Evolutionary genomics of pathogens

Laboratory of Evolutionary Genetics @UNINE

Publications

Preprints on BioRχiv
Preprints and datasets on Zenodo
Publications 2021 and in press

(lab members in bold)

Selected recent publications

Badet T, Fouché S, Hartmann FE, Zala M, Croll D. 2021. Machine-learning predicts genomic determinants of meiosis-driven structural variation in a eukaryotic pathogen. Nature Communications 12:3551. DOI (Open Access)

Stauber L, Thomas B, Feurtey A, Prospero S, Croll D. 2021. Emergence and diversification of a highly invasive chestnut pathogen lineage across south-eastern Europe. eLife 10:e56279. DOI (Open Access)

Dutta A, Hartmann FE, Sardinha Francisco C, McDonald BA, Croll D. 2021. Mapping the adaptive landscape of a major agricultural pathogen reveals evolutionary constraints across heterogeneous environments. The ISME Journal 15:1402–1419. DOI (Open Access)

Grossen C, Guillaume F, Keller LF, Croll D. 2020. Purging of highly deleterious mutations through severe bottlenecks in ibex. Nature Communications 11:1001. DOI (Open Access)

Fouche S, Badet T, Oggenfuss U, Plissonneau P, Sardinha Francisco C, Croll D. 2020. Stress-driven transposable element de-repression dynamics and virulence evolution in a fungal pathogen. Molecular Biology and Evolution 37(1):221–239. DOI. Free Access.

Sánchez-Vallet A, Fouché S, Fudal I, Hartmann FE, Soyer JL, Tellier A, Croll D. 2018. The Genome Biology of Effector Gene Evolution in Filamentous Plant Pathogens. Annual Review of Phytopathology 56:21-40. DOI. Free PDF

Hartmann FE, Croll D. 2018. Distinct Trajectories of Massive Recent Gene Gains and Losses in Populations of a Microbial Eukaryotic Pathogen. Molecular Biology and Evolution 34:2808-2822. DOI

Hartmann FE, Sanchez-Vallet A, McDonald BA, Croll D. 2017. A fungal wheat pathogen evolved host specialization by extensive chromosomal rearrangements. The ISME Journal 11:1189-1204. DOI


Preprints on BioRχiv

(manuscripts already published in a journal are only listed further down)

Tralamazza SM, Abraham L, Correa B, Croll D. Histone H3K27 methylation perturbs transcriptional robustness and underpins dispensability of highly conserved genes in fungi. DOI

Singh NK, Chanclud E, Croll D. Population-level deep sequencing reveals the interplay of clonal and sexual reproduction in the fungal wheat pathogen Zymoseptoria tritici. DOI

Oggenfuss U, Badet T, Wicker T, Hartmann FE, Kumar Singh N, Abraham LN, Karisto P, Vonlanthen T, Mundt CM, McDonald BA, Croll D. A population-level invasion by transposable elements triggers genome expansion in a fungal pathogen. DOI

Castroagudin V, Danelli A, Intra Moreira S, Teodora de Assis Reges J, Carvalho G, Nunes Maciel JL, Variani Bonato AL, Forcelini CA, Alves E, McDonald BA, Croll D, Ceresini P. The wheat blast pathogen Pyricularia graminis-tritici has complex origins and a disease cycle spanning multiple grass hosts. DOI


Preprints and datasets on Zenodo

Croll D. 2021. Whole-genome analyses of 286 Magnaporthe oryzae genomes suggest that an independent introduction of a global pandemic lineage is at the origin of the Zambia wheat blast outbreak. DOI

Temba et al. 2021. Multiplex amplicon sequencing dataset for genotyping pandemic populations of the wheat blast fungus. DOI

Mossion V, Croll D. 2021. A transcriptome for the early-branching fern Botrychium lunaria enables fine-grained resolution of population structure. DOI


Publications 2021 and in press

101. Mossion V, Dauphin B, Grant J, Zemp N, Croll D. A reference transcriptome for the early-branching fern Botrychium lunaria enables fine-grained resolution of population structure. Molecular Ecology Resources in press. DOI

100. Cadot S, Gfeller V, Hu L, Singh NK, Sanchez-Vallet A, Glauser G, Croll D, Erb M, van der Heijden M, Schlaeppi K. Soil composition and plant genotype determine benzoxazinoid-mediated plant-soil feedbacks in cereals. Plant, Cell & Environment in press. BioRχiv version: DOI

99. Kessler C, Brambilla A, Waldvogel D, Camenisch G, Biebach I, Leigh DM, Grossen C, Croll D. A robust sequencing assay of a thousand amplicons for the high-throughput population monitoring of Alpine ibex immunogenetics. Molecular Ecology Resources in press. DOI

98. Crous P, Lombard L, Sandoval-Denis M, …, Croll D, …, Thines M. Fusarium: more than a node or a foot-shaped basal cell. Studies in Mycology in press.

