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V Wood,
R Gwilliam,
M-A Rajandream,
M Lyne,
R Lyne,
A Stewart,
J Sgouros,
N Peat,
J Hayles,
S Baker, [......],
L Cerutti,
T Lowe, W R McCombie,
I Paulsen,
J Potashkin,
G V Shpakovski,
D Ussery,
B G Barrell,
P Nurse,
L Cerrutti
[show abstract]
[hide abstract]
ABSTRACT: We have sequenced and annotated the genome of fission yeast (Schizosaccharomyces pombe), which contains the smallest number of protein-coding genes yet recorded for a eukaryote: 4,824. The centromeres are between 35 and 110 kilobases (kb) and contain related repeats including a highly conserved 1.8-kb element. Regions upstream of genes are longer than in budding yeast (Saccharomyces cerevisiae), possibly reflecting more-extended control regions. Some 43% of the genes contain introns, of which there are 4,730. Fifty genes have significant similarity with human disease genes; half of these are cancer related. We identify highly conserved genes important for eukaryotic cell organization including those required for the cytoskeleton, compartmentation, cell-cycle control, proteolysis, protein phosphorylation and RNA splicing. These genes may have originated with the appearance of eukaryotic life. Few similarly conserved genes that are important for multicellular organization were identified, suggesting that the transition from prokaryotes to eukaryotes required more new genes than did the transition from unicellular to multicellular organization.
Nature 03/2002; 415(6874):871-80. · 36.28 Impact Factor
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Cell 07/2001; 105(5):571-4. · 32.40 Impact Factor
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E S Lander,
L M Linton,
B Birren,
C Nusbaum,
M C Zody,
J Baldwin,
K Devon,
K Dewar,
M Doyle,
W FitzHugh, [......],
K A Wetterstrand,
A Patrinos,
M J Morgan,
P de Jong,
J J Catanese,
K Osoegawa,
H Shizuya,
S Choi,
Y J Chen,
J Szustakowki
[show abstract]
[hide abstract]
ABSTRACT: The human genome holds an extraordinary trove of information about human development, physiology, medicine and evolution. Here we report the results of an international collaboration to produce and make freely available a draft sequence of the human genome. We also present an initial analysis of the data, describing some of the insights that can be gleaned from the sequence.
Nature 03/2001; 409(6822):860-921. · 36.28 Impact Factor
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S Tabata,
T Kaneko,
Y Nakamura,
H Kotani,
T Kato,
E Asamizu,
N Miyajima,
S Sasamoto,
T Kimura,
T Hosouchi, [......],
K Lemcke,
G Kolesov,
K Mayer,
S Rudd,
H Schoof,
C Schueller,
P Zaccaria,
H W Mewes,
M Bevan,
P Fransz
[show abstract]
[hide abstract]
ABSTRACT: The genome of the model plant Arabidopsis thaliana has been sequenced by an international collaboration, The Arabidopsis Genome Initiative. Here we report the complete sequence of chromosome 5. This chromosome is 26 megabases long; it is the second largest Arabidopsis chromosome and represents 21% of the sequenced regions of the genome. The sequence of chromosomes 2 and 4 have been reported previously and that of chromosomes 1 and 3, together with an analysis of the complete genome sequence, are reported in this issue. Analysis of the sequence of chromosome 5 yields further insights into centromere structure and the sequence determinants of heterochromatin condensation. The 5,874 genes encoded on chromosome 5 reveal several new functions in plants, and the patterns of gene organization provide insights into the mechanisms and extent of genome evolution in plants.
Nature 01/2001; 408(6814):823-6. · 36.28 Impact Factor
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G P Copenhaver,
K Nickel,
T Kuromori,
M I Benito,
S Kaul,
X Lin,
M Bevan,
G Murphy,
B Harris,
L D Parnell, W R McCombie,
R A Martienssen,
M Marra,
D Preuss
[show abstract]
[hide abstract]
ABSTRACT: High-precision genetic mapping was used to define the regions that contain centromere functions on each natural chromosome in Arabidopsis thaliana. These regions exhibited dramatic recombinational repression and contained complex DNA surrounding large arrays of 180-base pair repeats. Unexpectedly, the DNA within the centromeres was not merely structural but also encoded several expressed genes. The regions flanking the centromeres were densely populated by repetitive elements yet experienced normal levels of recombination. The genetically defined centromeres were well conserved among Arabidopsis ecotypes but displayed limited sequence homology between different chromosomes, excluding repetitive DNA. This investigation provides a platform for dissecting the role of individual sequences in centromeres in higher eukaryotes.
