The Genomic Aftermath of Hybridization in the Opportunistic Pathogen

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Human pathogens belong to different phylogenetic clades and it is clear that the ability to infect humans emerged several times independently. The sequencing and comparison of genomes from pathogenic and non-pathogenic species and strains paves the way to identify what genomic changes underlie the emergence of virulence. In this study we sequenced 11 globally-distributed clinical isolates of Candida metapsilosis, an emerging fungal pathogen of growing concern. We found that all isolates were the result of a single hybridization between two unidentified species, which points to hybridization as a mechanism for the origin of a virulent lineage. We found that the hybrids likely originated by sexual reproduction as they were diploids and retained genomic regions of opposite mating types. We reconstructed the aftermath of the genome merging by identifying where recombination led to the removal of one of the parental subgenomes. We finally compare the newly-sequenced genome with those of other pathogens from the Candida clade and establish global trends, such an enriched repertoire in cell-wall proteins in more virulent species. Our results provide insight into how hybridization may play a key role in the emergence of novel pathogenic lineages.

Vyšlo v časopise: The Genomic Aftermath of Hybridization in the Opportunistic Pathogen. PLoS Genet 11(10): e32767. doi:10.1371/journal.pgen.1005626
Kategorie: Research Article
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.pgen.1005626

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1. Morales L, Dujon B. Evolutionary role of interspecies hybridization and genetic exchanges in yeasts. Microbiol Mol Biol Rev MMBR. 2012;76: 721–739. doi: 10.1128/MMBR.00022-12 23204364

2. González SS, Barrio E, Gafner J, Querol A. Natural hybrids from Saccharomyces cerevisiae, Saccharomyces bayanus and Saccharomyces kudriavzevii in wine fermentations. FEMS Yeast Res. 2006;6: 1221–1234. 17156019

3. Louis VL, Despons L, Friedrich A, Martin T, Durrens P, Casarégola S, et al. Pichia sorbitophila, an Interspecies Yeast Hybrid, Reveals Early Steps of Genome Resolution After Polyploidization. G3 Bethesda Md. 2012;2: 299–311.

4. Xu J, Luo G, Vilgalys RJ, Brandt ME, Mitchell TG. Multiple origins of hybrid strains of Cryptococcus neoformans with serotype AD. Microbiol Read Engl. 2002;148: 203–212.

5. Baker E, Wang B, Bellora N, Peris D, Hulfachor AB, Koshalek JA, et al. The Genome Sequence of Saccharomyces eubayanus and the Domestication of Lager-Brewing Yeasts. Mol Biol Evol. 2015;

6. Wendland J. Lager yeast comes of age. Eukaryot Cell. 2014;13: 1256–1265. doi: 10.1128/EC.00134-14 25084862

7. Marcet-Houben M, Gabaldón T. Beyond the Whole-Genome Duplication: Phylogenetic Evidence for an Ancient Interspecies Hybridization in the Baker’s Yeast Lineage. PLoS Biol. 2015;13: e1002220. doi: 10.1371/journal.pbio.1002220 26252497

8. Pryszcz LP, Németh T, Gácser A, Gabaldón T. Genome comparison of Candida orthopsilosis clinical strains reveals the existence of hybrids between two distinct subspecies. Genome Biol Evol. 2014;6: 1069–1078. doi: 10.1093/gbe/evu082 24747362

9. Bovers M, Hagen F, Kuramae EE, Diaz MR, Spanjaard L, Dromer F, et al. Unique hybrids between the fungal pathogens Cryptococcus neoformans and Cryptococcus gattii. FEMS Yeast Res. 2006;6: 599–607. 16696655

10. Hagen F, Khayhan K, Theelen B, Kolecka A, Polacheck I, Sionov E, et al. Recognition of seven species in the Cryptococcus gattii/Cryptococcus neoformans species complex. Fungal Genet Biol FG B. 2015;78: 16–48. doi: 10.1016/j.fgb.2015.02.009 25721988

