Life with 6000 Genes

Department of Biochemistry, Stanford University, Palo Alto, California, United States
Science (Impact Factor: 33.61). 11/1996; 274(5287):546, 563-7. DOI: 10.1126/science.274.5287.546
Source: PubMed

ABSTRACT The genome of the yeast Saccharomyces cerevisiae has been completely sequenced through a worldwide collaboration. The sequence of 12,068 kilobases defines 5885 potential
protein-encoding genes, approximately 140 genes specifying ribosomal RNA, 40 genes for small nuclear RNA molecules, and 275
transfer RNA genes. In addition, the complete sequence provides information about the higher order organization of yeast's
16 chromosomes and allows some insight into their evolutionary history. The genome shows a considerable amount of apparent
genetic redundancy, and one of the major problems to be tackled during the next stage of the yeast genome project is to elucidate
the biological functions of all of these genes.

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    • "However, this is hardly ever the case: most of the genome sequences published are called ''unfinished'' as they are heavily fragmented, whereas the number of truly ''finished'' genomes remains remarkably low. Only the small, compact genomes of a few so-called ''model'' organisms have been fully assembled until now, mostly bacteria (such as Haemophilus influenzae and Escherichia coli [4] [5]) and fungi (e.g., Saccharomyces cerevisiae [6]) along with a single metazoan to date, the nematode Caenorhabditis elegans [7]. All other sequences consist of ''drafts'' of varying quality, including the human genome that still contains numerous gaps but is nevertheless the most complete mammalian reference assembly available [8] [9]. "
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    ABSTRACT: High-throughput DNA sequencing technologies are fuelling an accelerating trend to assemble de novo or resequence the genomes of numerous species as well as to complete unfinished assemblies. While current DNA sequencing technologies remain limited to reading stretches of a few hundreds or thousands of base pairs, experimental and computational methods are continuously improving with the goal of assembling entire genomes from large numbers of short DNA sequences. However, the algorithms that piece together DNA strands face important limitations due, notably, to the presence of repeated sequences or of multiple haplotypes within one genome, thus leaving many assemblies incomplete. Recently, the realization that the physical contacts experienced by a portion of a DNA molecule could be used as a robust and quantitative assay to determine its genomic position has led to the emerging field of contact genomics, which promises to revolutionize current genome assembly approaches by exploiting the flexible polymer properties of chromosomes. Here we review the current applications of contact genomics to genome scaffolding, haplotyping and metagenomic assembly, then outline the future developments we envision. Copyright © 2015. Published by Elsevier B.V.
    FEBS letters 04/2015; 40. DOI:10.1016/j.febslet.2015.04.034 · 3.17 Impact Factor
    • "lists the 93 S. cerevisiae strains sequenced in this study and seven strains that are isogenic with strains sequenced in other studies (Goffeau et al. 1996; RM11 2004; Wei et al. 2007; Doniger et al. 2008; Dowell et al. 2010; Nishant et al. 2010). All sequence-based analyses in this study are on the genomes of the 93 sequenced strains, as well as the reference S288c genome; all phenotypic and association analyses include all 100 strains, unless otherwise noted. "
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    ABSTRACT: Saccharomyces cerevisiae, a well-established model for species as diverse as humans and pathogenic fungi, is more recently a model for population and quantitative genetics. S. cerevisiae is found in multiple environments-one of which is the human body-as an opportunistic pathogen. To aid in the understanding of the S. cerevisiae population and quantitative genetics, as well as its emergence as an opportunistic pathogen, we sequenced, de novo assembled, and extensively manually edited and annotated the genomes of 93 S. cerevisiae strains from multiple geographic and environmental origins, including many clinical origin strains. These 93 S. cerevisiae strains, the genomes of which are near-reference quality, together with seven previously sequenced strains, constitute a novel genetic resource, the "100-genomes" strains. Our sequencing coverage, high-quality assemblies, and annotation provide unprecedented opportunities for detailed interrogation of complex genomic loci, examples of which we demonstrate. We found most phenotypic variation to be quantitative and identified population, genotype, and phenotype associations. Importantly, we identified clinical origin associations. For example, we found that an introgressed PDR5 was present exclusively in clinical origin mosaic group strains; that the mosaic group was significantly enriched for clinical origin strains; and that clinical origin strains were much more copper resistant, suggesting that copper resistance contributes to fitness in the human host. The 100-genomes strains are a novel, multipurpose resource to advance the study of S. cerevisiae population genetics, quantitative genetics, and the emergence of an opportunistic pathogen. © 2015 Strope et al.; Published by Cold Spring Harbor Laboratory Press.
    Genome Research 04/2015; 25(5). DOI:10.1101/gr.185538.114 · 14.63 Impact Factor
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    • "More than 50 years later, in 1976, Walter Fiers reported the complete sequence of the bacteriophage MS2 RNA genome (Fiers et al. 1976 ); in 1977 Frederick Sanger reported the fi rst sequence of a DNA (deoxyribonucleic acid) genome (Phage Ф X-174; Sanger et al. 1977 ). In the following years, the genomic sequences of representative organisms from the three different domains of life were reported, being Haemophilus infl uenzae , Saccharomyces cerevisiae , and Methanococcus jannaschii the fi rsts on their respective domains (Fleischmann et al. 1995 ; Goffeau et al. 1996 ; Bult et al. 1996 ). Furthermore, in 1986 the fi rst two chloroplast genomes came into view when two different Japanese research teams reported full sequences for the chloroplast genomes of Marchantia polymorpha and Nicotiana tabacum (Ohyama et al. 1986 ; Shinozaki et al. 1986 ). Nowadays, the next generation of DNA sequencing technologies has advanced in precision, time consumption and cost, to the point that genomic information for 10,904 organisms is now publicly available; among them only 197 genomes correspond to plants ( "
    PlantOmics: The Omics of Plant Science, 1 edited by Barh Debmalya, Khan Muhammad Sarwar, Davies Eric, 01/2015: chapter 18: pages 534-553; Spinger India., ISBN: 978-81-322-2172-2
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