Science 12/1999; 286(5449):2468-74. · 31.20 Impact Factor
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K Mayer,
C Schüller,
R Wambutt,
G Murphy,
G Volckaert,
T Pohl,
A Düsterhöft,
W Stiekema,
K D Entian,
N Terryn, [......],
S Granat,
N Shohdy,
A Hasegawa,
A Hameed,
M Lodhi,
A Johnson,
E Chen,
M Marra,
R Martienssen, W R McCombie
[show abstract]
[hide abstract]
ABSTRACT: The higher plant Arabidopsis thaliana (Arabidopsis) is an important model for identifying plant genes and determining their function. To assist biological investigations and to define chromosome structure, a coordinated effort to sequence the Arabidopsis genome was initiated in late 1996. Here we report one of the first milestones of this project, the sequence of chromosome 4. Analysis of 17.38 megabases of unique sequence, representing about 17% of the genome, reveals 3,744 protein coding genes, 81 transfer RNAs and numerous repeat elements. Heterochromatic regions surrounding the putative centromere, which has not yet been completely sequenced, are characterized by an increased frequency of a variety of repeats, new repeats, reduced recombination, lowered gene density and lowered gene expression. Roughly 60% of the predicted protein-coding genes have been functionally characterized on the basis of their homology to known genes. Many genes encode predicted proteins that are homologous to human and Caenorhabditis elegans proteins.
Nature 12/1999; 402(6763):769-77. · 36.28 Impact Factor
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K. Mayer,
C. Sch|[uuml]|ller,
R. Wambutt,
G. Murphy,
G. Volckaert,
T. Pohl,
A. D|[uuml]|sterh|[ouml]|ft,
W. Stiekema,
K.-D. Entian,
N. Terryn, [......],
S. Granat,
N. Shohdy,
A. Hasegawa,
A. Hameed,
M. Lodhi,
A. Johnson,
E. Chen,
M. Marra,
R. Martienssen, W. R. McCombie
[show abstract]
[hide abstract]
ABSTRACT: The higher plant Arabidopsis thaliana (Arabidopsis) is an important model for identifying plant genes and determining their function. To assist biological investigations and to define chromosome structure, a coordinated effort to sequence the Arabidopsis genome was initiated in late 1996. Here we report one of the first milestones of this project, the sequence of chromosome 4. Analysis of 17.38 megabases of unique sequence, representing about 17% of the genome, reveals 3,744 protein coding genes, 81 transfer RNAs and numerous repeat elements. Heterochromatic regions surrounding the putative centromere, which has not yet been completely sequenced, are characterized by an increased frequency of a variety of repeats, new repeats, reduced recombination, lowered gene density and lowered gene expression. Roughly 60% of the predicted protein-coding genes have been functionally characterized on the basis of their homology to known genes. Many genes encode predicted proteins that are homologous to human and Caenorhabditis elegans proteins.
Nature 12/1999; 402(6763):769-777. · 36.28 Impact Factor
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[show abstract]
[hide abstract]
ABSTRACT: The genomes of higher plants and animals are highly differentiated, and are composed of a relatively small number of genes and a large fraction of repetitive DNA. The bulk of this repetitive DNA constitutes transposable, and especially retrotransposable, elements. It has been hypothesized that most of these elements are heavily methylated relative to genes, but the evidence for this is controversial. We show here that repeat sequences in maize are largely excluded from genomic shotgun libraries by the selection of an appropriate host strain because of their sensitivity to bacterial restriction-modification systems. In contrast, unmethylated genic regions are preserved in these genetically filtered libraries if the insert size is less than the average size of genes. The representation of unique maize sequences not found in plant reference genomes is also greatly enriched. This demonstrates that repeats, and not genes, are the primary targets of methylation in maize. The use of restrictive libraries in genome shotgun sequencing in plant genomes should allow significant representation of genes, reducing the number of reactions required.
