The
            <i>Ashbya gossypii</i>
            Genome as a Tool for Mapping the Ancient
            <i>Saccharomyces cerevisiae</i>
            Genome

Dietrich, Fred S.; Voegeli, Sylvia; Brachat, Sophie; Lerch, Anita; Gates, Krista; Steiner, Sabine; Mohr, C.; Pöhlmann, Rainer; Luedi, Philippe P.; Choi, Sangdun; Wing, Rod A.; Flavier, Albert; Gaffney, Thomas; Philippsen, Peter

doi:10.1126/science.1095781

Cited by 594 publications

(552 citation statements)

References 18 publications

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“…The filamentous fungus A. gossypii and the budding yeast S. cerevisiae have different life styles (see Supplementary Movie S1) despite very similar gene contents and conserved domain compositions of gene products (Dietrich et al, 2004). Both organisms can establish polar growth but in S. cerevisiae periods of growth alternate with cell divisions, whereas A. gossypii cells (hyphae) grow for unlimited periods without undergoing divisions.…”

Section: Discussionmentioning

confidence: 99%

“…Using FASTA database searches (Pearson, 1990), we identified three formin homology members in the genome of A. gossypii (Dietrich et al, 2004). By combining information from homology searches with synteny, these proteins can be categorized as follows: one syntenic homolog to the S. cerevisiae BNI1 gene (AFR669W, in the following referred to as AgBNI1) and one syntenic and one nonsyntenic, telomerelocated homolog to the S. cerevisiae BNR1 gene (AFR301C and AGL364C, referred to as AgBNR1 and AgBNR2, respectively).…”

Section: The a Gossypii Formin Family Membersmentioning

confidence: 99%

“…The ascomycete Ashbya gossypii shows all the hallmarks of fungal filamentous growth, including tip splitting, although its recently completed genome sequence reveals an evolutionary relation with the Saccharomyces cerevisiae genome (Dietrich et al, 2004). A. gossypii is amenable to functional genome analysis using gene targeting methods or autonomously replicating plasmids (Wright and Philippsen, 1991;Steiner and Philippsen, 1994;Steiner et al, 1995;, which have promoted functional analyses of polarity genes in this fungus.…”

Section: Introductionmentioning

confidence: 99%

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From Function to Shape: A Novel Role of a Formin in Morphogenesis of the FungusAshbya gossypii

Schmitz

Kaufmann

Köhli

et al. 2006

MBoC

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Morphogenesis of filamentous ascomycetes includes continuously elongating hyphae, frequently emerging lateral branches, and, under certain circumstances, symmetrically dividing hyphal tips. We identified the formin AgBni1p of the model fungus Ashbya gossypii as an essential factor in these processes. AgBni1p is an essential protein apparently lacking functional overlaps with the two additional A. gossypii formins that are nonessential. Agbni1 null mutants fail to develop hyphae and instead expand to potato-shaped giant cells, which lack actin cables and thus tip-directed transport of secretory vesicles. Consistent with the essential role in hyphal development, AgBni1p locates to tips, but not to septa. The presence of a diaphanous autoregulatory domain (DAD) indicates that the activation of AgBni1p depends on Rho-type GTPases. Deletion of this domain, which should render AgBni1p constitutively active, completely changes the branching pattern of young hyphae. New axes of polarity are no longer established subapically (lateral branching) but by symmetric divisions of hyphal tips (tip splitting). In wild-type hyphae, tip splitting is induced much later and only at much higher elongation speed. When GTP-locked Rho-type GTPases were tested, only the young hyphae with mutated AgCdc42p split at their tips, similar to the DAD deletion mutant. Two-hybrid experiments confirmed that AgBni1p interacts with GTP-bound AgCdc42p. These data suggest a pathway for transforming one axis into two new axes of polar growth, in which an increased activation of AgBni1p by a pulse of activated AgCdc42p stimulates additional actin cable formation and tip-directed vesicle transport, thus enlarging and ultimately splitting the polarity site.

