pp 1-43 | Cite as

Transcriptome Sequencing Approaches to Elucidate Host–Microbe Interactions in Opportunistic Human Fungal Pathogens

  • Hrant Hovhannisyan
  • Toni Gabaldón
Part of the Current Topics in Microbiology and Immunology book series


Infections caused by opportunistic human fungal pathogens are a source of increasing medical concern, due to their growing incidence, the emergence of novel pathogenic species, and the lack of effective diagnostics tools. Fungal pathogens are phylogenetically diverse, and their virulence mechanisms can differ widely across species. Despite extensive efforts, the molecular bases of virulence in pathogenic fungi and their interactions with the human host remain poorly understood for most species. In this context, next-generation sequencing approaches hold the promise of helping to close this knowledge gap. In particular, high-throughput transcriptome sequencing (RNA-Seq) enables monitoring the transcriptional profile of both host and microbes to elucidate their interactions and discover molecular mechanisms of virulence and host defense. Here, we provide an overview of transcriptome sequencing techniques and approaches, and survey their application in studying the interplay between humans and fungal pathogens. Finally, we discuss novel RNA-Seq approaches in studying host–pathogen interactions and their potential role in advancing the clinical diagnostics of fungal infections.



TG group acknowledges support from the Spanish Ministry of Economy, Industry, and Competitiveness (MEIC) for the EMBL partnership and grants “Centro de Excelencia Severo Ochoa 2013–2017” SEV-2012-0208, and BFU2015-67107 cofounded by European Regional Development Fund (ERDF), from the CERCA Programme/Generalitat de Catalunya, from the Catalan Research Agency (AGAUR) SGR857, and grant from the European Union’s Horizon 2020 research and innovation programme under the grant agreement ERC-2016-724173 the Marie Sklodowska-Curie grant agreement No. H2020-MSCA-ITN-2014-642095.


  1. Abad A, Victoria Fernández-Molina J, Bikandi J et al (2010) What makes Aspergillus fumigatus a successful pathogen? Genes and molecules involved in invasive aspergillosis. Rev Iberoam Micol 27:155–182. Scholar
  2. Adams MD, Kelley JM, Gocayne JD et al (1991) Complementary DNA sequencing: expressed sequence tags and human genome project. Science 252:1651–1656. Scholar
  3. Alwine JC, Kemp DJ, Stark GR (1977) Method for detection of specific RNAs in agarose gels by transfer to diazobenzyloxymethyl-paper and hybridization with DNA probes. Proc Natl Acad Sci 74:5350–5354. Scholar
  4. Amorim-vaz S, Tran VDT, Pradervand S et al (2015) RNA enrichment method for quantitative transcriptional analysis of pathogens in vivo applied to the fungus Candida albicans. MBio 6:1–16. Scholar
  5. Anders S, Pyl PT, Huber W (2015) HTSeq–a Python framework to work with high-throughput sequencing data. Bioinformatics 31:166–169. Scholar
  6. Andes D, Lepak A, Pitula A et al (2005) A simple approach for estimating gene expression in Candida albicans directly from a systemic infection site. J Infect Dis 192:893–900. Scholar
  7. Andrews S (2010) FastQC: a quality control tool for high throughput sequence data. Available online at:
  8. Aprianto R, Slager J, Holsappel S, Veening JW (2016) Time-resolved dual RNA-seq reveals extensive rewiring of lung epithelial and pneumococcal transcriptomes during early infection. Genome Biol 17.
  9. Au KF, Sebastiano V, Afshar PT et al (2013) Characterization of the human ESC transcriptome by hybrid sequencing. Proc Natl Acad Sci.
  10. Avital G, Avraham R, Fan A et al (2017) scDual-Seq: Mapping the gene regulatory program of Salmonella infection by host and pathogen single-cell RNA-sequencing. Genome Biol.
  11. Avraham R, Haseley N, Brown D et al (2015) Pathogen Cell-to-Cell Variability Drives Heterogeneity in Host Immune Responses. Cell.
  12. Bainbridge MN, Warren RL, Hirst M et al (2006) Analysis of the prostate cancer cell line LNCaP transcriptome using a sequencing-by-synthesis approach. BMC Genomics 7.