Nature Genetics 12/1999; 23(3):305-8. · 35.53 Impact Factor
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[show abstract]
[hide abstract]
ABSTRACT: The yeast and human SKP1 genes regulate the mitotic cell cycle but are not yet known to be required for meiosis. Nine Arabidopsis SKP1 homologues have been uncovered and are named ASK1 through ASK9. Here, we report the isolation and characterization of a male sterile Arabidopsis mutant and show that the mutant defect was caused by a Ds transposon insertion into the ASK1 gene. In the ask1-1 mutant, abnormal microspores exhibit a range of sizes. Furthermore, during mutant male meiosis, although homologous chromosome pairing appeared normal at metaphase I, chromosome segregation at anaphase I is unequal, and some chromosomes are abnormally extended. Therefore, in ask1-1, at least some homologues remain associated after metaphase I. In addition, immunofluorescence microscopy indicates that the mutant spindle morphology at both metaphase I and early anaphase I is normal; thus, the abnormal chromosome segregation is not likely caused by a spindle defect. Because the yeast Skp1p is required for targeting specific proteins for ubiquitin-mediated proteolysis, we propose that ASK1 controls homologue separation by degrading or otherwise removing a protein that is required directly or indirectly for homologue association before anaphase I.
Proceedings of the National Academy of Sciences 10/1999; 96(20):11416-21. · 9.68 Impact Factor
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M Marra,
T Kucaba,
M Sekhon,
L Hillier,
R Martienssen,
A Chinwalla,
J Crockett,
J Fedele,
H Grover,
C Gund, W R McCombie,
K McDonald,
J McPherson,
N Mudd,
L Parnell,
J Schein,
R Seim,
P Shelby,
R Waterston,
R Wilson
[show abstract]
[hide abstract]
ABSTRACT: Arabidopsis thaliana has emerged as a model system for studies of plant genetics and development, and its genome has been targeted for sequencing by an international consortium (the Arabidopsis Genome Initiative; http://genome-www. stanford.edu/Arabidopsis/agi.html). To support the genome-sequencing effort, we fingerprinted more than 20,000 BACs (ref. 2) from two high-quality publicly available libraries, generating an estimated 17-fold redundant coverage of the genome, and used the fingerprints to nucleate assembly of the data by computer. Subsequent manual revision of the assemblies resulted in the incorporation of 19,661 fingerprinted BACs into 169 ordered sets of overlapping clones ('contigs'), each containing at least 3 clones. These contigs are ideal for parallel selection of BACs for large-scale sequencing and have supported the generation of more than 5.8 Mb of finished genome sequence submitted to GenBank; analysis of the sequence has confirmed the integrity of contigs constructed using this fingerprint data. Placement of contigs onto chromosomes can now be performed, and is being pursued by groups involved in both sequencing and positional cloning studies. To our knowledge, these data provide the first example of whole-genome random BAC fingerprint analysis of a eucaryote, and have provided a model essential to efforts aimed at generating similar databases of fingerprint contigs to support sequencing of other complex genomes, including that of human.
Nature Genetics 08/1999; 22(3):265-70. · 35.53 Impact Factor
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[show abstract]
[hide abstract]
ABSTRACT: Gene trap transposon mutagenesis can identify essential genes whose functions in later development are obscured by an early lethal phenotype. In higher plants, many genes are required for haploid gametophyte viability, so that the phenotypic effects of their disruption cannot be readily observed in the diploid plant body. The PROLIFERA (PRL) gene, identified by gene trap transposon mutagenesis in Arabidopsis, is required for megaga-metophyte and embryo development. Reporter gene expression patterns revealed that PRL was expressed in dividing cells throughout the plant. PRL is related to the MCM2-3-5 family of yeast genes that are required for the initiation of DNA replication.
