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1.
Nature ; 440(7088): 1194-8, 2006 Apr 27.
Article in English | MEDLINE | ID: mdl-16641997

ABSTRACT

After the completion of a draft human genome sequence, the International Human Genome Sequencing Consortium has proceeded to finish and annotate each of the 24 chromosomes comprising the human genome. Here we describe the sequencing and analysis of human chromosome 3, one of the largest human chromosomes. Chromosome 3 comprises just four contigs, one of which currently represents the longest unbroken stretch of finished DNA sequence known so far. The chromosome is remarkable in having the lowest rate of segmental duplication in the genome. It also includes a chemokine receptor gene cluster as well as numerous loci involved in multiple human cancers such as the gene encoding FHIT, which contains the most common constitutive fragile site in the genome, FRA3B. Using genomic sequence from chimpanzee and rhesus macaque, we were able to characterize the breakpoints defining a large pericentric inversion that occurred some time after the split of Homininae from Ponginae, and propose an evolutionary history of the inversion.


Subject(s)
Chromosomes, Human, Pair 3/genetics , Animals , Base Sequence , Chromosome Breakage/genetics , Chromosome Inversion/genetics , Contig Mapping , CpG Islands/genetics , DNA, Complementary/genetics , Evolution, Molecular , Expressed Sequence Tags , Human Genome Project , Humans , Macaca mulatta/genetics , Molecular Sequence Data , Pan troglodytes/genetics , Sequence Analysis, DNA , Synteny/genetics
2.
Nature ; 440(7082): 346-51, 2006 Mar 16.
Article in English | MEDLINE | ID: mdl-16541075

ABSTRACT

Human chromosome 12 contains more than 1,400 coding genes and 487 loci that have been directly implicated in human disease. The q arm of chromosome 12 contains one of the largest blocks of linkage disequilibrium found in the human genome. Here we present the finished sequence of human chromosome 12, which has been finished to high quality and spans approximately 132 megabases, representing approximately 4.5% of the human genome. Alignment of the human chromosome 12 sequence across vertebrates reveals the origin of individual segments in chicken, and a unique history of rearrangement through rodent and primate lineages. The rate of base substitutions in recent evolutionary history shows an overall slowing in hominids compared with primates and rodents.


Subject(s)
Chromosomes, Human, Pair 12/genetics , Animals , Base Composition , CpG Islands/genetics , Evolution, Molecular , Expressed Sequence Tags , Genes/genetics , Humans , Linkage Disequilibrium/genetics , Microsatellite Repeats/genetics , Molecular Sequence Data , Mutagenesis, Insertional/genetics , Pan troglodytes/genetics , Sequence Analysis, DNA , Sequence Deletion/genetics , Short Interspersed Nucleotide Elements/genetics , Synteny/genetics
3.
Genome Res ; 15(1): 1-18, 2005 Jan.
Article in English | MEDLINE | ID: mdl-15632085

ABSTRACT

We have sequenced the genome of a second Drosophila species, Drosophila pseudoobscura, and compared this to the genome sequence of Drosophila melanogaster, a primary model organism. Throughout evolution the vast majority of Drosophila genes have remained on the same chromosome arm, but within each arm gene order has been extensively reshuffled, leading to a minimum of 921 syntenic blocks shared between the species. A repetitive sequence is found in the D. pseudoobscura genome at many junctions between adjacent syntenic blocks. Analysis of this novel repetitive element family suggests that recombination between offset elements may have given rise to many paracentric inversions, thereby contributing to the shuffling of gene order in the D. pseudoobscura lineage. Based on sequence similarity and synteny, 10,516 putative orthologs have been identified as a core gene set conserved over 25-55 million years (Myr) since the pseudoobscura/melanogaster divergence. Genes expressed in the testes had higher amino acid sequence divergence than the genome-wide average, consistent with the rapid evolution of sex-specific proteins. Cis-regulatory sequences are more conserved than random and nearby sequences between the species--but the difference is slight, suggesting that the evolution of cis-regulatory elements is flexible. Overall, a pattern of repeat-mediated chromosomal rearrangement, and high coadaptation of both male genes and cis-regulatory sequences emerges as important themes of genome divergence between these species of Drosophila.


Subject(s)
Chromosomes/genetics , Drosophila/genetics , Evolution, Molecular , Genes, Insect/genetics , Genome , Sequence Analysis, DNA/methods , Animals , Chromosome Breakage/genetics , Chromosome Inversion/genetics , Chromosome Mapping/methods , Conserved Sequence/genetics , Drosophila melanogaster/genetics , Enhancer Elements, Genetic , Gene Rearrangement/genetics , Genetic Variation/genetics , Molecular Sequence Data , Predictive Value of Tests , Repetitive Sequences, Nucleic Acid/genetics
4.
Nature ; 428(6982): 493-521, 2004 Apr 01.
Article in English | MEDLINE | ID: mdl-15057822

ABSTRACT

The laboratory rat (Rattus norvegicus) is an indispensable tool in experimental medicine and drug development, having made inestimable contributions to human health. We report here the genome sequence of the Brown Norway (BN) rat strain. The sequence represents a high-quality 'draft' covering over 90% of the genome. The BN rat sequence is the third complete mammalian genome to be deciphered, and three-way comparisons with the human and mouse genomes resolve details of mammalian evolution. This first comprehensive analysis includes genes and proteins and their relation to human disease, repeated sequences, comparative genome-wide studies of mammalian orthologous chromosomal regions and rearrangement breakpoints, reconstruction of ancestral karyotypes and the events leading to existing species, rates of variation, and lineage-specific and lineage-independent evolutionary events such as expansion of gene families, orthology relations and protein evolution.


Subject(s)
Evolution, Molecular , Genome , Genomics , Rats, Inbred BN/genetics , Animals , Base Composition , Centromere/genetics , Chromosomes, Mammalian/genetics , CpG Islands/genetics , DNA Transposable Elements/genetics , DNA, Mitochondrial/genetics , Gene Duplication , Humans , Introns/genetics , Male , Mice , Models, Molecular , Mutagenesis , Polymorphism, Single Nucleotide/genetics , RNA Splice Sites/genetics , RNA, Untranslated/genetics , Rats , Regulatory Sequences, Nucleic Acid/genetics , Retroelements/genetics , Sequence Analysis, DNA , Telomere/genetics
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