11. Trofa D, Gácser A, Nosanchuk JD. Candida parapsilosis, an emerging fungal pathogen. Clin Microbiol Rev. 2008;21: 606–625. doi: 10.1128/CMR.00013-08 18854483

12. Tavanti A, Davidson AD, Gow NAR, Maiden MCJ, Odds FC. Candida orthopsilosis and Candida metapsilosis spp. nov. to replace Candida parapsilosis groups II and III. J Clin Microbiol. 2005;43: 284–292. 15634984

13. Cantón E, Pemán J, Quindós G, Eraso E, Miranda-Zapico I, Álvarez M, et al. Prospective multicenter study of the epidemiology, molecular identification, and antifungal susceptibility of Candida parapsilosis, Candida orthopsilosis, and Candida metapsilosis isolated from patients with candidemia. Antimicrob Agents Chemother. 2011;55: 5590–5596. doi: 10.1128/AAC.00466-11 21930869

14. Lockhart SR, Messer SA, Pfaller MA, Diekema DJ. Geographic distribution and antifungal susceptibility of the newly described species Candida orthopsilosis and Candida metapsilosis in comparison to the closely related species Candida parapsilosis. J Clin Microbiol. 2008;46: 2659–2664. doi: 10.1128/JCM.00803-08 18562582

15. Oliveira VKP, Paula CR, Colombo AL, Merseguel KB, Nishikaku AS, Moreira D, et al. Candidemia and death by Candida orthopsilosis and Candida metapsilosis in neonates and children. Pediatr Neonatol. 2014;55: 75–76. doi: 10.1016/j.pedneo.2013.07.006 24113226

16. Gácser A, Schäfer W, Nosanchuk JS, Salomon S, Nosanchuk JD. Virulence of Candida parapsilosis, Candida orthopsilosis, and Candida metapsilosis in reconstituted human tissue models. Fungal Genet Biol FG B. 2007;44: 1336–1341. 17391997

17. Gago S, García-Rodas R, Cuesta I, Mellado E, Alastruey-Izquierdo A. Candida parapsilosis, Candida orthopsilosis, and Candida metapsilosis virulence in the non-conventional host Galleria mellonella. Virulence. 2014;5: 278–285. doi: 10.4161/viru.26973 24193303

18. Németh T, Tóth A, Szenzenstein J, Horváth P, Nosanchuk JD, Grózer Z, et al. Characterization of virulence properties in the C. parapsilosis sensu lato species. PloS One. 2013;8: e68704. doi: 10.1371/journal.pone.0068704 23874732

19. Orsi CF, Colombari B, Blasi E. Candida metapsilosis as the least virulent member of the “C. parapsilosis” complex. Med Mycol. 2010;48: 1024–1033. doi: 10.3109/13693786.2010.489233 20507266

20. Bertini A, De Bernardis F, Hensgens LAM, Sandini S, Senesi S, Tavanti A. Comparison of Candida parapsilosis, Candida orthopsilosis, and Candida metapsilosis adhesive properties and pathogenicity. Int J Med Microbiol IJMM. 2013;303: 98–103. doi: 10.1016/j.ijmm.2012.12.006 23403338

21. Garcia-Effron G, Canton E, Pemán J, Dilger A, Romá E, Perlin DS. Epidemiology and echinocandin susceptibility of Candida parapsilosis sensu lato species isolated from bloodstream infections at a Spanish university hospital. J Antimicrob Chemother. 2012;67: 2739–2748. doi: 10.1093/jac/dks271 22868644

22. Bonfietti LX, Martins M dos A, Szeszs MW, Pukiskas SBS, Purisco SU, Pimentel FC, et al. Prevalence, distribution and antifungal susceptibility profiles of Candida parapsilosis, Candida orthopsilosis and Candida metapsilosis bloodstream isolates. J Med Microbiol. 2012;61: 1003–1008. doi: 10.1099/jmm.0.037812-0 22493277

