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1.
Eukaryot Cell ; 9(3): 449-59, 2010 Mar.
Artículo en Inglés | MEDLINE | ID: mdl-20048048

RESUMEN

Debaryomyces hansenii, a yeast that participates in the elaboration of foodstuff, displays important genetic diversity. Our recent phylogenetic classification of this species led to the subdivision of the species into three distinct clades. D. hansenii harbors the highest number of nuclear mitochondrial DNA (NUMT) insertions known so far for hemiascomycetous yeasts. Here we assessed the intraspecific variability of the NUMTs in this species by testing their presence/absence first in 28 strains, with 21 loci previously detected in the completely sequenced strain CBS 767(T), and second in a larger panel of 77 strains, with 8 most informative loci. We were able for the first time to structure populations in D. hansenii, although we observed little NUMT insertion variability within the clades. We determined the chronology of the NUMT insertions, which turned out to correlate with the previously defined taxonomy and provided additional evidence that colonization of nuclear genomes by mitochondrial DNA is a dynamic process in yeast. In combination with flow cytometry experiments, the NUMT analysis revealed the existence of both haploid and diploid strains, the latter being heterozygous and resulting from at least four crosses among strains from the various clades. As in the diploid pathogen Candida albicans, to which D. hansenii is phylogenetically related, we observed a differential loss of heterozygosity in the diploid strains, which can explain some of the large genetic diversity found in D. hansenii over the years.


Asunto(s)
ADN Mitocondrial/genética , Debaryomyces/genética , Diploidia , Genoma Fúngico/genética , Pérdida de Heterocigocidad/genética , Mutagénesis Insercional/genética , Polimorfismo Genético/genética , Secuencia de Bases/genética , Cromosomas Fúngicos/genética , ADN de Hongos/genética , Debaryomyces/clasificación , Evolución Molecular , Componentes Genómicos/genética , Haploidia , Heterocigoto , Datos de Secuencia Molecular , Plásmidos/genética , Reacción en Cadena de la Polimerasa , Homología de Secuencia de Ácido Nucleico
2.
Nature ; 430(6995): 35-44, 2004 Jul 01.
Artículo en Inglés | MEDLINE | ID: mdl-15229592

RESUMEN

Identifying the mechanisms of eukaryotic genome evolution by comparative genomics is often complicated by the multiplicity of events that have taken place throughout the history of individual lineages, leaving only distorted and superimposed traces in the genome of each living organism. The hemiascomycete yeasts, with their compact genomes, similar lifestyle and distinct sexual and physiological properties, provide a unique opportunity to explore such mechanisms. We present here the complete, assembled genome sequences of four yeast species, selected to represent a broad evolutionary range within a single eukaryotic phylum, that after analysis proved to be molecularly as diverse as the entire phylum of chordates. A total of approximately 24,200 novel genes were identified, the translation products of which were classified together with Saccharomyces cerevisiae proteins into about 4,700 families, forming the basis for interspecific comparisons. Analysis of chromosome maps and genome redundancies reveal that the different yeast lineages have evolved through a marked interplay between several distinct molecular mechanisms, including tandem gene repeat formation, segmental duplication, a massive genome duplication and extensive gene loss.


Asunto(s)
Evolución Molecular , Genes Fúngicos/genética , Genoma Fúngico , Levaduras/clasificación , Levaduras/genética , Cromosomas Fúngicos/genética , Secuencia Conservada/genética , Duplicación de Gen , Datos de Secuencia Molecular , ARN Ribosómico/genética , ARN de Transferencia/genética , Proteínas de Saccharomyces cerevisiae/genética , Sintenía/genética , Secuencias Repetidas en Tándem/genética
4.
FEMS Yeast Res ; 8(6): 846-57, 2008 Sep.
Artículo en Inglés | MEDLINE | ID: mdl-18673395

RESUMEN

Abstract Transfer of fragments of mtDNA to the nuclear genome is a general phenomenon that gives rise to NUMTs (NUclear sequences of MiTochondrial origin). We present here the first comparative analysis of the NUMT content of entirely sequenced species belonging to a monophyletic group, the hemiascomycetous yeasts (Candida glabrata, Kluyveromyces lactis, Kluyveromyces thermotolerans, Debaryomyces hansenii and Yarrowia lipolytica, along with the updated NUMT content of Saccharomyces cerevisiae). This study revealed a huge diversity in NUMT number and organization across the six species. Debaryomyces hansenii harbors the highest number of NUMTs (145), half of which are distributed in numerous large mosaics of up to eight NUMTs arising from multiple noncontiguous mtDNA fragments inserted at the same chromosomal locus. Most NUMTs, in all species, are found within intergenic regions including seven NUMTs in pseudogenes. However, five NUMTs overlap a gene, suggesting a positive impact of NUMTs on protein evolution. Contrary to the other species, K. lactis and K. thermotolerans harbor only a few diverged NUMTs, suggesting that mitochondrial transfer to the nuclear genome has decreased or ceased in these phylogenetic branches. The dynamics of NUMT acquisition and loss are illustrated here by their species-specific distribution.


Asunto(s)
Ascomicetos , Núcleo Celular/genética , ADN Mitocondrial/análisis , Variación Genética , Genoma Mitocondrial , Análisis de Secuencia de ADN , Ascomicetos/clasificación , Ascomicetos/genética , Secuencia de Bases , Genes Mitocondriales , Datos de Secuencia Molecular , Filogenia , Seudogenes , Especificidad de la Especie
5.
Genome Biol ; 5(9): R72, 2004.
Artículo en Inglés | MEDLINE | ID: mdl-15345056

RESUMEN

We have screened the genome of Saccharomyces cerevisiae for fragments that confer a growth-retardation phenotype when overexpressed in a multicopy plasmid with a tetracycline-regulatable (Tet-off) promoter. We selected 714 such fragments with a mean size of 700 base-pairs out of around 84,000 clones tested. These include 493 in-frame open reading frame fragments corresponding to 454 distinct genes (of which 91 are of unknown function), and 162 out-of-frame, antisense and intergenic genomic fragments, representing the largest collection of toxic inserts published so far in yeast.


Asunto(s)
Regulación Fúngica de la Expresión Génica/genética , Genoma Fúngico , Saccharomyces cerevisiae/crecimiento & desarrollo , Saccharomyces cerevisiae/genética , Clonación Molecular/métodos , ADN de Hongos/genética , Genes Fúngicos/genética , Genes Fúngicos/fisiología , Genes Letales/genética , Genes Supresores , Sistemas de Lectura Abierta/genética , Sistemas de Lectura Abierta/fisiología , Fenotipo , Sistemas de Lectura/genética , Transfección/métodos , Transgenes/fisiología
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