Open Access Highly Accessed Research article

Comparative genomics of emerging pathogens in the Candida glabrata clade

Toni Gabaldón113*, Tiphaine Martin2, Marina Marcet-Houben1, Pascal Durrens2, Monique Bolotin-Fukuhara3, Olivier Lespinet3, Sylvie Arnaise3, Stéphanie Boisnard3, Gabriela Aguileta1, Ralitsa Atanasova4, Christiane Bouchier5, Arnaud Couloux6, Sophie Creno5, Jose Almeida Cruz127, Hugo Devillers3, Adela Enache-Angoulvant113, Juliette Guitard4, Laure Jaouen3, Laurence Ma5, Christian Marck8, Cécile Neuvéglise9, Eric Pelletier6, Amélie Pinard3, Julie Poulain6, Julien Recoquillay3, Eric Westhof7, Patrick Wincker6, Bernard Dujon10, Christophe Hennequin4 and Cécile Fairhead3*

Author Affiliations

1 Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG) and UPF, Doctor Aiguader, 88, Barcelona, 08003, Spain

2 Université de Bordeaux 1, LaBRI, INRIA Bordeaux Sud-Ouest (MAGNOME), Talence, F-33405, France

3 Institut de Génétique et Microbiologie, UMR8621 CNRS-Université Paris Sud, Bât 400, UFR des Sciences, Orsay Cedex, F 91405, France

4 APHP, Hôpital St Antoine, Service de Parasitologie-Mycologie, and UMR S945, Inserm, Université P. M. Curie, Paris, France

5 Département Génomes et Génétique, Institut Pasteur, Plate-forme Génomique, rue du Dr. Roux, Paris, F-75015, France

6 CEA, IG, DSV, Genoscope, 2 rue Gaston Crémieux, Evry Cedex, 91057, France

7 Architecture et Réactivité de l‘ARN, Institut de Biologie Moléculaire et Cellulaire du CNRS, Université de Strasbourg, Strasbourg Cedex, F-67084, France

8 Institut de biologie et technologies de Saclay (iBiTec-S), Gif-sur-Yvette cedex, 91191, France

9 INRA, UMR 1319 Micalis, Thiverval-Grignon, F-78850, France

10 Institut Pasteur, Unité de Génétique moléculaires des levures, UMR3525 CNRS, UFR927, Université P. M. Curie, 25 rue du Docteur Roux, Paris Cedex15, F75724, France

11 APHP, Hôpital Bicêtre, Service de Microbiologie, Paris, France

12 Present adress: Champalimaud Foundation, Av. Brasília, Lisboa, 1400-038, Portugal

13 Comparative Genomics Group, CRG-Centre for Genomic Regulation, Doctor Aiguader, 88, Barcelona, 08003, Spain

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BMC Genomics 2013, 14:623  doi:10.1186/1471-2164-14-623

Published: 14 September 2013

Additional files

Additional file 1:

Assembly data.

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Additional file 2:

Flow cytometry of the Nakaseomyces. Species names are indicated above each panel. 1C, 2C, 4C indicate peaks corresponding to the DNA content of, respectively, one, two and four haploid genomes.

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Additional file 3:

Supplementary text containing additional results and references. Table S1. tRNA genes in the Nakaseomyces genomes. Table S2. GC inserts in the mitochondrial genomes of C. bracarensis and C. nivariensis.

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Additional file 4:

Pair-wise species identity between orthologous protein-coding genes. Each histogram represents the numbers of orthologous gene pairs according to their percentage of identity.

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Additional file 5:

Number of synteny blocks according to the mean length of synteny blocks. All pairwise comparisons of the genomes of the Nakaseomyces and S. cerevisiae (out-group) are shown. Genomes were divided into three groups according to their location in the phylogenetic tree (Figure 1): the ‘glabrata group’ (red); C. castellii and N. bacillisporus (green); S. cerevisiae (blue). Each dot corresponds to one pairwise comparison and is colored according to the groups of the two compared genomes.

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Additional file 6:

Alignment of putative Ho proteins. “LAGLIDADG” motifs and Nuclear Localization Signals are boxed.

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Additional file 7:

Histograms of Nakaseomyces genes according to the length of encoded proteins.

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Additional file 8:

Genes from S. cerevisiae that are absent from C. glabrata and their absence/presence in the Nakaseomyces.

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Additional file 9:

Glycolytic enzymes in the Nakaseomyces.

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Additional file 10:

The DAL cluster. The cluster from S. cerevisiae is shown at top. The cluster containing the additional DAL5 gene in C. castellii and N. bacillisporus is shown below, using the gene nomenclature from S. cerevisiae. In these two genomes, the cluster differs only by the synteny on the left. Genes are represented by arrows, genes in black are DAL genes.

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Additional file 11:

Duplicated ribosomal protein genes in the Nakaseomyces.

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Additional file 12:

Scenarios for positive selection tests.

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