23. Nosek J, Holesova Z, Kosa P, Gacser A, Tomaska L. Biology and genetics of the pathogenic yeast Candida parapsilosis. Curr Genet. 2009;55: 497–509. doi: 10.1007/s00294-009-0268-4 19662416

24. Butler G, Rasmussen MD, Lin MF, Santos MAS, Sakthikumar S, Munro CA, et al. Evolution of pathogenicity and sexual reproduction in eight Candida genomes. Nature. 2009;459: 657–662. doi: 10.1038/nature08064 19465905

25. Riccombeni A, Vidanes G, Proux-Wéra E, Wolfe KH, Butler G. Sequence and analysis of the genome of the pathogenic yeast Candida orthopsilosis. PloS One. 2012;7: e35750. doi: 10.1371/journal.pone.0035750 22563396

26. Pryszcz LP, Németh T, Gácser A, Gabaldón T. Unexpected genomic variability in clinical and environmental strains of the pathogenic yeast Candida parapsilosis. Genome Biol Evol. 2013;5: 2382–2392. doi: 10.1093/gbe/evt185 24259314

27. Safonova Y, Bankevich A, Pevzner PA. dipSPAdes: Assembler for Highly Polymorphic Diploid Genomes. In: Sharan R, editor. Research in Computational Molecular Biology. Springer International Publishing; 2014. pp. 265–279. Available: http://link.springer.com/chapter/10.1007/978-3-319-05269-4_21

28. Gunisova S, Elboher E, Nosek J, Gorkovoy V, Brown Y, Lucier J-F, et al. Identification and comparative analysis of telomerase RNAs from Candida species reveal conservation of functional elements. RNA. 2009;15: 546–559. doi: 10.1261/rna.1194009 19223441

29. Valach M, Pryszcz LP, Tomaska L, Gacser A, Gabaldón T, Nosek J. Mitochondrial genome variability within the Candida parapsilosis species complex. Mitochondrion. 2012;12: 514–519. doi: 10.1016/j.mito.2012.07.109 22824459

30. Rycovska A, Valach M, Tomaska L, Bolotin-Fukuhara M, Nosek J. Linear versus circular mitochondrial genomes: intraspecies variability of mitochondrial genome architecture in Candida parapsilosis. Microbiol Read Engl. 2004;150: 1571–1580.

31. Kosa P, Valach M, Tomaska L, Wolfe KH, Nosek J. Complete DNA sequences of the mitochondrial genomes of the pathogenic yeasts Candida orthopsilosis and Candida metapsilosis: insight into the evolution of linear DNA genomes from mitochondrial telomere mutants. Nucleic Acids Res. 2006;34: 2472–2481. 16684995

32. Bennett RJ, Forche A, Berman J. Rapid mechanisms for generating genome diversity: whole ploidy shifts, aneuploidy, and loss of heterozygosity. Cold Spring Harb Perspect Med. 2014;4.

33. Louis VL, Despons L, Friedrich A, Martin T, Durrens P, Casarégola S, et al. Pichia sorbitophila, an Interspecies Yeast Hybrid, Reveals Early Steps of Genome Resolution After Polyploidization. G3 Bethesda Md. 2012;2: 299–311.

34. Alby K, Bennett RJ. Interspecies pheromone signaling promotes biofilm formation and same-sex mating in Candida albicans. Proc Natl Acad Sci U S A. 2011;108: 2510–2515. doi: 10.1073/pnas.1017234108 21262815

35. Hull CM, Johnson AD. Identification of a mating type-like locus in the asexual pathogenic yeast Candida albicans. Science. 1999;285: 1271–1275. 10455055

36. Sai S, Holland LM, McGee CF, Lynch DB, Butler G. Evolution of mating within the Candida parapsilosis species group. Eukaryot Cell. 2011;10: 578–587. doi: 10.1128/EC.00276-10 21335529

37. Hensgens LAM, Tavanti A, Mogavero S, Ghelardi E, Senesi S. AFLP genotyping of Candida metapsilosis clinical isolates: evidence for recombination. Fungal Genet Biol FG B. 2009;46: 750–758. doi: 10.1016/j.fgb.2009.06.006 19559094