97. Badet T, Fouché S, Hartmann FE, Zala M, Croll D. Machine-learning predicts genomic determinants of meiosis-driven structural variation in a eukaryotic pathogen. Nature Communications 12:3551. DOI

96. Singh NK, Badet T, Abraham LN, Croll D. Rapid sequence evolution driven by transposable elements at a virulence locus in a fungal wheat pathogen. BMC Genomics 22:329. DOI

95. Dutta A, Croll D, McDonald BA, Krattinger SG. Genome-Wide Association Study Reveals Genetic Architecture of Septoria Tritici Blotch Resistance in a Historic Landrace Collection. Euphytica 217:108. DOI

94. Stauber L, Thomas B, Prospero S, Croll D. Emergence and diversification of a highly invasive chestnut pathogen lineage across south-eastern Europe. eLife 10:e56279. DOI

93. Hendier A, Chatelain C, Du Pasquier PE, Paris M, Ouattara K, Koné I, Croll D, Zuberbühler K. A new method to determine the diet of pygmy hippopotamus in Taï National Park, Côte d’Ivoire. African Journal of Ecology. DOI

92. Croll D, Crous PW, Pereira D, Mordecai EA, McDonald BA, Brunner PC. Genome-scale phylogenies reveal relationships among Parastagonospora species infecting domesticated and wild grasses. Persoonia DOI

91. Pereira D, Oggenfuss U, McDonald BA, Croll D. The population genomics of transposable element activation in the highly repressive genome of an agricultural pathogen. Microbial Genomics in press. BioRχiv version: DOI

90. Lorrain C, Oggenfuss U, Croll D, Duplessis S, Stukenbrock E. Transposable Elements in Fungi: Coevolution With the Host Genome Shapes Genome Architecture, Plasticity and Adaptation. Chapter in Encyclopedia of Mycology. Elsevier. ISBN 9780128199909. Link

89. Singh NK, Dutta A, Puccetti G, Croll D. Tackling microbial threats in agriculture with integrative imaging and computational approaches. Computational and Structural Biotechnology Journal 19:372-383. DOI (Open Access)

88. Dutta A, Hartmann FE, Sardinha Francisco C, McDonald BA, Croll D. Mapping the adaptive landscape of a major agricultural pathogen reveals evolutionary constraints across heterogeneous environments. The ISME Journal 15:1402–1419. DOI (Open Access)

87. Hartmann FE, Vonlanthen T, Singh NK, McDonald M, Milgate A, Croll D. The complex genomic basis of rapid convergent adaptation to pesticides across continents in a fungal plant pathogen. Molecular Ecology. DOI (Open Access)

86. Dutta A, Croll D, McDonald BA, Barrett LG. Maintenance of variation in virulence and reproduction in populations of an agricultural plant pathogen. Evolutionary Applications. DOI (Open Access)


2020

85. Pereira D, McDonald BA, Croll D. The genetic architecture of emerging fungicide resistance in populations of a global wheat pathogen. Genome Biology and Evolution 12(12):2231–2244. DOI (Open Access)

84. Stauber L, Prospero S, Croll D. Comparative genomics analyses of lifestyle transitions at the origin of an invasive fungal pathogen in the genus Cryphonectria. mSphere 5:e00737-20. DOI (Open Access)

83. Fokkens L+, Guo L+, Dora S, Wang B, Ye K*, Sanchez-Rodriguez C*, Croll D*. A chromosome-scale genome assembly for the Fusarium oxysporum strain Fo5176 to establish a model Arabidopsis-fungal pathosystem. G3: Genes|Genomes|Genetics 10(10):3549-3555. DOI (Open Access) +) joint first, *) joint senior/corresponding authors