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Section: Discussionmentioning

confidence: 99%

Section: The a Gossypii Formin Family Membersmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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From Function to Shape: A Novel Role of a Formin in Morphogenesis of the FungusAshbya gossypii

Schmitz

Kaufmann

Köhli

et al. 2006

MBoC

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“…In S. cerevisiae, 85% of the duplicate pairs that resulted from WGD 100 Mya are now deleted [28][29][30]. Similarly, only 13-18% of duplicated genes that remain in the Arabidopsis thaliana genome are considered to be the result of an old polyploidization or aneuploidization event at 170-300 Mya [31].…”

Section: Introductionmentioning

confidence: 99%

Timing and mechanism of ancient vertebrate genome duplications – the adventure of a hypothesis

2005

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“…It is a mild pathogen of cotton, and has been used industrially to produce high vitamin B 2 levels. The haploid genome sequence was recently completed (Dietrich et al 2004) (http://agd.unibas.ch/). Aspergillus nidulans is a common soil mold from the order Eurotiales.…”

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confidence: 99%

Highly efficient concerted evolution in the ribosomal DNA repeats: Total rDNA repeat variation revealed by whole-genome shotgun sequence data

Ganley¹,

Kobayashi²

2007

Genome Res.

328

268

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Repeat families within genomes are often maintained with similar sequences. Traditionally, this has been explained by concerted evolution, where repeats in an array evolve "in concert" with the same sequence via continual turnover of repeats by recombination. Another form of evolution, birth-and-death evolution, can also explain this pattern, although in this case selection is the critical force maintaining the repeats. The level of intragenomic variation is the key difference between these two forms of evolution. The prohibitive size and repetitive nature of large repeat arrays have made determination of the absolute level of intragenomic repeat variability difficult, thus there is little evidence to support concerted evolution over birth-and-death evolution for many large repeat arrays. Here we use whole-genome shotgun sequence data from the genome projects of five fungal species to reveal absolute levels of sequence variation within the ribosomal RNA gene repeats (rDNA). The level of sequence variation is remarkably low. Furthermore, the polymorphisms that are detected are not functionally constrained and seem to exist beneath the level of selection. These results suggest the rDNA is evolving via concerted evolution. Comparisons with a repeat array undergoing birth-and-death evolution provide a clear contrast in the level of repeat array variation between these two forms of evolution, confirming that the rDNA indeed does evolve via concerted evolution. These low levels of intra-genomic variation are consistent with a model of concerted evolution in which homogenization is very rapid and efficiently maintains highly similar repeat arrays.[Supplemental material is available online at www.genome.org.]Repetitive elements are an abundant feature of genomes (Britten and Kohne 1968) and play critical roles in cell biology, genome structure, and adaptive evolution (Andersson et al. 1998;Shapiro and von Sternberg 2005). In many cases, repeats from a repeat family are highly similar to one another within a genome, a pattern that persists through evolutionary time even though sequence differences are apparent between species (Brown et al. 1972). Thus, the repeats seem to be maintained as a coherent family. This pattern is contrary to the expectations of conventional evolution, where repeats are expected to evolve independently ( Fig. 1) and diverge with time. This unusual mode of evolution, where repeats within a genome are more similar to each other than they are to "orthologous" repeats in a related species, is defined as concerted evolution (Zimmer et al. 1980). The molecular process responsible for concerted evolution is known as homogenization (Dover 1982), and although not fully elucidated, is thought to involve continual turnover of repeat copies by unequal recombination (e.g., Smith 1973;Szostak and Wu 1980;Kobayashi et al. 1998). However, recent studies have shown that several repeat families previously thought to evolve by concerted evolution actually evolve via a different evolutionary process known as birth-...

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The Ashbya gossypii Genome as a Tool for Mapping the Ancient Saccharomyces cerevisiae Genome

Cited by 594 publications

References 18 publications

From Function to Shape: A Novel Role of a Formin in Morphogenesis of the FungusAshbya gossypii

From Function to Shape: A Novel Role of a Formin in Morphogenesis of the FungusAshbya gossypii

Timing and mechanism of ancient vertebrate genome duplications – the adventure of a hypothesis

Highly efficient concerted evolution in the ribosomal DNA repeats: Total rDNA repeat variation revealed by whole-genome shotgun sequence data

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