38. Gabaldón T. Large-scale assignment of orthology: back to phylogenetics? Genome Biol. 2008;9: 235. doi: 10.1186/gb-2008-9-10-235 18983710

39. Huerta-Cepas J, Capella-Gutiérrez S, Pryszcz LP, Marcet-Houben M, Gabaldón T. PhylomeDB v4: zooming into the plurality of evolutionary histories of a genome. Nucleic Acids Res. 2014;42: D897–902. doi: 10.1093/nar/gkt1177 24275491

40. Gácser A, Trofa D, Schäfer W, Nosanchuk JD. Targeted gene deletion in Candida parapsilosis demonstrates the role of secreted lipase in virulence. J Clin Invest. 2007;117: 3049–3058. 17853941

41. Trofa D, Soghier L, Long C, Nosanchuk JD, Gacser A, Goldman DL. A rat model of neonatal candidiasis demonstrates the importance of lipases as virulence factors for Candida albicans and Candida parapsilosis. Mycopathologia. 2011;172: 169–178. doi: 10.1007/s11046-011-9429-3 21667319

42. Gácser A, Stehr F, Kröger C, Kredics L, Schäfer W, Nosanchuk JD. Lipase 8 affects the pathogenesis of Candida albicans. Infect Immun. 2007;75: 4710–4718. 17646357

43. Schofield DA, Westwater C, Warner T, Balish E. Differential Candida albicans lipase gene expression during alimentary tract colonization and infection. FEMS Microbiol Lett. 2005;244: 359–365. 15766791

44. Stehr F, Felk A, Gácser A, Kretschmar M, Mähnss B, Neuber K, et al. Expression analysis of the Candida albicans lipase gene family during experimental infections and in patient samples. FEMS Yeast Res. 2004;4: 401–408. 14734020

45. Naglik JR, Challacombe SJ, Hube B. Candida albicans secreted aspartyl proteinases in virulence and pathogenesis. Microbiol Mol Biol Rev MMBR. 2003;67: 400–428, table of contents. 12966142

46. Horváth P, Nosanchuk JD, Hamari Z, Vágvölgyi C, Gácser A. The identification of gene duplication and the role of secreted aspartyl proteinase 1 in Candida parapsilosis virulence. J Infect Dis. 2012;205: 923–933. doi: 10.1093/infdis/jir873 22301631

47. Gabaldón T, Martin T, Marcet-Houben M, Durrens P, Bolotin-Fukuhara M, Lespinet O, et al. Comparative genomics of emerging pathogens in the Candida glabrata clade. BMC Genomics. 2013;14: 623. doi: 10.1186/1471-2164-14-623 24034898

48. Ghannoum MA, Jurevic RJ, Mukherjee PK, Cui F, Sikaroodi M, Naqvi A, et al. Characterization of the oral fungal microbiome (mycobiome) in healthy individuals. PLoS Pathog. 2010;6: e1000713. doi: 10.1371/journal.ppat.1000713 20072605

49. Dohm JC, Minoche AE, Holtgräwe D, Capella-Gutiérrez S, Zakrzewski F, Tafer H, et al. The genome of the recently domesticated crop plant sugar beet (Beta vulgaris). Nature. 2014;505: 546–549. doi: 10.1038/nature12817 24352233

50. Luo R, Liu B, Xie Y, Li Z, Huang W, Yuan J, et al. SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. GigaScience. 2012;1: 18. doi: 10.1186/2047-217X-1-18 23587118

51. Huang S, Chen Z, Huang G, Yu T, Yang P, Li J, et al. HaploMerger: reconstructing allelic relationships for polymorphic diploid genome assemblies. Genome Res. 2012;22: 1581–1588. doi: 10.1101/gr.133652.111 22555592

52. Boetzer M, Henkel CV, Jansen HJ, Butler D, Pirovano W. Scaffolding pre-assembled contigs using SSPACE. Bioinforma Oxf Engl. 2011;27: 578–579.