Science 06/1995; 268(5212):877-80. · 31.20 Impact Factor
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V Wood,
R Gwilliam,
M A Rajandream,
M Lyne,
R. Lyne,
A Stewart,
J. Sgouros,
N. Peat,
J Hayles,
S Baker, [......],
S L Forsburg,
L Cerutti,
T. Lowe, W R McCombie,
I Paulsen,
J Potashkin,
G V Shpakovski,
D. Ussery,
B G Barrell,
P Nurse
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R. H. Waterston,
K. Lindblad-Toh,
E. Birney,
J. Rogers,
J. F. Abril,
P. Agarwal,
R. Agarwala,
R. Ainscough,
M. Alexandersson,
P. An, [......],
S. Williams,
R. K. Wilson,
E. Winter,
K. C. Worley,
D. Wyman,
S. Yang,
S. P. Yang,
E. M. Zdobnov,
M. C. Zody,
E. S. Lander
[show abstract]
[hide abstract]
ABSTRACT: The sequence of the mouse genome is a key informational tool for understanding the contents of the human genome and a key experimental tool for biomedical research. Here, we report the results of an international collaboration to produce a high-quality draft sequence of the mouse genome. We also present an initial comparative analysis of the mouse and human genomes, describing some of the insights that can be gleaned from the two sequences. We discuss topics including the analysis of the evolutionary forces shaping the size, structure and sequence of the genomes; the conservation of large-scale synteny across most of the genomes; the much lower extent of sequence orthology covering less than half of the genomes; the proportions of the genomes under selection; the number of protein-coding genes; the expansion of gene families related to reproduction and immunity; the evolution of proteins; and the identification of intraspecies polymorphism.
NATURE. 420(6915):520-62.
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R. H. Waterston,
K. Lindblad-Toh,
E. Birney,
J. Rogers,
J. F. Abril,
P. Agarwal,
R. Agarwala,
R. Ainscough,
M. Alexandersson,
P. An, [......],
S. Williams,
R. K. Wilson,
E. Winter,
K. C. Worley,
D. Wyman,
S. Yang,
S. P. Yang,
E. M. Zdobnov,
M. C. Zody,
E. S. Lander
[show abstract]
[hide abstract]
ABSTRACT: The sequence of the mouse genome is a key informational tool for understanding the contents of the human genome and a key experimental tool for biomedical research. Here, we report the results of an international collaboration to produce a high-quality draft sequence of the mouse genome. We also present an initial comparative analysis of the mouse and human genomes, describing some of the insights that can be gleaned from the two sequences. We discuss topics including the analysis of the evolutionary forces shaping the size, structure and sequence of the genomes; the conservation of large-scale synteny across most of the genomes; the much lower extent of sequence orthology covering less than half of the genomes; the proportions of the genomes under selection; the number of protein-coding genes; the expansion of gene families related to reproduction and immunity; the evolution of proteins; and the identification of intraspecies polymorphism.
NATURE. 420(6915):520-62.
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R. H. Waterston,
K. Lindblad-Toh,
E. Birney,
J. Rogers,
J. F. Abril,
P. Agarwal,
R. Agarwala,
R. Ainscough,
M. Alexandersson,
P. An, [......],
S. Williams,
R. K. Wilson,
E. Winter,
K. C. Worley,
D. Wyman,
S. Yang,
S. P. Yang,
E. M. Zdobnov,
M. C. Zody,
E. S. Lander
[show abstract]
[hide abstract]
ABSTRACT: The sequence of the mouse genome is a key informational tool for understanding the contents of the human genome and a key experimental tool for biomedical research. Here, we report the results of an international collaboration to produce a high-quality draft sequence of the mouse genome. We also present an initial comparative analysis of the mouse and human genomes, describing some of the insights that can be gleaned from the two sequences. We discuss topics including the analysis of the evolutionary forces shaping the size, structure and sequence of the genomes; the conservation of large-scale synteny across most of the genomes; the much lower extent of sequence orthology covering less than half of the genomes; the proportions of the genomes under selection; the number of protein-coding genes; the expansion of gene families related to reproduction and immunity; the evolution of proteins; and the identification of intraspecies polymorphism.
NATURE. 420(6915):520-62.