82. Torres DE+, Oggenfuss U+, Croll D*, Seidl MF*. Genome evolution in fungal plant pathogens: looking beyond the two-speed genome model. Fungal Biology Reviews 34(3):136-143. DOI (Open Access). +) joint first, *) joint senior/corresponding authors

81. Vesga P, Flury P, Vacheron J, Keel C*, Croll D*, Maurhofer M*. Transcriptome plasticity underlying plant root colonization and insect invasion by Pseudomonas protegens. The ISME Journal 14:2766–2782. DOI (Open Access) *) joint senior/corresponding authors

80. Feurtey A, Lorrain C, Croll D, Eschenbrenner C, Freitag M, Habig M, Haueisen J, Moller M, Schotanus K, Stukenbrock EH. Genome compartmentalization predates species divergence in the plant pathogen genus Zymoseptoria. BMC Genomics 21(588). DOI (Open Access)

79. Sánchez-Vallet A, Tian H, Rodriguez-Moreno L, Valkenburg DJ, Saleem-Batcha R, Wawra S, Kombrink A, Verhage L, de Jonge R, van Esse HP, Zuccaro A, Croll D, Mesters JR, Thomma BPHJ. A secreted LysM effector protects fungal hyphae through chitin-dependent homodimer polymerization. PLOS Pathogens 16(6):e1008652. DOI (Open Access)

78. Badet T, Croll D. The rise and fall of genes: origins and functions of plant pathogen pangenomes. Current Opinion in Plant Biology 56:65-73. DOI (Open Access)

77. Aubry S, Reyes Avila SC, Croll D, Christ B. Omics-based detection, identification and quantification of GM food and feed: current challenges and perspectives. Chapter in Foodomics. Royal Society of Chemistry. ISBN 978-1-78801-884-5. Link

76. Pereira D, Croll D, Brunner P, McDonald BA. Natural selection drives population divergence for local adaptation in a wheat pathogen. Fungal Genetics & Biology 141:103398. DOI

75. Heinzelmann R, Rigling R, Sipos G, Münsterkötter M, Croll D. Chromosomal assembly and analyses of genome-wide recombination rates in the forest pathogenic fungus Armillaria ostoyae. Heredity 124:699–713. DOI

74. Grossen C, Guillaume F, Keller LF, Croll D. Purging of highly deleterious mutations through severe bottlenecks in ibex. Nature Communications 11:1001. DOI (Open Access)

73. Badet T, Oggenfuss U, Abraham LN, McDonald BA, Croll D. A 19-isolate reference-quality global pangenome for the fungal wheat pathogen Zymoseptoria tritici. BMC Biology 18:12. DOI (Open Access)

72. Fouche S, Badet T, Oggenfuss U, Plissonneau P, Sardinha Francisco C, Croll D. Stress-driven transposable element de-repression dynamics and virulence evolution in a fungal pathogen. Molecular Biology and Evolution 37(1):221–239. DOI. Free Access.


2019

71. Tralamazza S, Oliveira Rocha L, Oggenfuss U, Correa B, Croll D. Complex evolutionary origins of specialized metabolite gene cluster diversity among the plant pathogenic fungi of the *Fusarium graminearum *species complex. Genome Biology and Evolution 11:3106–3122. DOI (Open Access)

70. Mohd-Assaad N, McDonald BA, Croll D. The emergence of the multi-species NIP1 effector in Rhynchosporium was accompanied by high rates of gene duplications and losses. Environmental Microbiology 21: 2677-2695. DOI

69. McDonald M, Renkin M, Spackman M, Orchard B, Croll D, Solomon P, Milgate A. Rapid parallel evolution of azole fungicide resistance in Australian populations of the wheat pathogen Zymoseptoria tritici. Applied and Environmental Microbiology 85(4):e01908-18. DOI

68. Gupta DR, Sarai CRA, Win J, Soanes DM, Ryder LS, Croll D, Bhattacharjee P, Hossain MS, Mahmud NU, Mehbub MS, Surovy MZ, Talbot NJ, Kamoun S, Islam I. Cautionary Notes on Use of the MoT3 Diagnostic Assay for Magnaporthe oryzae Wheat and Rice Blast Isolates. Phytopathology 109(4):504–508. DOI