  13. Baruzzo G, Hayer KE, Kim EJ et al (2017) Simulation-based comprehensive benchmarking of RNA-seq aligners. Nat Methods 14:135–139. Scholar
  14. Berenguer J, Buck M, Witebsky F et al (1993) Lysis-centrifugation blood cultures in the detection of tissue-proven invasive candidiasis disseminated versus single-organ infection. Diagn Microbiol Infect Dis 17:103–109. Scholar
  15. Binkley J, Arnaud MB, Inglis DO et al (2014) The Candida Genome Database: the new homology information page highlights protein similarity and phylogeny. Nucleic Acids Res 42:D711–D716. Scholar
  16. Bitar D, Lortholary O, Le Strat Y et al (2014) Population-based analysis of invasive fungal infections, France, 2001–2010. Emerg Infect Dis 20:1149–1155. Scholar
  17. Black MB, Parks BB, Pluta L et al (2014) Comparison of microarrays and RNA-Seq for gene expression analyses of dose-response experiments. Toxicol Sci 137:385–403. Scholar
  18. Blackwell M (2011) The fungi: 1, 2, 3 … 5.1 million species? Am J Bot 98:426–438. Scholar
  19. Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114–2120. Scholar
  20. Borodina T, Adjaye J, Sultan M (2011) A Strand-Specific Library Preparation Protocol for RNA Sequencing. In: Methods in enzymology. pp 79–98Google Scholar
  21. Brandão F, Esher SK, Ost KS et al (2018) HDAC genes play distinct and redundant roles in Cryptococcus neoformans virulence. Sci Rep.
  22. Brandt ME, Lockhart SR (2012) Recent taxonomic developments with candida and other opportunistic yeasts. Curr Fungal Infect Rep 6:170–177. Scholar
  23. Bray NL, Pimentel H, Melsted P, Pachter L (2016) Near-optimal probabilistic RNA-seq quantification. Nat Biotechnol 34:525–527. Scholar
  24. Brown GD, Denning DW, Gow NAR et al (2012) Hidden killers: human fungal infections. Sci. Transl, Med, p 4Google Scholar
  25. Brown NA, Ries LNA, Reis TF et al (2016) RNAseq reveals hydrophobins that are involved in the adaptation of Aspergillus nidulans to lignocellulose. Biotechnol Biofuels 9.
  26. Bruno VM, Shetty AC, Yano J et al (2015) Transcriptomic Analysis of Vulvovaginal Candidiasis Identifies a Role for the NLRP3 Inflammasome. MBio 6:1–15. Scholar
  27. Bullard JH, Purdom E, Hansen KD, Dudoit S (2010) Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments. BMC Bioinformatics 11:94. Scholar
  28. Byrne A, Beaudin AE, Olsen HE et al (2017) Nanopore long-read RNAseq reveals widespread transcriptional variation among the surface receptors of individual B cells. Nat Commun.
  29. Campbell JD, Liu G, Luo L et al (2015) Assessment of microRNA differential expression and detection in multiplexed small RNA sequencing data. RNA.
  30. Castel SE, Levy-Moonshine A, Mohammadi P et al (2015) Tools and best practices for data processing in allelic expression analysis. Genome Biol 16:195. Scholar
  31. Cerqueira GC, Arnaud MB, Inglis DO et al (2014) The Aspergillus Genome Database: multispecies curation and incorporation of RNA-Seq data to improve structural gene annotations. Nucleic Acids Res 42:D705–D710. Scholar
  32. Chalupová J, Raus M, Sedlářová M, Šebela M (2014) Identification of fungal microorganisms by MALDI-TOF mass spectrometry. Biotechnol Adv 32:230–241Google Scholar
  33. Chapman B, Slavin M, Marriott D et al (2017) Changing epidemiology of candidaemia in Australia. J Antimicrob Chemother 72:1103–1108. Scholar
  34. Chen SY, Deng F, Jia X et al (2017) A transcriptome atlas of rabbit revealed by PacBio single-molecule long-read sequencing. Sci Rep.
  35. Chen JJ, Hsueh HM, Delongchamp RR et al (2007) Reproducibility of microarray data: a further analysis of microarray quality control (MAQC) data. BMC Bioinformatics 8.
  36. Chen L, Kostadima M, Martens JHA et al (2014a) Transcriptional diversity during lineage commitment of human blood progenitors. Science.
  37. Chen Y, Toffaletti DL, Tenor JL et al (2014b) The Cryptococcus neoformans transcriptome at the site of human meningitis. MBio 5.
  38. Chen F, Zhang C, Jia X et al (2015) Transcriptome profiles of human lung epithelial cells A549 interacting with Aspergillus fumigatus by RNA-Seq. PLoS One 10.
