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The genome of the filamentous fungus Ashbya gossypii: annotation and evolutionary implications

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Comparative Genomics

Part of the book series: Topics in Current Genetics ((TCG,volume 15))

Abstract

The 9.2 Mb genome of the filamentous fungus Ashbya gossypii consists of seven chromosomes carrying 4718 protein coding genes, 194 tRNA genes, at least 60 small RNA genes, and 40-50 copies of rRNA genes. With respect to both, the size and the number of genes, this presently represents the smallest known genome of a free-living eukaryote. Over 95% of the A. gossypii open reading frames encode proteins with homology to Saccharomyces cerevisiae proteins. In addition, 90% of A. gossypii genes show both, homology and a particular pattern of synteny (conservation of gene order), with the genome of budding yeast. Gene orders in the two species are not strictly co-linear because individual clusters of A. gossypii genes are always syntenic to two distinct S. cerevisiae chromosomal regions but frequently homologous genes are missing in either of the two regions. These gene clusters of ancient synteny (CLAS) were found to cover over 90% of both genomes. Specifically, 95% of the S. cerevisiae genes can be paired in duplicate blocks that match the gene order of single A. gossypii gene groups. The almost complete coverage of both genomes by clusters of ancient synteny provides compelling evidence that both species originate from a common ancestor and that the evolution of S. cerevisiae included a whole genome duplication subsequently followed by random deletions of one gene copy in 90% of the duplicated genes. The alignment of both genomes revealed a complete list of the 10% still remaining duplicated genes (twin genes) in today’s genome of S. cerevisiae. The analysis of this comprehensive set of ancient twin genes in S. cerevisiae suggests that their evolution is asynchronous. Finally, interpretation of the synteny pattern between the sixteen S. cerevisiae centromere regions and the homologous gene regions in A. gossypii suggests that the common ancestor of the two species most likely carried eight chromosomes. The postulated reduction to seven chromosomes in the A. gossypii lineage very likely marked a key event in the development of this filamentous yeast as a novel species.

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  1. Biozentrum Universität Basel, Klingelbergstrasse 50, CH-4056 Basel, Switzerland

    Sophie Brachat, Fred Dietrich, Sylvia Voegeli & Peter Philippsen

  2. Novartis-Pharma (Basel),  

    Sophie Brachat

  3. Department of Molecular Genetics and Microbiology, Duke University, Medical Center, Research Drive, Durham, NC 27710, USA

    Fred Dietrich

  4. Syngenta Biotechnology Inc., 3054 Cornwallis Road, Research Triangle Park, NC 27709, USA

    Tom Gaffney

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Brachat, S., Dietrich, F., Voegeli, S., Gaffney, T., Philippsen, P. The genome of the filamentous fungus Ashbya gossypii: annotation and evolutionary implications. In: Sunnerhagen, P., Piskur, J. (eds) Comparative Genomics. Topics in Current Genetics, vol 15. Springer, Berlin, Heidelberg. https://doi.org/10.1007/4735_114

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