ORCID Profile
0000-0002-2316-1005
Current Organisation
Inria Centre de recherche Bordeaux Sud-Ouest
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Publisher: Elsevier BV
Date: 08-2011
DOI: 10.1016/J.CRVI.2011.05.004
Abstract: The Génolevures online database (URL: www.genolevures.org) stores and provides the data and results obtained by the Génolevures Consortium through several c aigns of genome annotation of the yeasts in the Saccharomycotina subphylum (hemiascomycetes). This database is dedicated to large-scale comparison of these genomes, storing not only the different chromosomal elements detected in the sequences, but also the logical relations between them. The database is ided into a public part, accessible to anyone through Internet, and a private part where the Consortium members make genome annotations with our Magus annotation system this system is used to annotate several related genomes in parallel. The public database is widely consulted and offers structured data, organized using a REST web site architecture that allows for automated requests. The implementation of the database, as well as its associated tools and methods, is evolving to cope with the influx of genome sequences produced by Next Generation Sequencing (NGS).
Publisher: Oxford University Press (OUP)
Date: 16-11-2008
DOI: 10.1093/NAR/GKN859
Publisher: Cold Spring Harbor Laboratory
Date: 12-06-2009
Abstract: Our knowledge of yeast genomes remains largely dominated by the extensive studies on Saccharomyces cerevisiae and the consequences of its ancestral duplication, leaving the evolution of the entire class of hemiascomycetes only partly explored. We concentrate here on five species of Saccharomycetaceae , a large sub ision of hemiascomycetes, that we call “protoploid” because they erged from the S. cerevisiae lineage prior to its genome duplication. We determined the complete genome sequences of three of these species: Kluyveromyces (Lachancea) thermotolerans and Saccharomyces (Lachancea) kluyveri (two members of the newly described Lachancea clade), and Zygosaccharomyces rouxii . We included in our comparisons the previously available sequences of Kluyveromyces lactis and Ashbya ( Eremothecium) gossypii . Despite their broad evolutionary range and significant in idual variations in each lineage, the five protoploid Saccharomycetaceae share a core repertoire of approximately 3300 protein families and a high degree of conserved synteny. Synteny blocks were used to define gene orthology and to infer ancestors. Far from representing minimal genomes without redundancy, the five protoploid yeasts contain numerous copies of paralogous genes, either dispersed or in tandem arrays, that, altogether, constitute a third of each genome. Ancient, conserved paralogs as well as novel, lineage-specific paralogs were identified.
Publisher: Oxford University Press (OUP)
Date: 12-2014
DOI: 10.1093/GBE/EVU251
Location: France
No related grants have been discovered for David James Sherman.