  39. Cheon SA, Thak EJ, Bahn YS, Kang HA (2017) A novel bZIP protein, Gsb1, is required for oxidative stress response, mating, and virulence in the human pathogen Cryptococcus neoformans. Sci Rep 7.
  40. Chhangawala S, Rudy G, Mason CE, Rosenfeld JA (2015) The impact of read length on quantification of differentially expressed genes and splice junction detection. Genome Biol 16:131. Scholar
  41. Chowdhary A, Sharma C, Meis JF (2017) Candida auris: A rapidly emerging cause of hospital-acquired multidrug-resistant fungal infections globally. PLoS Pathog. 13Google Scholar
  42. Cock PJA, Fields CJ, Goto N et al (2009) The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants. Nucleic Acids Res 38:1767–1771. Scholar
  43. Conesa A, Madrigal P, Tarazona S et al (2016) A survey of best practices for RNA-seq data analysis. Genome Biol 17:13. Scholar
  44. Cottier F, Tan ASM, Chen J et al (2015) The transcriptional stress response of Candida albicans to weak organic acids. G3 (Bethesda) 5:497–505.
  45. D’Souza CA, Kronstad JW, Taylor G et al (2011) Genome variation in Cryptococcus gattii, an emerging pathogen of immunocompetent hosts. MBio 2.
  46. Dagenais TRT, Keller NP (2009) Pathogenesis of Aspergillus fumigatus in invasive aspergillosis. Clin Microbiol Rev 22:447–465Google Scholar
  47. Dijksterhuis J, Houbraken J, Samson RA (2013) Fungal spoilage of crops and food. In: Agricultural Applications, 2nd Edition. pp 35–56Google Scholar
  48. Dinel S, Bolduc C, Belleau P et al (2005) Reproducibility, bioinformatic analysis and power of the SAGE method to evaluate changes in transcriptome. Nucleic Acids Res 33:1–8. Scholar
  49. Dobin A, Davis CA, Schlesinger F et al (2013) STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29:15–21. Scholar
  50. Dobin A, Gingeras TR (2013) Comment on “TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions” by Kim et al. bioRxiv 000851.
  51. Dutton LC, Paszkiewicz KH, Silverman RJ et al (2016) Transcriptional landscape of trans-kingdom communication between Candida albicans and Streptococcus gordonii. Mol Oral Microbiol 31:136–161. Scholar
  52. Emmert-Streib F, Glazko GV (2011) Pathway analysis of expression data: deciphering functional building blocks of complex diseases. PLoS Comput Biol. Scholar
  53. Fan HC, Fu GK, Fodor SPA, Önnerfjord P (2015) Expression profiling. Combinatorial labeling of single cells for gene expression cytometry. Science.
  54. Ferrareze PAG, Streit RSA, dos Santos PR et al (2017) Transcriptional Analysis Allows Genome Reannotation and Reveals that Cryptococcus gattii VGII Undergoes Nutrient Restriction during Infection. Microorganisms 5:49. Scholar
  55. Flevari A, Theodorakopoulou M, Velegraki A et al (2013) Treatment of invasive candidiasis in the elderly: a review. Clin Interv Aging 8:1199–1208Google Scholar
  56. Francis WR, Christianson LM, Kiko R et al (2013) A comparison across non-model animals suggests an optimal sequencing depth for de novo transcriptome assembly. BMC Genom 14:1–12. Scholar
  57. Fuller KK, Cramer RA, Zegans ME et al (2016) Aspergillus fumigatus photobiology illuminates the marked heterogeneity between isolates. MBio 7.
  58. Gabaldón T, Carreté L (2016) The birth of a deadly yeast: tracing the evolutionary emergence of virulence traits in Candida glabrata. FEMS Yeast Res. 16Google Scholar
  59. Gabaldón T, Naranjo-Ortíz MA, Marcet-Houben M (2016) Evolutionary genomics of yeast pathogens in the Saccharomycotina. FEMS Yeast Res. 16Google Scholar
  60. Garalde DR, Snell EA, Jachimowicz D et al (2018) Highly parallel direct RN A sequencing on an array of nanopores. Nat Methods. Scholar
  61. Geiss GK, Bumgarner RE, Birditt B et al (2008) Direct multiplexed measurement of gene expression with color-coded probe pairs. Nat Biotechnol 26:317–325. Scholar
  62. Gibbons JG, Beauvais A, Beau R et al (2012) Global transcriptome changes underlying colony growth in the opportunistic human pathogen Aspergillus fumigatus. Eukaryot Cell 11:68–78. Scholar
  63. Gonzalez-Hilarion S, Paulet D, Lee KT et al (2016) Intron retention-dependent gene regulation in Cryptococcus neoformans. Sci Rep. Scholar
  64. Goodwin S, McPherson JD, McCombie WR (2016) Coming of age: ten years of next-generation sequencing technologies. Nat Rev Genet 17:333–351. Scholar
