitis C virus (HCV) circulates as a population of different but closely related genomes: quasispecies nature of HCV genome distribution.

Abstract: Sequencing of multiple recombinant clones generated from polymerase chain reaction-amplified products demonstrated that the degree of heterogeneity of two well-conserved regions of the hepatitis C virus (HCV) genome within individual plasma samples from a single patient was consistent with a quasispecies structure of HCV genomic RNA. About half of circulating RNA molecules were identical, while the remaining consisted of a spectrum of mutants differing from each other in one to four nucleotides. Mutant sequence diversity ranged from silent mutations to appearance of in-frame stop codons and included both conservative and nonconservative amino acid substitutions. From the relative proportion of essentially defective sequences, we estimated that most circulating particles should contain defective genomes. These observations might have important implications in the physiopathology of HCV infection and underline the need for a population-based approach when one is analyzing HCV genomes.

The chloroplast genome.

Abstract: Chloroplasts are intracellular organelles in plants which contain the entire machinery necessary for the process of photosynthesis. They also participate in the biosynthesis of amino acids, nucleotides, lipids and starch. Mendel’s law was rediscovered at the beginning of this century, and in 1909 Baur and Correns separately published the first reports of non-Mendelian inheritance based on studies of variegation in higher plants. Some of the green-and-white variegated leaves were shown to be caused by factors inherited in a non-Mendelian manner. Further analysis of variegation in higher plants revealed that the genetic determinants for these characters were associated with chloroplasts. However, the difficulty of obtaining specific chloroplast mutations has limited the study of non-Mendelian genetics in higher plants. Our knowledge of extranuclear genetics came primarily from studies using the unicellular alga Chlamydomonas.

Function and evolution of a minimal plastid genome from a nonphotosynthetic parasitic plant

Abstract: Complete nucleotide sequencing shows that the plastid genome of Epifagus virginiana, a nonphotosynthetic parasitic flowering plant, lacks all genes for photosynthesis and chlororespiration found in chloroplast genomes of green plants. The 70,028-base-pair genome contains only 42 genes, at least 38 of which specify components of the gene-expression apparatus of the plastid. Moreover, all chloroplast-encoded RNA polymerase genes and many tRNA and ribosomal protein genes have been lost. Since the genome is functional, nuclear gene products must compensate for some gene losses by means of previously unsuspected import mechanisms that may operate in all plastids. At least one of the four unassigned protein genes in Epifagus plastid DNA must have a nongenetic and nonbioenergetic function and, thereby, serve as the reason for the maintenance of an active genome. Many small insertions in the Epifagus plastid genome create tandem duplications and presumably arose by slippage mispairing during DNA replication. The extensive reduction in genome size in Epifagus reflects an intensification of the same processes of length mutation that govern the amount of noncoding DNA in chloroplast genomes. Remarkably, this massive pruning occurred with a virtual absence of gene order change.

Gene targeting in animal cells using isogenic DNA constructs

Abstract: The present invention provides novel methods for modifying the genome of an animal cell which typically comprise the steps of: constructing a DNA molecule in which desired sequence modifications are contained in a segment of DNA (a ''targeting DNA'') that is substantially isogenic with a DNA in the cell genome (a ''target DNA''); introducing the targeting DNA construct into the cell (e.g., by microinjection, electroporation, transfection, or calcium phosphate precipitation); and selecting cells in which the desired sequence modifications have been introduced into the genome via homologous recombination.

The C. elegans genome sequencing project: a beginning.

Abstract: The long-term goal of this project is the elucidation of the complete sequence of the Caenorhabditis elegans genome. During the first year methods have been developed and a strategy implemented that is amenable to large-scale sequencing. The three cosmids sequenced in this initial phase are surprisingly rich in genes, many of which have mammalian homologues.

Primary structure of the herpesvirus saimiri genome.

Abstract: This report describes the complete nucleotide sequence of the genome of herpesvirus saimiri, the prototype of gammaherpesvirus subgroup 2 (rhadinoviruses). The unique low-G + C-content DNA region has 112,930 bp with an average base composition of 34.5% G + C and is flanked by about 35 noncoding high-G + C-content DNA repeats of 1,444 bp (70.8% G + C) in tandem orientation. We identified 76 major open reading frames and a set of seven U-RNA genes for a total of 83 potential genes. The genes are closely arranged, with only a few regions of sizable noncoding sequences. For 60 of the predicted proteins, homologous sequences are found in other herpesviruses. Genes conserved between herpesvirus saimiri and Epstein-Barr virus (gammaherpesvirus subgroup 1) show that their genomes are generally collinear, although conserved gene blocks are separated by unique genes that appear to determine the particular phenotype of these viruses. Several deduced protein sequences of herpesvirus saimiri without counterparts in most of the other sequenced herpesviruses exhibited significant homology with cellular proteins of known function. These include thymidylate synthase, dihydrofolate reductase, complement control proteins, the cell surface antigen CD59, cyclins, and G protein-coupled receptors. Searching for functional protein motifs revealed that the virus may encode a cytosine-specific methylase and a tyrosine-specific protein kinase. Several herpesvirus saimiri genes are potential candidates to cooperate with the gene for saimiri transformation-associated protein of subgroup A (STP-A) in T-lymphocyte growth stimulation.

