title: Comparative genomics of emerging pathogens in the Candida glabrata clade.
abstract: BACKGROUND
  Candida glabrata follows C. albicans as the second or third most prevalent cause of candidemia worldwide. These two pathogenic yeasts are distantly related, C. glabrata being part of the Nakaseomyces, a group more closely related to Saccharomyces cerevisiae. Although C. glabrata was thought to be the only pathogenic Nakaseomyces, two new pathogens have recently been described within this group: C. nivariensis and C. bracarensis. To gain insight into the genomic changes underlying the emergence of virulence, we sequenced the genomes of these two, and three other non-pathogenic Nakaseomyces, and compared them to other sequenced yeasts.
  
  
  RESULTS
  Our results indicate that the two new pathogens are more closely related to the non-pathogenic N. delphensis than to C. glabrata. We uncover duplications and accelerated evolution that specifically affected genes in the lineage preceding the group containing N. delphensis and the three pathogens, which may provide clues to the higher propensity of this group to infect humans. Finally, the number of Epa-like adhesins is specifically enriched in the pathogens, particularly in C. glabrata.
  
  
  CONCLUSIONS
  Remarkably, some features thought to be the result of adaptation of C. glabrata to a pathogenic lifestyle, are present throughout the Nakaseomyces, indicating these are rather ancient adaptations to other environments. Phylogeny suggests that human pathogenesis evolved several times, independently within the clade. The expansion of the EPA gene family in pathogens establishes an evolutionary link between adhesion and virulence phenotypes. Our analyses thus shed light onto the relationships between virulence and the recent genomic changes that occurred within the Nakaseomyces.
  Nakaseomyces delphensis: CAPT01000001 to CAPT01000179Candida bracarensis: CAPU01000001 to CAPU01000251Candida nivariensis: CAPV01000001 to CAPV01000123Candida castellii: CAPW01000001 to CAPW01000101Nakaseomyces bacillisporus: CAPX01000001 to CAPX01000186.
authors.affiliation: Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG) and UPF, Doctor Aiguader, 88, Barcelona, 08003, Spain. toni.gabaldon@crg.eu.
authors.forename: Toni
authors.initials: T
authors.lastname: Gabaldón
authors.forename: Tiphaine
authors.initials: T
authors.lastname: Martin
authors.forename: Marina
authors.initials: M
authors.lastname: Marcet-Houben
authors.forename: Pascal
authors.initials: P
authors.lastname: Durrens
authors.forename: Monique
authors.initials: M
authors.lastname: Bolotin-Fukuhara
authors.forename: Olivier
authors.initials: O
authors.lastname: Lespinet
authors.forename: Sylvie
authors.initials: S
authors.lastname: Arnaise
authors.forename: Stéphanie
authors.initials: S
authors.lastname: Boisnard
authors.forename: Gabriela
authors.initials: G
authors.lastname: Aguileta
authors.forename: Ralitsa
authors.initials: R
authors.lastname: Atanasova
authors.forename: Christiane
authors.initials: C
authors.lastname: Bouchier
authors.forename: Arnaud
authors.initials: A
authors.lastname: Couloux
authors.forename: Sophie
authors.initials: S
authors.lastname: Creno
authors.forename: Jose
authors.initials: J
authors.lastname: Almeida Cruz
authors.forename: Hugo
authors.initials: H
authors.lastname: Devillers
authors.forename: Adela
authors.initials: A
authors.lastname: Enache-Angoulvant
authors.forename: Juliette
authors.initials: J
authors.lastname: Guitard
authors.forename: Laure
authors.initials: L
authors.lastname: Jaouen
authors.forename: Laurence
authors.initials: L
authors.lastname: Ma
authors.forename: Christian
authors.initials: C
authors.lastname: Marck
authors.forename: Cécile
authors.initials: C
authors.lastname: Neuvéglise
authors.forename: Eric
authors.initials: E
authors.lastname: Pelletier
authors.forename: Amélie
authors.initials: A
authors.lastname: Pinard
authors.forename: Julie
authors.initials: J
authors.lastname: Poulain
authors.forename: Julien
authors.initials: J
authors.lastname: Recoquillay
authors.forename: Eric
authors.initials: E
authors.lastname: Westhof
authors.forename: Patrick
authors.initials: P
authors.lastname: Wincker
authors.forename: Bernard
authors.initials: B
authors.lastname: Dujon
authors.forename: Christophe
authors.initials: C
authors.lastname: Hennequin
authors.forename: Cécile
authors.initials: C
authors.lastname: Fairhead
mesh_terms: D041221:Candida glabrata / Q000145:classification* / Q000235:genetics; D004271:DNA, Fungal / Q000235:genetics; D019143:Evolution, Molecular; D016681:Genome, Fungal; D010802:Phylogeny; D004718:Saccharomycetales / Q000145:classification* / Q000235:genetics; D012641:Selection, Genetic; D017422:Sequence Analysis, DNA
chemical_list: D004271:DNA, Fungal
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