Showing papers by "Kenneth H. Wolfe published in 2016"
Joint Genome Institute1, University College Dublin2, Universidade Federal de Minas Gerais3, Great Lakes Bioenergy Research Center4, Deutsche Sammlung von Mikroorganismen und Zellkulturen5, Vanderbilt University6, University of Wisconsin-Madison7, National Academy of Sciences of Ukraine8, Ohio State University9, Royal Netherlands Academy of Arts and Sciences10, National Center for Agricultural Utilization Research11, Louisiana State University12
TL;DR: The comparative genome analysis of 29 taxonomically and biotechnologically important yeasts, including 16 newly sequenced, enables correlation of genes to useful metabolic properties and showed the synteny of the mating-type locus to be conserved over a billion years of evolution.
Abstract: Ascomycete yeasts are metabolically diverse, with great potential for biotechnology. Here, we report the comparative genome analysis of 29 taxonomically and biotechnologically important yeasts, including 16 newly sequenced. We identify a genetic code change, CUG-Ala, in Pachysolen tannophilus in the clade sister to the known CUG-Ser clade. Our well-resolved yeast phylogeny shows that some traits, such as methylotrophy, are restricted to single clades, whereas others, such as l-rhamnose utilization, have patchy phylogenetic distributions. Gene clusters, with variable organization and distribution, encode many pathways of interest. Genomics can predict some biochemical traits precisely, but the genomic basis of others, such as xylose utilization, remains unresolved. Our data also provide insight into early evolution of ascomycetes. We document the loss of H3K9me2/3 heterochromatin, the origin of ascomycete mating-type switching, and panascomycete synteny at the MAT locus. These data and analyses will facilitate the engineering of efficient biosynthetic and degradative pathways and gateways for genomic manipulation.
273 citations
TL;DR: The genome sequences of 27 isolates of the pathogenic yeast Candida orthopsilosis are reported, finding that most isolates are diploid hybrids, products of mating between two unknown parental species (A and B) that are 5% divergent in sequence.
Abstract: Mating between different species produces hybrids that are usually asexual and stuck as diploids, but can also lead to the formation of new species. Here, we report the genome sequences of 27 isolates of the pathogenic yeast Candida orthopsilosis. We find that most isolates are diploid hybrids, products of mating between two unknown parental species (A and B) that are 5% divergent in sequence. Isolates vary greatly in the extent of homogenization between A and B, making their genomes a mosaic of highly heterozygous regions interspersed with homozygous regions. Separate phylogenetic analyses of SNPs in the A- and B-derived portions of the genome produces almost identical trees of the isolates with four major clades. However, the presence of two mutually exclusive genotype combinations at the mating type locus, and recombinant mitochondrial genomes diagnostic of inter-clade mating, shows that the species C. orthopsilosis does not have a single evolutionary origin but was created at least four times by separate interspecies hybridizations between parents A and B. Older hybrids have lost more heterozygosity. We also identify two isolates with homozygous genomes derived exclusively from parent A, which are pure non-hybrid strains. The parallel emergence of the same hybrid species from multiple independent hybridization events is common in plant evolution, but is much less documented in pathogenic fungi.
64 citations
TL;DR: It is reported that centromeres of the methylotrophic yeast Komagataella phaffii (formerly called Pichia pastoris) are structurally defined, demonstrating that evolutionary transitions in centromere organization have occurred in multiple yeast clades.
Abstract: Centromere organization has evolved dramatically in one clade of fungi, the Saccharomycotina. These yeasts have lost the ability to make normal eukaryotic heterochromatin with histone H3K9 methylation, which is a major component of pericentromeric regions in other eukaryotes. Following this loss, several different types of centromere emerged, including two types of sequence-defined ("point") centromeres, and the epigenetically defined "small regional" centromeres of Candida albicans Here we report that centromeres of the methylotrophic yeast Komagataella phaffii (formerly called Pichia pastoris) are structurally defined. Each of its four centromeres consists of a 2-kb inverted repeat (IR) flanking a 1-kb central core (mid) region. The four centromeres are unrelated in sequence. CenH3 (Cse4) binds strongly to the cores, with a decreasing gradient along the IRs. This mode of organization resembles Schizosaccharomyces pombe centromeres but is much more compact and lacks the extensive flanking heterochromatic otr repeats. Different isolates of K. phaffii show polymorphism for the orientation of the mid regions, due to recombination in the IRs. CEN4 is located within a 138-kb region that changes orientation during mating-type switching, but switching does not induce recombination of centromeric IRs. Our results demonstrate that evolutionary transitions in centromere organization have occurred in multiple yeast clades.
40 citations
TL;DR: This minireview highlights the contributions of the late Austin L. Hughes to two areas of molecular evolution: the role of positive (Darwinian) selection, and the impact of gene duplications during genome evolution.
Abstract: In this minireview, we highlight the contributions of the late Austin L. Hughes to two areas of molecular evolution: the role of positive (Darwinian) selection, and the impact of gene duplications during genome evolution.
5 citations
TL;DR: This research presents a novel probabilistic approach to estimating the response of the immune system to laser-spot assisted, 3D image analysis of central nervous system injury.
Abstract: There is an error in the Data Availability Statement. Specifically, the accession number PRJNA238968 is obsolete, and the accession number PRJEB1698 should be used to access the sequencing data deposited in the EBI-ENA database (http://www.ebi.ac.uk/ena/data/view/PRJEB1698).
4 citations
TL;DR: It is reported that centromeres of the methylotrophic yeast Komagataella phaffii (formerly called Pichia pastoris) are structurally-defined, and this mode of organization resembles Schizosaccharomyces pombe centromres but is much more compact and lacks the extensive flanking heterochromatic otr repeats.
Abstract: Centromere organization has evolved dramatically in one clade of fungi, the Saccharomycotina. These yeasts have lost the ability to make normal eukaryotic heterochromatin with histone H3K9 methylation, which is a major component of pericentromeric regions in other eukaryotes. Following this loss, several different types of centromere emerged, including two types of sequence-defined ("point") centromeres, and the epigenetically-defined "small regional" centromeres of Candida albicans. Here we report that centromeres of the methylotrophic yeast Komagataella phaffii (formerly called Pichia pastoris) are structurally-defined. Each of its four centromeres consists of a 2-kb inverted repeat (IR) flanking a 1-kb central core (mid) region. The four centromeres are unrelated in sequence. CenH3 (Cse4) binds strongly to the cores, with a decreasing gradient along the IRs. This mode of organization resembles Schizosaccharomyces pombe centromeres but is much more compact and lacks the extensive flanking heterochromatic otr repeats. Different isolates of K. phaffii show polymorphism for the orientation of the mid regions, due to recombination in the IRs. CEN4 is located within a 138-kb region that changes orientation during mating-type switching, but switching does not induce recombination of centromeric IRs. The existing genetic toolbox for K. phaffii should facilitate analysis of the relationship between the IRs and the establishment and maintenance of centromeres in this species.
3 citations