53. Stanke M, Keller O, Gunduz I, Hayes A, Waack S, Morgenstern B. AUGUSTUS: ab initio prediction of alternative transcripts. Nucleic Acids Res. 2006;34: W435–439. 16845043

54. Pryszcz LP, Huerta-Cepas J, Gabaldón T. MetaPhOrs: orthology and paralogy predictions from multiple phylogenetic evidence using a consistency-based confidence score. Nucleic Acids Res. 2011;39: e32. doi: 10.1093/nar/gkq953 21149260

55. Quevillon E, Silventoinen V, Pillai S, Harte N, Mulder N, Apweiler R, et al. InterProScan: protein domains identifier. Nucleic Acids Res. 2005;33: W116–120. 15980438

56. Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012;9: 357–359. doi: 10.1038/nmeth.1923 22388286

57. McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 2010;20: 1297–1303. doi: 10.1101/gr.107524.110 20644199

58. Untergasser A, Cutcutache I, Koressaar T, Ye J, Faircloth BC, Remm M, et al. Primer3—new capabilities and interfaces. Nucleic Acids Res. 2012;40: e115. 22730293

59. Schwartz DC, Cantor CR. Separation of yeast chromosome-sized DNAs by pulsed field gradient gel electrophoresis. Cell. 1984;37: 67–75. 6373014

60. Chu G, Vollrath D, Davis RW. Separation of large DNA molecules by contour-clamped homogeneous electric fields. Science. 1986;234: 1582–1585. 3538420

61. Frith MC, Hamada M, Horton P. Parameters for accurate genome alignment. BMC Bioinformatics. 2010;11: 80.: doi: 10.1186/1471-2105-11-80 20144198

62. Huerta-Cepas J, Capella-Gutierrez S, Pryszcz LP, Denisov I, Kormes D, Marcet-Houben M, et al. PhylomeDB v3.0: an expanding repository of genome-wide collections of trees, alignments and phylogeny-based orthology and paralogy predictions. Nucleic Acids Res. 2011;39: D556–560. doi: 10.1093/nar/gkq1109 21075798

63. Smith TF, Waterman MS. Identification of common molecular subsequences. J Mol Biol. 1981;147: 195–197. 7265238

64. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004;32: 1792–1797. 15034147

65. Katoh K, Toh H. Recent developments in the MAFFT multiple sequence alignment program. Brief Bioinform. 2008;9: 286–298. doi: 10.1093/bib/bbn013 18372315

66. Lassmann T, Frings O, Sonnhammer ELL. Kalign2: high-performance multiple alignment of protein and nucleotide sequences allowing external features. Nucleic Acids Res. 2009;37: 858–865. doi: 10.1093/nar/gkn1006 19103665

67. Wallace IM, O’Sullivan O, Higgins DG, Notredame C. M-Coffee: combining multiple sequence alignment methods with T-Coffee. Nucleic Acids Res. 2006;34: 1692–1699. 16556910

68. Capella-Gutiérrez S, Silla-Martínez JM, Gabaldón T. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinforma Oxf Engl. 2009;25: 1972–1973.

69. Guindon S, Dufayard J-F, Lefort V, Anisimova M, Hordijk W, Gascuel O. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol. 2010;59: 307–321. doi: 10.1093/sysbio/syq010 20525638

70. Stamatakis A, Ludwig T, Meier H. RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees. Bioinforma Oxf Engl. 2005;21: 456–463.

71. Dray S., Dufour A.B. The ade4 package: implementing the duality diagram for ecologists. J Stat Softw. 2007;22: 1–20.

72. Wehe A, Bansal MS, Burleigh JG, Eulenstein O. DupTree: a program for large-scale phylogenetic analyses using gene tree parsimony. Bioinforma Oxf Engl. 2008;24: 1540–1541.

73. Huerta-Cepas J, Dopazo J, Gabaldón T. ETE: a python Environment for Tree Exploration. BMC Bioinformatics. 2010;11: 24. doi: 10.1186/1471-2105-11-24 20070885