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Complete DNA Sequence of Kuraishia capsulata Illustrates Novel Genomic Features among Budding Yeasts (Saccharomycotina)

The numerous yeast genome sequences presently available provide a rich source of information for functional as well as evolutionary genomics but unequally cover the large phylogenetic diversity of extant yeasts. We present here the complete sequence of the nuclear genome of the haploid-type strain o...

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Autores principales: Morales, Lucia, Noel, Benjamin, Porcel, Betina, Marcet-Houben, Marina, Hullo, Marie-Francoise, Sacerdot, Christine, Tekaia, Fredj, Leh-Louis, Véronique, Despons, Laurence, Khanna, Varun, Aury, Jean-Marc, Barbe, Valérie, Couloux, Arnaud, Labadie, Karen, Pelletier, Eric, Souciet, Jean-Luc, Boekhout, Teun, Gabaldon, Toni, Wincker, Patrick, Dujon, Bernard
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2013
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3879985/
https://www.ncbi.nlm.nih.gov/pubmed/24317973
http://dx.doi.org/10.1093/gbe/evt201
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author Morales, Lucia
Noel, Benjamin
Porcel, Betina
Marcet-Houben, Marina
Hullo, Marie-Francoise
Sacerdot, Christine
Tekaia, Fredj
Leh-Louis, Véronique
Despons, Laurence
Khanna, Varun
Aury, Jean-Marc
Barbe, Valérie
Couloux, Arnaud
Labadie, Karen
Pelletier, Eric
Souciet, Jean-Luc
Boekhout, Teun
Gabaldon, Toni
Wincker, Patrick
Dujon, Bernard
author_facet Morales, Lucia
Noel, Benjamin
Porcel, Betina
Marcet-Houben, Marina
Hullo, Marie-Francoise
Sacerdot, Christine
Tekaia, Fredj
Leh-Louis, Véronique
Despons, Laurence
Khanna, Varun
Aury, Jean-Marc
Barbe, Valérie
Couloux, Arnaud
Labadie, Karen
Pelletier, Eric
Souciet, Jean-Luc
Boekhout, Teun
Gabaldon, Toni
Wincker, Patrick
Dujon, Bernard
author_sort Morales, Lucia
collection PubMed
description The numerous yeast genome sequences presently available provide a rich source of information for functional as well as evolutionary genomics but unequally cover the large phylogenetic diversity of extant yeasts. We present here the complete sequence of the nuclear genome of the haploid-type strain of Kuraishia capsulata (CBS1993(T)), a nitrate-assimilating Saccharomycetales of uncertain taxonomy, isolated from tunnels of insect larvae underneath coniferous barks and characterized by its copious production of extracellular polysaccharides. The sequence is composed of seven scaffolds, one per chromosome, totaling 11.4 Mb and containing 6,029 protein-coding genes, ∼13.5% of which being interrupted by introns. This GC-rich yeast genome (45.7%) appears phylogenetically related with the few other nitrate-assimilating yeasts sequenced so far, Ogataea polymorpha, O. parapolymorpha, and Dekkera bruxellensis, with which it shares a very reduced number of tRNA genes, a novel tRNA sparing strategy, and a common nitrate assimilation cluster, three specific features to this group of yeasts. Centromeres were recognized in GC-poor troughs of each scaffold. The strain bears MAT alpha genes at a single MAT locus and presents a significant degree of conservation with Saccharomyces cerevisiae genes, suggesting that it can perform sexual cycles in nature, although genes involved in meiosis were not all recognized. The complete absence of conservation of synteny between K. capsulata and any other yeast genome described so far, including the three other nitrate-assimilating species, validates the interest of this species for long-range evolutionary genomic studies among Saccharomycotina yeasts.