67. Ceresini PC, Castroagudín VL, Rodrigues FA, Rios JA, Aucique-Pérez CE, Moreira SI, Croll D, Alves E, de Carvalho G, Nunes Maciel JL, McDonald BA. Wheat blast: from its origins in South America to its emergence as a global threat. Molecular Plant Pathology 20:155-172. DOI


2018

66. Attarian R, Hu G, Sánchez-León E, Caza M, Croll D, Do E, Bach H, Missall T, Lodge J, Jung WH, Kronstad J. The monothiol glutaredoxin Grx4 regulates iron homeostasis and virulence in Cryptococcus neoformans. mBio 9(6):e02377-18. DOI (Open Access)

65. Krishnan P, Meile L, Plissonneau C, Ma X, Hartmann FE, Croll D, McDonald BA, Sánchez-Vallet A. Transposable element insertions shape gene regulation and melanin production in a fungal pathogen of wheat. BMC Biology 16:78. DOI (Open Access)

64. Fouche S, Plissonneau C, McDonald BA, Croll D. Meiosis leads to pervasive copy-number variation and distorted inheritance of accessory chromosomes of the wheat pathogen Zymoseptoria tritici. Genome Biology and Evolution 10:1416–1429. DOI (Open Access)

63. Mohd-Assaad N, McDonald BA, Croll D. Genome-wide detection of genes under positive selection in worldwide populations of the barley scald pathogen. Genome Biology and Evolution 10:1315–1332. DOI (Open Access)

62. Hartmann FE, McDonald BA, Croll D. Genome-wide evidence for divergent selection between populations of a major agricultural pathogen. Molecular Ecology. 27:2725-2741. DOI

61. Sánchez-Vallet A, Fouché S, Fudal I, Hartmann FE, Soyer JL, Tellier A, Croll D. The Genome Biology of Effector Gene Evolution in Filamentous Plant Pathogens. Annual Review of Phytopathology 56:21-40. DOI. Free PDF

60. Ceresini PC, Castroagudín VL, Rodrigues FA, Rios JA, Aucique-Pérez CE, Moreira SI, Alves E, Croll D, Nunes Maciel JL. Wheat Blast: Past, Present, and Future. Annual Review of Phytopathology 56:427-456. DOI. Free PDF

59. Benevenuto J, Texeira-Silva NS, Kuramae EE, Croll D*, Vitorello CBM*. Comparative genomics of smut pathogens: insights from orphans and positively selected genes into host specialization. Frontiers in Microbiology 06 April. DOI (Open Access) *) joint senior/corresponding authors

58. Meile L, Croll D, Brunner PC, Plissonneau C, Hartmann FE, McDonald BA, Sanchez-Vallet* A. A fungal avirulence factor encoded in a highly plastic genomic region triggers partial resistance to septoria tritici blotch. New Phytologist 219:1048–1061. DOI

57. Schirrmann MK, Zoller S, Croll D, Stukenbrock EH, Leuchtmann A, Fior S. Genome-wide signatures of selection in Epichloë reveal candidate genes for host specialization. Molecular Ecology 27(15):3070-3086 DOI

56. Fouché S, Plissonneau C, Croll D. The birth and death of effectors in rapidly evolving filamentous pathogen genomes. Current Opinion in Microbiology 46:34-42. DOI PDF

55. Plissonneau C, Hartmann FE, Croll D. Pangenome analyses of the wheat pathogen Zymoseptoria tritici reveal the structural basis of a highly plastic eukaryotic genome. BMC Biology 16:5. DOI (Open Access)

54. Kretschmer M, Lambie S, Croll D, Kronstad JW. Acetate provokes mitochondrial stress and cell death in Ustilago maydis. Molecular Microbiology . 107:488-507. DOI

53. Sanchez-Vallet A, Hartmann FE, Marcel T, Croll D. Nature’s genetic screens: using genome-wide association studies for effector discovery. Molecular Plant Pathology . 19:3-6. DOI

52. Grossen C, Biebach I, Angelone-Alasaad S, Keller LF, Croll D. Population genomics analyses of European ibex species show lower diversity and higher inbreeding in reintroduced populations. Evolutionary Applications . 11:123–139. DOI

51. Stewart EL, Croll D, Lendenmann MH, Sanchez Vallet A, Hartmann FE, Palma Guerrero J, Ma X, McDonald BA. QTL mapping reveals complex genetic architecture of quantitative virulence in the wheat pathogen Zymoseptoria tritici. Molecular Plant Pathology 19:201-216. DOI