Global and local genome mapping in Arabidopsis thaliana by using recombinant inbred lines and random amplified polymorphic DNAs

Abstract: A population of Arabidopsis thaliana recombinant inbred lines was constructed and used to develop a high-density genetic linkage map containing 252 random amplified polymorphic DNA markers and 60 previously mapped restriction fragment length polymorphisms. Linkage groups were correlated to the classical genetic map by inclusion of nine phenotypic markers in the mapping cross. We also applied a technique for local mapping that allows targeting of markers to a selected genome region by pooling DNA from recombinant inbred lines based on their genotype. We conclude that random amplified polymorphic DNAs, used in conjunction with a recombinant inbred population, can facilitate the genetic and physical characterization of the Arabidopsis genome and that this method is generally applicable to other organisms for which appropriate populations either are available or can be developed.

Gene order comparisons for phylogenetic inference: evolution of the mitochondrial genome.

Abstract: Detailed knowledge of gene maps or even complete nucleotide sequences for small genomes leads to the feasibility of evolutionary inference based on the macrostructure of entire genomes, rather than on the traditional comparison of homologous versions of a single gene in different organisms. The mathematical modeling of evolution at the genomic level, however, and the associated inferential apparatus are qualitatively different from the usual sequence comparison theory developed to study evolution at the level of individual gene sequences. We describe the construction of a database of 16 mitochondrial gene orders from fungi and other eukaryotes by using complete or nearly complete genomic sequences; propose a measure of gene order rearrangement based on the minimal set of chromosomal inversions, transpositions, insertions, and deletions necessary to convert the order in one genome to that of the other; report on algorithm design and the development of the DERANGE software for the calculation of this measure; and present the results of analyzing the mitochondrial data with the aid of this tool.

A highly conserved repeated DNA element located in the chromosome of Streptococcus pneumoniae.

Abstract: We report the discovery of a group of highly conserved DNA sequences located, in those cases studied, within intergenic regions of the chromosome of the Gram positive Streptococcus pneumoniae. The S. pneumoniae genome contains about 25 of these elements called BOX. From 5' to 3', BOX elements are composed of three subunits (boxA, boxB, and boxC) which are 59, 45 and 50 nucleotides long, respectively. BOX elements containing one, two and four copies of boxB have been observed; boxB alone was also detected in one instance. These elements are unrelated to the two most thoroughly documented families of repetitive DNA sequences present in the genomes of enterobacteria. BOX sequences have the potential to form stable stem-loop structures and one of these, at least, is transcribed. Most of these elements are located in the immediate vicinity of genes whose product has been implicated at some stage in the process of genetic transformation or in virulence of S. pneumoniae. This location raises the intriguing possibility that BOX sequences are regulatory elements shared by several coordinately controlled genes, including competence-specific and virulence-related genes.

Effects of ionizing radiation on a plant genome: analysis of two Arabidopsis transparent testa mutations.

Abstract: Ionizing radiation is known to cause chromosomal alterations such as inversions and deletions and has been used extensively for inducing mutations. In Arabidopsis, two methods for the isolation of genes identified on the basis of mutant phenotypes--genomic subtraction and chromosome walking--either rely on or are greatly facilitated by the availability of these types of mutations. This article gives a detailed characterization of ionizing radiation-induced mutations in plants. The Arabidopsis genes encoding chalcone flavanone isomerase (CHI) and dihydroflavonol 4-reductase (DFR) were cloned and found to correspond to two transparent testa loci. A CHI allele, generated by fast-neutron irradiation, consisted of an inversion within the gene. A 272-bp fragment from 38 centimorgans away on the same chromosome was transferred to one end of this inversion. A DFR allele, induced by x-irradiation, contained two deletions and an inversion of the 2.8-centimorgan intervening region. Sequence analysis of the break points in both mutants indicate that repair of radiation-induced damage involves mechanisms similar or identical to those that mediate the integration of foreign sequences into the genome. The chromosome rearrangements found in these mutants have important implications for the use of ionizing radiation-induced alleles in classical and molecular genetic experiments in plants.

Over- and under-representation of short oligonucleotides in DNA sequences.

