Genomic Exploration of the Hemiascomycetous Yeasts: 2. Data generation and processing

Artiguenave, François; Wincker, Patrick; Brottier, Phillippe; Duprat, Simone; Jovelin, Fabien; Scarpelli, Claude; Verdier, Jean; Vico, Virginie; Weissenbach, Jean; Saurin, William

doi:10.1016/s0014-5793(00)02273-0

Cited by 48 publications

(35 citation statements)

References 10 publications

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“…Plasmid puri¢cation, sequencing reactions and sequence data processing were performed as described [12]. S. kluyveri RSTs were compared with S. cerevisiae predicted open reading frame (ORF) products, and with all available predicted proteomes as well as with a ¢ltered SwissProt database as described [13].…”

Section: Sequencing Strategy Rst Analysis and Annotationmentioning

confidence: 99%

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Genomic Exploration of the Hemiascomycetous Yeasts: 9. Saccharomyces kluyveri

et al. 2000

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The genome of Saccharomyces kluyveri was explored through 2528 random sequence tags with an average length of 981 bp. The complete nuclear ribosomal DNA unit was found to be 8656 bp in length. Sequences homologous to retroelements of the gypsy and copia types were identified as well as numerous solo long terminal repeats. We identified at least 1406 genes homologous to Saccharomyces cerevisiae open reading frames, with on average 58.1% and 72.4% amino acid identity and similarity, respectively. In addition, by comparison with completely sequenced genomes and the SwissProt database, we found 27 novel S. kluyveri genes. Most of these genes belong to pathways or have functions absent from S. cerevisiae, such as the catabolic pathway of purines or pyrimidines, melibiose fermentation, sorbitol utilization, or degradation of pollutants. The sequences are deposited in EMBL under the accession numbers AL404849^AL407376. ß

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Section: Sequencing Strategy Rst Analysis and Annotationmentioning

confidence: 99%

“…Most inserts (1213) were sequenced for both ends [12]. The average size of the inserts is 4.21 þ 1.29 kb.…”

Section: Properties Of the Dna Librarymentioning

confidence: 99%

Genomic Exploration of the Hemiascomycetous Yeasts: 9. Saccharomyces kluyveri

et al. 2000

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“…Restriction fragments of 3^5 kb were size selected on a 1% agarose gel and puri¢ed using GeneClean II kit (Bio 101, USA). The pBAM3 vector [12] was digested with SmaI (Gibco BRL, USA) and dephosphorylated using alkaline phosphatase (Boehringer Mannheim, Germany). Vector (8 ng) and fragments (10^50 ng) were incubated overnight at 4³C with T4 DNA ligase (Gibco BRL, USA).…”

Section: Yeast Strainmentioning

confidence: 99%

“…A total number of 2570 random sequence tags (RSTs) (average size of 898 bp) were sequenced [12]. Overall, 1178 inserts were sequenced at both ends.…”

Section: Properties Of the Dna Library And Contigsmentioning

confidence: 99%

Genomic Exploration of the Hemiascomycetous Yeasts: 7. Saccharomyces servazzii

Casarégola¹,

Lépingle²,

Bon³

et al. 2000

FEBS Letters

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The genome of Saccharomyces servazzii was analyzed with 2570 random sequence tags totalling 2.3 Mb. BLASTX comparisons revealed a minimum of 1420 putative open reading frames with significant homology to Saccharomyces cerevisiae (58% aa identity on average), two with Schizosaccharomyces pombe and one with a human protein, confirming that S. servazzii is closely related to S. cerevisiae. About 25% of the S. servazzii genes were identified, assuming that the gene complement is identical in both yeasts. S. servazzii carries very few transposable elements related to Ty elements in S. cerevisiae. Most of the mitochondrial genes were identified in eight contigs altogether spanning 25 kb for a predicted size of 29 kb. A significant match with the Kluyveromyces lactis linear DNA plasmid pGKL-1 encoded RF4 killer protein suggests that a related plasmid exists in S. servazzii. The sequences have been deposited with EMBL under the accession numbers AL402279Â L404848. ß 2000 Federation of European Biochemical Societies. Published by Elsevier Science B.V. All rights reserved.

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“…A total of 5082 sequences were produced by GENOSCOPE [10], corresponding to a total amount of sequences of ca. 4.9 Mb (4.7 Mb correspond to nuclear DNA, with an average GC content of 47.6%).…”

Section: Characteristics Of the Sequences And Calculation Of The Genomentioning

confidence: 99%

Genomic Exploration of the Hemiascomycetous Yeasts: 13. Pichia angusta

et al. 2000

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As part of a comparative genomics project on 13 hemiascomycetous yeasts, the Pichia angusta type strain was studied using a partial random sequencing strategy. With coverage of 0.5 genome equivalents, about 2500 novel proteincoding genes were identified, probably corresponding to more than half of the P. angusta protein-coding genes, 6% of which do not have homologs in Saccharomyces cerevisiae. Some of them contain one or two introns, on average three times shorter than those in S. cerevisiae. We also identified 28 tRNA genes, a few retrotransposons similar to Ty5 of S. cerevisiae, solo long terminal repeats, the whole ribosomal DNA cluster, and segments of mitochondrial DNA. The P. angusta sequences were deposited in EMBL under the accession numbers AL430961 to AL436044. ß 2000 Federation of European Biochemical Societies. Published by Elsevier Science B.V. All rights reserved.

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Genomic Exploration of the Hemiascomycetous Yeasts: 2. Data generation and processing

Cited by 48 publications

References 10 publications

Genomic Exploration of the Hemiascomycetous Yeasts: 9. Saccharomyces kluyveri

Genomic Exploration of the Hemiascomycetous Yeasts: 9. Saccharomyces kluyveri

Genomic Exploration of the Hemiascomycetous Yeasts: 7. Saccharomyces servazzii

Genomic Exploration of the Hemiascomycetous Yeasts: 13. Pichia angusta

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