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spelling pubmed-38799852014-01-03 Complete DNA Sequence of Kuraishia capsulata Illustrates Novel Genomic Features among Budding Yeasts (Saccharomycotina) Morales, Lucia Noel, Benjamin Porcel, Betina Marcet-Houben, Marina Hullo, Marie-Francoise Sacerdot, Christine Tekaia, Fredj Leh-Louis, Véronique Despons, Laurence Khanna, Varun Aury, Jean-Marc Barbe, Valérie Couloux, Arnaud Labadie, Karen Pelletier, Eric Souciet, Jean-Luc Boekhout, Teun Gabaldon, Toni Wincker, Patrick Dujon, Bernard Genome Biol Evol Research Article The numerous yeast genome sequences presently available provide a rich source of information for functional as well as evolutionary genomics but unequally cover the large phylogenetic diversity of extant yeasts. We present here the complete sequence of the nuclear genome of the haploid-type strain of Kuraishia capsulata (CBS1993(T)), a nitrate-assimilating Saccharomycetales of uncertain taxonomy, isolated from tunnels of insect larvae underneath coniferous barks and characterized by its copious production of extracellular polysaccharides. The sequence is composed of seven scaffolds, one per chromosome, totaling 11.4 Mb and containing 6,029 protein-coding genes, ∼13.5% of which being interrupted by introns. This GC-rich yeast genome (45.7%) appears phylogenetically related with the few other nitrate-assimilating yeasts sequenced so far, Ogataea polymorpha, O. parapolymorpha, and Dekkera bruxellensis, with which it shares a very reduced number of tRNA genes, a novel tRNA sparing strategy, and a common nitrate assimilation cluster, three specific features to this group of yeasts. Centromeres were recognized in GC-poor troughs of each scaffold. The strain bears MAT alpha genes at a single MAT locus and presents a significant degree of conservation with Saccharomyces cerevisiae genes, suggesting that it can perform sexual cycles in nature, although genes involved in meiosis were not all recognized. The complete absence of conservation of synteny between K. capsulata and any other yeast genome described so far, including the three other nitrate-assimilating species, validates the interest of this species for long-range evolutionary genomic studies among Saccharomycotina yeasts. Oxford University Press 2013 2013-12-06 /pmc/articles/PMC3879985/ /pubmed/24317973 http://dx.doi.org/10.1093/gbe/evt201 Text en © The Author(s) 2013. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. http://creativecommons.org/licenses/by-nc/3.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
spellingShingle Research Article
Morales, Lucia
Noel, Benjamin
Porcel, Betina
Marcet-Houben, Marina
Hullo, Marie-Francoise
Sacerdot, Christine
Tekaia, Fredj
Leh-Louis, Véronique
Despons, Laurence
Khanna, Varun
Aury, Jean-Marc
Barbe, Valérie
Couloux, Arnaud
Labadie, Karen
Pelletier, Eric
Souciet, Jean-Luc
Boekhout, Teun
Gabaldon, Toni
Wincker, Patrick
Dujon, Bernard
Complete DNA Sequence of Kuraishia capsulata Illustrates Novel Genomic Features among Budding Yeasts (Saccharomycotina)
title Complete DNA Sequence of Kuraishia capsulata Illustrates Novel Genomic Features among Budding Yeasts (Saccharomycotina)
title_full Complete DNA Sequence of Kuraishia capsulata Illustrates Novel Genomic Features among Budding Yeasts (Saccharomycotina)
title_fullStr Complete DNA Sequence of Kuraishia capsulata Illustrates Novel Genomic Features among Budding Yeasts (Saccharomycotina)
title_full_unstemmed Complete DNA Sequence of Kuraishia capsulata Illustrates Novel Genomic Features among Budding Yeasts (Saccharomycotina)
title_short Complete DNA Sequence of Kuraishia capsulata Illustrates Novel Genomic Features among Budding Yeasts (Saccharomycotina)
title_sort complete dna sequence of kuraishia capsulata illustrates novel genomic features among budding yeasts (saccharomycotina)
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3879985/
https://www.ncbi.nlm.nih.gov/pubmed/24317973
http://dx.doi.org/10.1093/gbe/evt201
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