Gene flow contributes to diversification of the major fungal pathogen $Candida\ albicans$

Jeanne Ropars (1, 2) , Corinne Maufrais (3) , Dorothée Diogo (2) , Marina Marcet-Houben (4, 5) , Aurélie Perin (2) , Natacha Sertour (2) , Kevin Mosca (2) , Emmanuelle Permal (6) , Guillaume Laval (7, 3) , Christiane Bouchier (8, 9) , Laurence Ma (8, 9) , Katja Schwartz (10) , Kerstin Voelz (11) , Robin C May (11) , Julie Poulain (12, 13, 14) , Christophe Battail (12) , Patrick Wincker (12, 13, 14) , Andrew M Borman (15) , Anuradha Chowdhary (16) , Shangrong Fan (17) , Soo Hyun Kim (18) , Patrice Le Pape (19) , Orazio Romeo (20, 21) , Jong Hee Shin (18) , Toni Gabaldon (22, 23) , Gavin Sherlock (10) , Marie-Elisabeth Bougnoux (24, 25) , Christophe D'Enfert (2)

1 ESE - Ecologie Systématique et Evolution
2 BPF - Biologie et Pathogénicité fongiques
3 C3BI - Centre de Bioinformatique, Biostatistique et Biologie Intégrative
4 CRG-UPF - Center for Genomic Regulation
5 UPF - Universitat Pompeu Fabra [Barcelona]
6 URGI - Unité de Recherche Génomique Info
7 Génétique Evolutive Humaine - Human Evolutionary Genetics
8 Génomique (Plate-Forme) - Genomics Platform
9 CITECH - Centre de Recherche et Innovation Technologique
10 Stanford University
11 University of Birmingham [Birmingham]
12 JACOB - Institut de Biologie François JACOB
13 GENOSCOPE - Genoscope - Centre national de séquençage [Evry]
14 UMR 8030 - Génomique métabolique
15 Public Health England [London]
16 University of Delhi
17 Peking University [Beijing]
18 Chonnam National University [Gwangju]
19 IICiMed - Cibles et Médicaments des Infections et de l'Immunité
20 University of Messina
21 IRCCS Messina - Centro Neurolesi Bonino Pulejo Messina
22 CRG - Centro de Regulación Genómica
23 Department of Experimental and Health Sciences - ICREA Infection Biology Laboratory
24 UPD5 - Université Paris Descartes - Paris 5
25 CHU Necker - Enfants Malades [AP-HP]

Elucidating population structure and levels of genetic diversity and recombination is necessary to understand the evolution and adaptation of species. $Candida\ albicans$ is the second most frequent agent of human fungal infections worldwide, causing high-mortality rates. Here we present the genomic sequences of 182 C. $albicans$ isolates collected worldwide, including commensal isolates, as well as ones responsible for superficial and invasive infections, constituting the largest dataset to date for this major fungal pathogen. Although, C. $albicans$ shows a predominantly clonal population structure, we find evidence of gene flow between previously known and newly identified genetic clusters, supporting the occurrence of (para)sexuality in nature. A highly clonal lineage, which experimentally shows reduced fitness, has undergone pseudogenization in genes required for virulence and morphogenesis, which may explain its niche restriction. $Candida\ albicans$ thus takes advantage of both clonality and gene flow to diversify.

Keywords: Microbial genetics; Pathogens; Population genetics

Domains: Life Sciences [q-bio]; Life Sciences [q-bio]; Microbiology and Parasitology; Mycology

Jeanne Ropars, Corinne Maufrais, Dorothée Diogo, Marina Marcet-Houben, Aurélie Perin, et al.. Gene flow contributes to diversification of the major fungal pathogen $Candida\ albicans$. Nature Communications, 2018, 9 (1), pp.2253. ⟨10.1038/s41467-018-04787-4⟩. ⟨pasteur-01815656⟩