2017

50. Heinzelmann R, Croll D, Zoller S, Sipos G, Münsterkötter M, Güldener U, Rigling D. High-density genetic mapping identifies the genetic basis of a natural colony morphology mutant in the root rot pathogen Armillaria ostoyae. Fungal Genetics & Biology 108:44-54. DOI

49. Hartmann FE, Croll D. Distinct Trajectories of Massive Recent Gene Gains and Losses in Populations of a Microbial Eukaryotic Pathogen. Molecular Biology and Evolution 34:2808-2822. DOI

48. Plissonneau C, Benevenuto J, Mohd-Assaad N, Fouché S, Hartmann FE, Croll D. Using population and comparative genomics to understand the genetic basis of effector-driven fungal pathogen evolution. Frontiers in Plant Science 8:119. DOI PDF

47. Palma-Guerrero J, Ma X, Torriani SFF, Zala M, Francisco CS, Hartmann FE, Croll D, McDonald BA. Comparative transcriptome analyses in Zymoseptoria tritici reveal significant differences in gene expression among strains during plant infection. Molecular Plant-Microbe Interactions. 30:231-244. DOI

46. Zhong Z+, Marcel T+, Hartmann FE, Ma X, Plissonneau C, Zala M, Ducasse A, Confais J, Compain J, Lapalu N, Amselem J, McDonald BA, Croll D*, Palma-Guerrero J*. A small secreted protein in Zymoseptoria tritici is responsible for avirulence on wheat cultivars carrying the Stb6 resistance gene. New Phytologist 214:619-631 +) joint first authors *) joint senior/corresponding authors. DOI

45. Kokko H, Chaturvedi A, Croll D, Fischer MC, Guillaume F, Karrenberg S, Kerr B, Rolshausen G, Stapley J. Can evolution supply what ecology demands? Trends in Ecology & Evolution. 32:187-197. DOI

44. Hartmann FE, Sanchez-Vallet A, McDonald BA, Croll D. A fungal wheat pathogen evolved host specialization by extensive chromosomal rearrangements. The ISME Journal. 11:1189-1204. DOI

43. Croll D, McDonald BA. The genetic basis of local adaptation for pathogenic fungi in agricultural ecosystems. Molecular Ecology . 26:2027-2040. DOI

42. Kretschmer M, Croll D, Kronstad JW. Chloroplast-associated metabolic functions influence the susceptibility of maize to Ustilago maydis. Molecular Plant Pathology. 18:1210-1221. DOI

41. Kretschmer M, Croll D, Kronstad JW. Maize susceptibility to Ustilago maydis is influenced by genetic and chemical perturbation of carbohydrate allocation. Molecular Plant Pathology. 18:1222-1237. DOI

40. Lambie S, Kretschmer M, Croll D, Haslam TM, Kunst L, Klose J, Kronstad JW. The putative phospholipase Lip2 counteracts oxidative damage and influences the virulence of Ustilago maydis. Molecular Plant Pathology 18(2):210–221. DOI


2016

39. Mohd-Assaad N, McDonald BA, Croll D. Multi-locus resistance evolution to azole fungicides in fungal plant pathogen populations. Molecular Ecology 25:6124–6142 . DOI

38. Plissonneau C, Stürchler A, Croll D. The evolution of orphan regions in genomes of a fungal pathogen of wheat. mBio 7 (5):e01231-16. DOI PDF

37. Croll D. Evolution in the absence of sex: Ideas revisited in the post-genomics age. BioEssays 38 (12): 1191. DOI

36. Islam TM, Croll D, Gladieux P, Soanes DM, Persoons A, Bhattacharjee P, Hossain S, Gupta DR, Rahman M, Mahboob GM, Cook N, Salam MU, Surovy MZ, Sancho VB, Maciel JLN, Júnior AN, Castroagudín VL, de Assis Reges JT, Ceresini PC, Ravel S, Kellner R, Fournier E, Tharreau D, Lebrun MH, McDonald BA, Stitt T, Swan D, Talbot NJ, Saunders DGO, Win J, Kamoun S. Emergence of wheat blast in Bangladesh was caused by a South American lineage of Magnaporthe oryzae. BMC Biology 14:84. DOI