  65. Griffin AT, Hanson KE (2014) Update on fungal diagnostics. Curr Infect Dis Rep 16.
  66. Guinea J (2014) Global trends in the distribution of Candida species causing candidemia. Clin Microbiol Infect 20:5–10Google Scholar
  67. Guo Y, Zhao S, Li C-I et al (2014) RNAseqPS: A Web Tool for Estimating Sample Size and Power for RNAseq Experiment. Cancer Inform 13:1–5. Scholar
  68. Haas BJ, Papanicolaou A, Yassour M et al (2013) De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. Nat Protoc 8:1494–1512. Scholar
  69. Hart SN, Therneau TM, Zhang Y et al (2013) Calculating Sample Size Estimates for RNA Sequencing Data. J Comput Biol 20:970–978. Scholar
  70. Havlickova B, Czaika VA, Friedrich M (2008) Epidemiological trends in skin mycoses worldwide. Mycoses 51:2–15Google Scholar
  71. Hawksworth DL, Lücking R (2017) Fungal Diversity Revisited: 2.2 to 3.8 Million Species. Microbiol Spectr 5.
  72. Heward JA, Lindsay MA (2014) Long non-coding RNAs in the regulation of the immune response. Trends ImmunolGoogle Scholar
  73. Hu G, Chen SH, Qiu J et al (2014) Microevolution during serial mouse passage demonstrates FRE3 as a virulence adaptation gene in Cryptococcus neoformans. MBio. Scholar
  74. Hu B, Xie G, Lo C-C et al (2011) Pathogen comparative genomics in the next-generation sequencing era: genome alignments, pangenomics and metagenomics. Brief Funct Genomics 10:322–333. Scholar
  75. Idnurm A, Walton FJ, Floyd A et al (2009) Identification of ENA1 as a virulence gene of the human pathogenic fungus Cryptococcus neoformans through signature-tagged insertional mutagenesis. Eukaryot Cell. Scholar
  76. Irmer H, Tarazona S, Sasse C et al (2015) RNAseq analysis of Aspergillus fumigatus in blood reveals a just wait and see resting stage behavior. BMC Genom 16:640. Scholar
  77. Jain M, Koren S, Miga KH et al (2018) Nanopore sequencing and assembly of a human genome with ultra-long reads. Nat Biotechnol. Scholar
  78. Jamuar SS Tan EC (2015) Clinical application of next-generation sequencing for Mendelian diseases. Hum. GenomicsGoogle Scholar
  79. Janbon G, Ormerod KL, Paulet D et al (2014) Analysis of the Genome and Transcriptome of Cryptococcus neoformans var. grubii Reveals Complex RNA Expression and Microevolution Leading to Virulence Attenuation. PLoS Genet 10.
  80. Jia X, Chen F, Pan W et al (2014) Gliotoxin promotes Aspergillus fumigatus internalization into type II human pneumocyte A549 cells by inducing host phospholipase D activation. Microbes Infect 16:491–501. Scholar
  81. Jiang H, Lei R, Ding S-W, Zhu S (2014) Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads. BMC Bioinformatics 15:182. Scholar
  82. Jiang C, Li Z, Zhang L et al (2016) Significance of hyphae formation in virulence of Candida tropicalis and transcriptomic analysis of hyphal cells. Microbiol Res 192:65–72. Scholar
  83. Jiang M, Zhang S, Yang Z et al (2018) Self-Recognition of an Inducible Host lncRNA by RIG-I Feedback Restricts Innate Immune Response. Cell. Scholar
  84. Jung WH, Hu G, Kuo W, Kronstad JW (2009) Role of ferroxidases in iron uptake and virulence of Cryptococcus neoformans. Eukaryot Cell. Scholar
  85. Kale SD, Ayubi T, Chung D et al (2017) Modulation of Immune Signaling and Metabolism Highlights Host and Fungal Transcriptional Responses in Mouse Models of Invasive Pulmonary Aspergillosis. Sci Rep 7.