-
R. H. Waterston,
K. Lindblad-Toh,
E. Birney,
J. Rogers,
J. F. Abril,
P. Agarwal,
R. Agarwala,
R. Ainscough,
M. Alexandersson,
P. An, [......],
S. Williams,
R. K. Wilson,
E. Winter,
K. C. Worley,
D. Wyman,
S. Yang,
S. P. Yang,
E. M. Zdobnov,
M. C. Zody,
E. S. Lander
[show abstract]
[hide abstract]
ABSTRACT: The sequence of the mouse genome is a key informational tool for understanding the contents of the human genome and a key experimental tool for biomedical research. Here, we report the results of an international collaboration to produce a high-quality draft sequence of the mouse genome. We also present an initial comparative analysis of the mouse and human genomes, describing some of the insights that can be gleaned from the two sequences. We discuss topics including the analysis of the evolutionary forces shaping the size, structure and sequence of the genomes; the conservation of large-scale synteny across most of the genomes; the much lower extent of sequence orthology covering less than half of the genomes; the proportions of the genomes under selection; the number of protein-coding genes; the expansion of gene families related to reproduction and immunity; the evolution of proteins; and the identification of intraspecies polymorphism.
Nature. 420(6915):520-62.
-
R. H. Waterston,
K. Lindblad-Toh,
E. Birney,
J. Rogers,
J. F. Abril,
P. Agarwal,
R. Agarwala,
R. Ainscough,
M. Alexandersson,
P. An, [......],
S. Williams,
R. K. Wilson,
E. Winter,
K. C. Worley,
D. Wyman,
S. Yang,
S. P. Yang,
E. M. Zdobnov,
M. C. Zody,
E. S. Lander
[show abstract]
[hide abstract]
ABSTRACT: The sequence of the mouse genome is a key informational tool for understanding the contents of the human genome and a key experimental tool for biomedical research. Here, we report the results of an international collaboration to produce a high-quality draft sequence of the mouse genome. We also present an initial comparative analysis of the mouse and human genomes, describing some of the insights that can be gleaned from the two sequences. We discuss topics including the analysis of the evolutionary forces shaping the size, structure and sequence of the genomes; the conservation of large-scale synteny across most of the genomes; the much lower extent of sequence orthology covering less than half of the genomes; the proportions of the genomes under selection; the number of protein-coding genes; the expansion of gene families related to reproduction and immunity; the evolution of proteins; and the identification of intraspecies polymorphism.
Nature. 420(6915):520-62.
-
R. H. Waterston,
K. Lindblad-Toh,
E. Birney,
J. Rogers,
J. F. Abril,
P. Agarwal,
R. Agarwala,
R. Ainscough,
M. Alexandersson,
P. An, [......],
S. Williams,
R. K. Wilson,
E. Winter,
K. C. Worley,
D. Wyman,
S. Yang,
S. P. Yang,
E. M. Zdobnov,
M. C. Zody,
E. S. Lander
[show abstract]
[hide abstract]
ABSTRACT: The sequence of the mouse genome is a key informational tool for understanding the contents of the human genome and a key experimental tool for biomedical research. Here, we report the results of an international collaboration to produce a high-quality draft sequence of the mouse genome. We also present an initial comparative analysis of the mouse and human genomes, describing some of the insights that can be gleaned from the two sequences. We discuss topics including the analysis of the evolutionary forces shaping the size, structure and sequence of the genomes; the conservation of large-scale synteny across most of the genomes; the much lower extent of sequence orthology covering less than half of the genomes; the proportions of the genomes under selection; the number of protein-coding genes; the expansion of gene families related to reproduction and immunity; the evolution of proteins; and the identification of intraspecies polymorphism.
Nature. 420(6915):520-62.
-
E. S. Lander,
L. M. Linton,
B. Birren,
C. Nusbaum,
M. C. Zody,
J. Baldwin,
K. Devon,
K. Dewar,
M. Doyle,
W. FitzHugh, [......],
K. A. Wetterstrand,
A. Patrinos,
M. J. Morgan,
J. Szustakowki,
P. de Jong,
J. J. Catanese,
K. Osoegawa,
H. Shizuya,
S. Choi,
Y. J. Chen
[show abstract]
[hide abstract]
ABSTRACT: The human genome holds an extraordinary trove of information about human development, physiology, medicine and evolution. Here we report the results of an international collaboration to produce and make freely available a draft sequence of the human genome. We also present an initial analysis of the data, describing some of the insights that can be gleaned from the sequence.
Nature. 409(6822):860-921.