35. Croll D, Laine AL. What the population genetic structures of host and pathogen tell us about disease evolution. New Phytologist. 212 (3): 537–539. DOI

34. Grossen C, Seneviratne S, Croll D, Irwin DE. Strong reproductive isolation and narrow genomic tracts of differentiation among three woodpecker species in secondary contact. Molecular Ecology. 25 (17): 4247–4266. DOI

33. Palma-Guerrero J, Torriani SFF, Zala M, Carter D, Courbot M, Rudd JJ, McDonald BA, Croll D. Comparative transcriptome analyses of Zymoseptoria tritici strains show complex lifestyle transitions and intra-specific variability in transcription profiles. Molecular Plant Pathology. 17 (6): 845–859. DOI

32. Lendenmann M, Croll D, Palma-Guerrero J, Stewart E, McDonald BA. QTL Mapping of Temperature Sensitivity Reveals Candidate Genes for Thermal Adaptation and Growth Morphology in the Plant Pathogenic Fungus Zymoseptoria tritici. Heredity 116:384-394. DOI

31. Geddes JMH, Caza M, Croll D, Stoynov N, Foster LJ, Kronstad JW. Analysis of the Protein Kinase A-regulated proteome of Cryptococcus neoformans identifies a role for the ubiquitin-proteasome pathway in capsule formation. mBio 7 (1): e01862-15. DOI PDF


2015

30. Croll D, Lendenmann MH, Stewart E, McDonald BA. Impact of recombination hotspots on genome evolution of a fungal plant pathogen. Genetics 201(3):1213-1228. DOI

29. Geddes JMH, Croll D, Caza M, Stoynov N, Foster LJ, Kronstad JW. Secretome Profiling of Cryptococcus neoformans Reveals Regulation of a Subset of Virulence-Associated Proteins and Potential Biomarkers by Protein Kinase A. BMC Microbiology 15 (1):206. DOI PDF

28. Lendenmann MH, Croll D, McDonald BA. QTL Mapping of Fungicide Sensitivity Reveals Novel Genes and Pleiotropy with Melanization in the Pathogen Zymoseptoria tritici. Fungal Genetics & Biology 80:53-67. DOI

27. Jung WH, Croll D, Cho JH, Kim YR, Lee YW. Analysis of the Nasal Vestibule Mycobiome in Patients with Allergic Rhinitis. Mycoses 58 (3):167-172. DOI


2014

26. Lendenmann MH, Croll D, Stewart EL, McDonald BA. Quantitative Trait Locus Mapping of Melanization in the Plant Pathogenic Fungus Zymoseptoria tritici. G3:Genes|Genomes|Genetics 4(12):2519-2533.DOI PDF

25. Billmyre B, Croll D, Li W, Mieczkowski P, Carter DA, Cuomo C, Kronstad JW, Heitman J. Highly recombinant VGII Cryptococcus gattii population develops clonal outbreak clusters through both sexual macroevolution and asexual microevolution. **mBio **5 (4): e01494-14.DOI PDF

24. Grossen C, Keller L, Biebach I, The International Goat Genome Consortium, Croll D. Introgression from domestic goat generated variation at the major histocompatibility complex of Alpine ibex. PLoS Genetics 10(6):e1004438 DOI PDF

23. Brunner PC, Torriani SFF, Croll D, Stukenbrock EH, McDonald BA. Hitchhiking selection is driving intron gain in a pathogenic fungus. Molecular Biology and Evolution 31(7):1741-1749DOI

22. Stukenbrock E, Croll D. The evolving fungal genome. Fungal Biology Reviews 28:1-12DOI

21. Stefansson T, Willi Y, Croll D, McDonald BA. An assay for quantitative virulence in Rhynchosporium commune reveals an association between effector genotype and virulence. Plant Pathology 63:405-414. DOI

20. Croll D. Learn from the fungi: Adaptive evolution without sex in fungal pathogens. BioEssays 36:334 DOI


2013

19. Croll D, Zala M, McDonald BA. Breakage-fusion-bridge cycles and large insertions contribute to the rapid evolution of accessory chromosomes in a fungal pathogen. PLoS Genetics 9 (6):e1003567. DOI PDF

18. Brunner PC, Torriani SFF, Croll D, Stukenbrock EH, McDonald BA. Coevolution and life cycle specialization of plant cell wall degrading enzymes in a hemibiotrophic pathogen. Molecular Biology and Evolution 30:1337–1347. DOI