Abstract: Strand-symmetric relative abundance functionals for di-, tri-, and tetranucleotides are introduced and applied to sequences encompassing a broad phylogenetic range to discern tendencies and anomalies in the occurrences of these short oligonucleotides within and between genomic sequences. For dinucleotides, TA is almost universally under-represented, with the exception of vertebrate mitochondrial genomes, and CG is strongly under-represented in vertebrates and in mitochondrial genomes. The traditional methylation/deamination/mutation hypothesis for the rarity of CG does not adequately account for the observed deficiencies in certain sequences, notably the mitochondrial genomes, yeast, and Neurospora crassa, which lack the standard CpG methylase. Homodinucleotides (AA.TT, CC.GG) and larger homooligonucleotides are over-represented in many organisms, perhaps due to polymerase slippage events. For trinucleotides, GCA.TGC tends to be under-represented in phage, human viral, and eukaryotic sequences, and CTA.TAG is strongly under-represented in many prokaryotic, eukaryotic, and viral sequences. The CCA.TGG triplet is ubiquitously over-represented in human viral and eukaryotic sequences. Among the tetranucleotides, several four-base-pair palindromes tend to be under-represented in phage sequences, probably as a means of restriction avoidance. The tetranucleotide CTAG is observed to be rare in virtually all bacterial genomes and some phage genomes. Explanations for these over- and under-representations in terms of DNA/RNA structures and regulatory mechanisms are considered.

copia-like retrotransposons are ubiquitous among plants

Abstract: Transposable genetic elements are assumed to be a feature of all eukaryotic genomes Their identification, however, has largely been haphazard, limited principally to organisms subjected to molecular or genetic scrutiny We assessed the phylogenetic distribution of copia-like retrotransposons, a class of transposable element that proliferates by reverse transcription, using a polymerase chain reaction assay designed to detect copia-like element reverse transcriptase sequences copia-like retrotransposons were identified in 64 plant species as well as the photosynthetic protist Volvox carteri The plant species included representatives from 9 of 10 plant divisions, including bryophytes, lycopods, ferns, gymnosperms, and angiosperms DNA sequence analysis of 29 cloned PCR products and of a maize retrotransposon cDNA confirmed the identity of these sequences as copia-like reverse transcriptase sequences, thereby demonstrating that this class of retrotransposons is a ubiquitous component of plant genomes

Disruption of either the E1 or the E2 regulatory gene of human papillomavirus type 16 increases viral immortalization capacity

Abstract: The "high-risk" human papillomavirus types 16 (HPV-16) and 18 (HPV-18) have been etiologically implicated in the majority of human cervical carcinomas. In these cancers, the viral DNAs are often integrated into the host genome so that expression of the E1 and the E2 genes is lost, suggesting that disruption of these regulatory genes plays an important role in carcinogenic progression. Previous studies defining the viral genes affecting HPV-16 transformation functions have used the "prototype" viral genome, which was cloned from a human cervical carcinoma and later discovered to harbor a mutation in the E1 gene. In this study, we have corrected this mutation and have evaluated the effect of mutations of either the E1 or the E2 gene on the efficiency of HPV-16 immortalization of human keratinocytes. Mutation of either the E1 gene or the E2 gene in the background of a "wild-type" HPV-16 genome markedly increased immortalization capacity. Mutations were also generated in the E2-binding sites located upstream of the P97 promoter, which directs synthesis of the viral E6 and E7 transforming genes. E2 negatively regulates the P97 promoter through binding at adjacent sites. Surprisingly, the mutation of these sites only partially relieved the negative effect of E2 on viral immortalization, implicating additional mechanisms in the E2 repression of viral immortalization functions. Our results provide genetic evidence that the E1 and E2 gene products each can repress HPV-16 immortalization and support the hypothesis that a selective growth advantage is provided by integration of the viral genome in a manner that causes the loss of expression of either E1 or E2.

The small genome of Arabidopsis contains at least six expressed alpha-tubulin genes.

Abstract: The goal of our investigations is to define the genetic control of microtubule-based processes in a higher plant. The available evidence suggests that we have achieved our first objective: the characterization of the complete alpha-tubulin and beta-tubulin gene families of Arabidopsis. Four additional alpha-tubulin genes (TUA2, TUA4, TUA5, and TUA6) of Arabidopsis have been cloned and sequenced to complete the analysis of the gene structure for all six alpha-tubulin genes detectable on DNA gel blots of Arabidopsis genomic DNA hybridized with alpha-tubulin coding sequences. TUA1 and TUA3 were characterized earlier in our laboratory. Noncoding gene-specific hybridization probes have been constructed for all six alpha-tubulin genes and used in RNA gel blot analyses to demonstrate that all six genes are transcribed. The six genes encode four different alpha-tubulin isoforms; TUA2 and TUA4 encode a single isoform, as do TUA3 and TUA5. Two-dimensional protein gel immunoblot analyses have resolved at least four alpha-tubulin isoforms from plant tissues, suggesting that all of the predicted TUA gene products are synthesized in vivo.

