Topic
Genome
About: Genome is a research topic. Over the lifetime, 74231 publications have been published within this topic receiving 3819713 citations.
Papers published on a yearly basis
Papers
More filters
TL;DR: A model is presented whereby the formation of gene clusters in bacteria is mediated by transfer of DNA within and among taxa, and predicts a mosaic structure of modern genomes in which ancestral chromosomal material is interspersed with novel, horizontally transferred operons providing peripheral metabolic functions.
Abstract: A model is presented whereby the formation of gene clusters in bacteria is mediated by transfer of DNA within and among taxa. Bacterial operons are typically composed of genes whose products contribute to a single function. If this function is subject to weak selection or to long periods with no selection, the contributing genes may accumulate mutations and be lost by genetic drift. From a cell's perspective, once several genes are lost, the function can be restored only if all missing genes were acquired simultaneously by lateral transfer. The probability of transfer of multiple genes increases when genes are physically proximate. From a gene's perspective, horizontal transfer provides a way to escape evolutionary loss by allowing colonization of organisms lacking the encoded functions. Since organisms bearing clustered genes are more likely to act as successful donors, clustered genes would spread among bacterial genomes. The physical proximity of genes may be considered a selfish property of the operon since it affects the probability of successful horizontal transfer but may provide no physiological benefit to the host. This process predicts a mosaic structure of modern genomes in which ancestral chromosomal material is interspersed with novel, horizontally transferred operons providing peripheral metabolic functions.
679 citations
TL;DR: It is proposed that the cancer genome is shaped through a process of cumulative haploinsufficiency and triplosensitivity, and the distribution and potency of TSGs, OGs, and essential genes on chromosomes can predict the complex patterns of aneuploidy and copy number variation characteristic of cancer genomes.
679 citations
University of Pretoria1, Universidade Católica de Brasília2, Empresa Brasileira de Pesquisa Agropecuária3, United States Department of Energy4, Oak Ridge National Laboratory5, Joint Genome Institute6, Ghent University7, Institut national de la recherche agronomique8, University of Toulouse9, University of British Columbia10, University of Münster11, University of Düsseldorf12, Oregon State University13, University of São Paulo14, Federal University of Rio de Janeiro15, Australian National University16, Indian Institute of Chemical Technology17, University of Arizona18, Universidade Federal de Viçosa19, Universidade Federal do Rio Grande do Sul20, Department of Environment and Primary Industries21, University of Melbourne22, University of Tasmania23, University of the Sunshine Coast24, University of Brasília25
TL;DR: Of 36,376 predicted protein-coding genes, 34% occur in tandem duplications, the largest proportion thus far in plant genomes, which shows the highest diversity of genes for specialized metabolites such as terpenes that act as chemical defence and provide unique pharmaceutical oils.
Abstract: Eucalypts are the world's most widely planted hardwood trees. Their outstanding diversity, adaptability and growth have made them a global renewable resource of fibre and energy. We sequenced and assembled >94% of the 640-megabase genome of Eucalyptus grandis. Of 36,376 predicted protein-coding genes, 34% occur in tandem duplications, the largest proportion thus far in plant genomes. Eucalyptus also shows the highest diversity of genes for specialized metabolites such as terpenes that act as chemical defence and provide unique pharmaceutical oils. Genome sequencing of the E. grandis sister species E. globulus and a set of inbred E. grandis tree genomes reveals dynamic genome evolution and hotspots of inbreeding depression. The E. grandis genome is the first reference for the eudicot order Myrtales and is placed here sister to the eurosids. This resource expands our understanding of the unique biology of large woody perennials and provides a powerful tool to accelerate comparative biology, breeding and biotechnology.
679 citations
Joint Genome Institute1, University of California, Berkeley2, National Institute for Medical Research3, Genetic Information Research Institute4, National Institutes of Health5, Rice University6, University of California, Irvine7, University of Manchester8, Los Alamos National Laboratory9, United States Department of Health and Human Services10, Washington University in St. Louis11, Okinawa Institute of Science and Technology12, St. Jude Children's Research Hospital13, Nara Institute of Science and Technology14, University of Maryland, Baltimore15, University of Évry Val d'Essonne16, University of Rochester Medical Center17, University of Houston18, University of Calgary19, Cincinnati Children's Hospital Medical Center20, Yale University21
TL;DR: The western clawed frog Xenopus tropicalis is an important model for vertebrate development that combines experimental advantages of the African clawed frogs Xenopus laevis with more tractable genetics.
Abstract: The western clawed frog Xenopus tropicalis is an important model for vertebrate development that combines experimental advantages of the African clawed frog Xenopus laevis with more tractable genetics. Here we present a draft genome sequence assembly of X. tropicalis. This genome encodes more than 20,000 protein-coding genes, including orthologs of at least 1700 human disease genes. Over 1 million expressed sequence tags validated the annotation. More than one-third of the genome consists of transposable elements, with unusually prevalent DNA transposons. Like that of other tetrapods, the genome of X. tropicalis contains gene deserts enriched for conserved noncoding elements. The genome exhibits substantial shared synteny with human and chicken over major parts of large chromosomes, broken by lineage-specific chromosome fusions and fissions, mainly in the mammalian lineage.
679 citations
TL;DR: The demonstrable and potential roles of HTDV/HERV-K as well as of other human elements in disease and in maintaining genome plasticity are illustrated.
Abstract: Human endogenous retroviruses (HERVs) are very likely footprints of ancient germ-cell infections. HERV sequences encompass about 1% of the human genome. HERVs have retained the potential of other retroelements to retrotranspose and thus to change genomic structure and function. The genomes of almost all HERV families are highly defective. Recent progress has allowed the identification of the biologically most active family, HTDV/HERV-K, which codes for viral proteins and particles and is highly expressed in germ-cell tumors. The demonstrable and potential roles of HTDV/HERV-K as well as of other human elements in disease and in maintaining genome plasticity are illustrated.
678 citations