17. Drabešová J, Ryšánek P, Brunner PC, McDonald BA, Croll D. 2013. Population genetic structure of Mycosphaerella graminicola and Quinone Outside Inhibitor (QoI) resistance in the Czech Republic.** European Journal of Plant Pathology **135:211–224. DOI


2012

16. Croll D, McDonald BA. 2012. Intron gains and losses in the evolution of Fusarium and Cryptococcus fungi. Genome Biology and Evolution 4:1148-1161. DOI PDF

15. Ehinger M, Croll D, Koch AM, Sanders IR. 2012 . Significant genetic and phenotypic changes arising from clonal growth of a single spore of an arbuscular mycorrhizal fungus over multiple generations. New Phytologist 196:853-861. DOI

14. Croll D, McDonald BA. 2012 The accessory genome as a cradle for adaptive evolution in pathogens.** PLoS Pathogens** 8(4):e1002608. DOI PDF

13. Hofstetter V, Buyck B, Croll D, Viret O, Couloux A, Gindro K. 2012. What if esca disease of grapevine were not a fungal disease? Fungal Diversity 54:51-67. DOI

12. Tisserant E, Kohler A, Dozolme-Seddas P, Balestrini R, Benabdellah K, Colard A, Croll D, Da Silva C, Gomez SK, Koul R, et al. 2012. The transcriptome of the arbuscular mycorrhizal fungus Glomus intraradices (DAOM 197198) reveals functional tradeoffs in an obligate symbiont. New Phytologist 193:755-769. DOI


2011

11. Torriani SFF, Stukenbrock EH, Brunner PC, McDonald BA, Croll D. 2011. Evidence for Extensive Recent Intron Transposition in Closely Related Fungi. Current Biology 21:2017-2022. DOI

10. Stöck M, Croll D, Dumas Z, Biollay S, Wang J, Perrin N. 2011. A cryptic heterogametic transition revealed by sex-linked DNA markers in Palearctic green toads.** Journal Of Evolutionary Biology** 24:1064-1070. DOI


2010

9. Sanders IR, Croll D. 2010. Arbuscular mycorrhiza: the challenge to understand the genetics of the fungal partner. Annual Review of Genetics 44:271-292. DOI

8. Angelard C, Colard A, Niculita-Hirzel H, Croll D, Sanders IR. 2010. Segregation in a mycorrhizal fungus alters rice growth and symbiosis-specific gene transcription. Current Biology 20:1216-1221. DOI


2009

7. Croll D, Sanders IR. 2009. Recombination in Glomus intraradices, a supposed ancient asexual arbuscular mycorrhizal fungus. BMC Evolutionary Biology 9:13. DOI

6. Corradi N, Ruffner B, Croll D, Colard A, Horák A, Sanders IR. 2009. High-level molecular diversity of copper-zinc superoxide dismutase genes among and within species of arbuscular mycorrhizal fungi. Applied and Environmental Microbiology 75:1970-1978. DOI

5. Croll D, Giovannetti M, Koch AM, Sbrana C, Ehinger M, Lammers PJ, Sanders IR. 2009. Nonself vegetative fusion and genetic exchange in the arbuscular mycorrhizal fungus Glomus intraradices. New Phytologist 181:924-937. DOI


- 2008

4. Croll D, Corradi N, Gamper HA, Sanders IR. 2008. Multilocus genotyping of arbuscular mycorrhizal fungi and marker suitability for population genetics. New Phytologist 180:564-568. DOI

3. Croll D, Wille L, Gamper HA, Mathimaran N, Lammers PJ, Corradi N, Sanders IR. 2008. Genetic diversity and host plant preferences revealed by simple sequence repeat and mitochondrial markers in a population of the arbuscular mycorrhizal fungus Glomus intraradices. New Phytologist 178:672-687. DOI

2. Corradi N, Croll D, Colard A, Kuhn G, Ehinger M, Sanders IR. 2007. Gene copy number polymorphisms in an arbuscular mycorrhizal fungal population. Applied and Environmental Microbiology 73:366-369. DOI

1. Koch AM, Croll D, Sanders IR. 2006. Genetic variability in a population of arbuscular mycorrhizal fungi causes variation in plant growth. Ecology Letters 9:103-110. DOI