Cloning the Arabidopsis GA7 Locus by Genomic Subtraction

Abstract: Arabidopsis thaliana ga l mutants are gibberellin-responsive dwarfs. We used the genomic subtraction technique to clone DNA sequences that are present in wild-type Arabidopsis (ecotype Landsberg erecta, Ler) but are missing in a presumptive g a l deletion mutant, gal-3. The cloned sequences correspond to a 5.0-kb deletion in the gal-3 genome. Three lines of evidence indicated that the 5.0-kb deletion in the gal-3 mutant is located at the GAl locus. First, restriction fragment length polymorphism mapping showed that DNA sequences within the 5.0-kb deletion map to the GAl locus. Second, cosmid clones that contain wild-type DNA inserts spanning the deletion in gal-3 complemented the dwarf phenotype when integrated into the gal-3 genome by Agrobacterium tumefaciens-mediated transformation. Third, we identified molecular lesions in four additional ga l alleles within the 5.0-kb region deleted in mutant gal-3. One of these lesions is a large insertion or inversion located within the most distal intron encoded by the GAl locus. The three other lesions are all single base changes located within the two most distal exons. RNA gel blot analysis indicated that the GAl locus encodes a 2.8-kb mRNA. We calculated a recombination rate of 10-5 cM per nucleotide for the GAl region of the Arabidopsis genome.

Cloning the Arabidopsis GA1 Locus by Genomic Subtraction.

Abstract: Arabidopsis thaliana ga1 mutants are gibberellin-responsive dwarfs. We used the genomic subtraction technique to clone DNA sequences that are present in wild-type Arabidopsis (ecotype Landsberg erecta, Ler) but are missing in a presumptive ga1 deletion mutant, ga1-3. The cloned sequences correspond to a 5.0-kb deletion in the ga1-3 genome. Three lines of evidence indicated that the 5.0-kb deletion in the ga1-3 mutant is located at the GA1 locus. First, restriction fragment length polymorphism mapping showed that DNA sequences within the 5.0-kb deletion map to the GA1 locus. Second, cosmid clones that contain wild-type DNA inserts spanning the deletion in ga1-3 complemented the dwarf phenotype when integrated into the ga1-3 genome by Agrobacterium tumefaciens-mediated transformation. Third, we identified molecular lesions in four additional ga1 alleles within the 5.0-kb region deleted in mutant ga1-3. One of these lesions is a large insertion or inversion located within the most distal intron encoded by the GA1 locus. The three other lesions are all single base changes located within the two most distal exons. RNA gel blot analysis indicated that the GA1 locus encodes a 2.8-kb mRNA. We calculated a recombination rate of 10-5 cM per nucleotide for the GA1 region of the Arabidopsis genome.

Analysis of the Escherichia coli genome: DNA sequence of the region from 84.5 to 86.5 minutes.

Abstract: The DNA sequence of 91.4 kilobases of the Escherichia coli K-12 genome, spanning the region between rrnC at 84.5 minutes and rrnA at 86.5 minutes on the genetic map (85 to 87 percent on the physical map), is described. Analysis of this sequence identified 82 potential coding regions (open reading frames) covering 84 percent of the sequenced interval. The arrangement of these open reading frames, together with the consensus promoter sequences and terminator-like sequences found by computer searches, made it possible to assign them to proposed transcriptional units. More than half the open reading frames correlated with known genes or functions suggested by similarity to other sequences. Those remaining encode still unidentified proteins. The sequenced region also contains several RNA genes and two types of repeated sequence elements were found. Intergenic regions include three "gray holes," 0.6 to 0.8 kilobases, with no recognizable functions.

RFLP-based genetic map of the homoeologous group 3 chromosomes of wheat and rye.

Abstract: Genetic maps of chromosomes 3A, 3B and 3D of wheat and 3R of rye were developed using 22 DNA probes and two isozyme marker systems. Analysis of the 49 loci mapped showed extreme clustering around the centromere in all four maps, with large 'gaps' in the distal chromosome regions, which is interpreted as being due to strong localisation of recombination towards the ends of the wheat and rye chromosomes. In the centromeric regions gene orders are highly conserved between the three wheat genomes and the rye genome. However, the unpredictable behaviour of the DNA clones that map in distal chromosome locations may indicate that the genomes are diverging most rapidly in the regions of higher recombination. A comparison of cDNA and genomic probes showed the latter to be much more efficient for revealing RFLP. Some classes of gDNA clones, i.e. chromosome-specific sequences and those hybridizing in a non-homoeologous manner, were seen to be most polymorphic. Correlations between map locations and RFLP levels showed no clear relationship. In addition to anonymous DNA clones, the locations of known function clones, sedoheptulose-1,7-bisphosphatase (XSbp), carboxypeptidase I (XCxp1) and a bZIP protein (XEmbp), were ascertained along with those for two isozyme loci, Mal-1 and Est-5.