Browsing School of Genetics & Microbiology by Author "WOLFE, KENNETH"
Now showing items 1-20 of 23
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Additions, losses, and rearrangements on the evolutionary route from a reconstructed ancestor to the modern Saccharomyces cerevisiae genome.
GORDON, JONATHAN; BYRNE, KEVIN PATRICK; WOLFE, KENNETH (PLoS, 2009)Comparative genomics can be used to infer the history of genomic rearrangements that occurred during the evolution of a species. We used the principle of parsimony, applied to aligned synteny blocks from 11 yeast species, ... -
Changes in alternative splicing of human and mouse genes are accompanied by faster evolution of constitutive exons
WOLFE, KENNETH (Oxford University Press, 2005)Alternative splicing is known to be an important source of protein sequence variation, but its evolutionary impact has not been explored in detail. Studying alternative splicing requires extensive sampling of the transcriptome, ... -
Chromosomal G + C content evolution in yeasts: systematic interspecies differences, and GC-poor troughs at centromeres.
WOLFE, KENNETH (2010)The G + C content at synonymous codon positions (GC3s) in genes varies along chromosomes in most eukaryotes. In Saccharomyces cerevisiae, regions of high GC3s are correlated with recombination hot spots, probably due to ... -
Clusters of co-expressed genes in mammalian genomes are conserved by natural selection
WOLFE, KENNETH (Oxford University Press, 2005)Genes that belong to the same functional pathways are often packaged into operons in prokaryotes. However, aside from examples in nematode genomes, this form of transcriptional regulation appears to be absent in eukaryotes. ... -
Complete DNA sequences of the mitochondrial genomes of the pathogenic yeasts Candida orthopsilosis and Candida metapsilosis: Insight into the evolution of linear DNA genomes from mitochondrial telomere mutants.
WOLFE, KENNETH (Oxford University Press, 2006)We determined complete mitochondrial DNA sequences of the two yeast species, Candida orthopsilosis and Candida metapsilosis, and compared them with the linear mitochondrial genome of their close relative, C.parapsilosis. ... -
Elusive origins of the extra genes in Aspergillus oryzae
WOLFE, KENNETH (PLoS, 2008)The genome sequence of Aspergillus oryzae revealed unexpectedly that this species has approximately 20% more genes than its congeneric species A. nidulans and A. fumigatus. Where did these extra genes come from? Here, we ... -
Evidence for horizontal transfer of a secondary metabolite gene cluster between fungi
WOLFE, KENNETH (BioMed Central, 2008)Background Filamentous fungi synthesize many secondary metabolites and are rich in genes encoding proteins involved in their biosynthesis. Genes from the same pathway are often clustered and co-expressed in particular ... -
Evidence from comparative genomics for a complete sexual cycle in the "asexual" pathogenic yeast Candida glabrata
FARES, MARIO ALI; WOLFE, KENNETH (BioMed Central, 2003)BACKGROUND: Candida glabrata is a pathogenic yeast of increasing medical concern. It has been regarded as asexual since it was first described in 1917, yet phylogenetic analyses have revealed that it is more closely related ... -
Evolutionary Origins of the Fumonisin Secondary Metabolite Gene Cluster in Fusarium verticillioides and Aspergillus niger
WOLFE, KENNETH (SAGE-Hindawi, 2011)The secondary metabolite gene clusters of euascomycete fungi are among the largest known clusters of functionally related genes in eukaryotes. Most of these clusters are species specific or genus specific, and little is ... -
Fourfold faster rate of genome rearrangement in nematodes than in Drosophila
WOLFE, KENNETH (2002)We compared the genome of the nematode Caenorhabditis elegans to 13% of that of Caenorhabditis briggsae, identifying 252 conserved segments along their chromosomes. We detected 517 chromosomal rearrangements, with the ratio ... -
Functional Partitioning of Yeast Co-Expression Networks after Genome Duplication
WOLFE, KENNETH (Public Library of Science, 2006)Several species of yeast, including the baker?s yeast Saccharomyces cerevisiae, underwent a genome duplication roughly 100 million years ago. We analyze genetic networks whose members were involved in this duplication. ... -
Genome survey sequencing of the wine spoilage yeast Dekkera (Brettanomyces) bruxellensis.
WOLFE, KENNETH (American Society for Microbiology, 2007)The hemiascomycete yeast Dekkera bruxellensis, also known as Brettanomyces bruxellensis, is a major cause of wine spoilage worldwide. Wines infected with D. bruxellensis develop distinctive, unpleasant aromas due to volatile ... -
Genomic islands in the pathogenic filamentous fungus Aspergillus fumigatus
WOLFE, KENNETH (PLoS, 2008)We present the genome sequences of a new clinical isolate of the important human pathogen, Aspergillus fumigatus, A1163, and two closely related but rarely pathogenic species, Neosartorya fischeri NRRL181 and Aspergillus ... -
Increased glycolytic flux as an outcome of whole-genome duplication in yeast
WOLFE, KENNETH (BioMed Central, 2007)After whole-genome duplication (WGD), deletions return most loci to single copy. However, duplicate loci may survive through selection for increased dosage. Here, we show how the WGD increased copy number of some glycolytic ... -
Localized hypermutation and associated gene losses in legume chloroplast genomes
KAVANAGH, THOMAS; WOLFE, KENNETH; POWELL, ANTOINETTE (2010)Point mutations result from errors made during DNA replication or repair, so they are usually expected to be homogeneous across all regions of a genome. However, we have found a region of chloroplast DNA in plants related ... -
Mechanisms of Chromosome Number Evolution in Yeast
BYRNE, KEVIN PATRICK; WOLFE, KENNETH (PLoS, 2011)The whole-genome duplication (WGD) that occurred during yeast evolution changed the basal number of chromosomes from 8 to 16. However, the number of chromosomes in post-WGD species now ranges between 10 and 16, and the ... -
Multiple rounds of speciation associated with reciprocal gene loss in polyploid yeasts.
BYRNE, KEVIN PATRICK; WOLFE, KENNETH (2006)A whole-genome duplication occurred in a shared ancestor of the yeast species Saccharomyces cerevisiae, Saccharomyces castellii and Candida glabrata. Here we trace the subsequent losses of duplicated genes, and show that ... -
PubCrawler: keeping up comfortably with PubMed and GenBank
HOKAMP, KARSTEN; WOLFE, KENNETH (Oxford University Press, 2004)The free PubCrawler web service (http://www.pubcrawler.ie) has been operating for five years and so far has brought literature and sequence updates to over 22 000 users. It provides information on a personalized web page ... -
Rate asymmetry after genome duplication causes substantial long-branch attraction artifacts in the phylogeny of Saccharomyces species
WOLFE, KENNETH (Oxford University Press, 2006)Whole-genome duplication (WGD) produces sets of gene pairs that are all of the same age. We therefore expect that phylogenetic trees that relate these pairs to their orthologs in other species should show a single consistent ... -
SMURF: genomic mapping of fungal secondary metabolite clusters
WOLFE, KENNETH (2010)Fungi produce an impressive array of secondary metabolites (SMs) including mycotoxins, antibiotics and pharmaceuticals. The genes responsible for their biosynthesis, export, and transcriptional regulation are often found ...