  86. Kathiravan, MK, Salake AB, Chothe AS, Dudhe PB, Watode RP, Mukta MS, Gadhwe S (2012). The biology and chemistry of antifungal agents: A review. Bioorganic Med Chem 20(19):5678–5698.
  87. Khot PD, Fredricks DN (2009) PCR-based diagnosis of human fungal infections. Expert Rev Anti Infect Ther 7:1201–1221. Scholar
  88. Kim D, Langmead B, Salzberg SL (2015) HISAT: a fast spliced aligner with low memory requirements. Nat Methods 12:357–360. Scholar
  89. Kim D, Pertea G, Trapnell C et al (2013) TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol 14:R36. Scholar
  90. Kim J, Sudbery P (2011) Candida albicans, a major human fungal pathogen. J Microbiol 49:171–177. Scholar
  91. Klingspor L, Tortorano AM, Peman J et al (2015) Invasive Candida infections in surgical patients in intensive care units: a prospective, multicentre survey initiated by the European Confederation of Medical Mycology (ECMM) (2006-2008). Clin Microbiol Infect 21:87.e1-87.e10.
  92. Kolisko M, Boscaro V, Burki F et al (2014) Single-cell transcriptomics for microbial eukaryotes. Curr, BiolGoogle Scholar
  93. Kolodziejczyk AA, Kim JK, Svensson V et al (2015) The Technology and Biology of Single-Cell RNA Sequencing. Mol. CellGoogle Scholar
  94. Kowalski CH, Beattie SR, Fuller KK et al (2016) Heterogeneity among isolates reveals that fitness in low oxygen correlates with Aspergillus fumigatus virulence. MBio 7.
  95. Kozel TR, Wickes B (2014) Fungal diagnostics. Cold Spring Harb Perspect Med 4.
  96. Kwon-Chung KJ, Boekhout T, Wickes BL, Fell JW (2011). Systematics of the genus Cryptococcus and its type species C. neoformans. In Cryptococcus: 3–15. American Society of MicrobiologyGoogle Scholar
  97. Kwon-Chung KJ, Fraser JA, Doering TÁL et al (2015) Cryptococcus neoformans and Cryptococcus gattii, the etiologic agents of cryptococcosis. Cold Spring Harb Perspect Med. Scholar
  98. Kwon-Chung KJ, Sugui JA (2013) Aspergillus fumigatus-What Makes the Species a Ubiquitous Human Fungal Pathogen? PLoS Pathog 9:1–4. Scholar
  99. Latgé JP (1999) Aspergillus fumigatus and Aspergillosis. Clin Microbiol Rev 12:310–350Google Scholar
  100. Levin JZ, Yassour M, Adiconis X et al (2010) Comprehensive comparative analysis of strand-specific RNA sequencing methods. Nat Methods 7:709–715. Scholar
  101. Liao Y, Smyth GK, Shi W (2014) featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics 30:923–930. Scholar
  102. Lin JQ, Zhao XX, Zhi QQ et al (2013) Transcriptomic profiling of Aspergillus flavus in response to 5-azacytidine. Fungal Genet Biol 56:78–86. Scholar
  103. Lister R, O’Malley RC, Tonti-Filippini J et al (2008) Highly Integrated Single-Base Resolution Maps of the Epigenome in Arabidopsis. Cell 133:523–536. Scholar
  104. Liu Y, Ferguson JF, Xue C et al (2013) Evaluating the Impact of Sequencing Depth on Transcriptome Profiling in Human Adipose. PLoS One 8.
  105. Liu Y, Filler SG (2011) Candida albicans Als3, a multifunctional adhesin and invasin. Eukaryot Cell 10:168–173Google Scholar
  106. Liu Y, Shetty AC, Schwartz JA et al (2015) New signaling pathways govern the host response to C. albicans infection in various niches. Genome Res 125:679–689. Scholar
  107. Liu TB, Subbian S, Pan W et al (2014a) Cryptococcus inositol utilization modulates the host protective immune response during brain infection. Cell Commun Signal 12:1–17. Scholar
  108. Liu Y, Zhou J, White KP (2014b) RNA-seq differential expression studies: more sequence or more replication? Bioinformatics 30:301–304. Scholar
  109. Lockhart DJ, Dong H, Byrne MC et al (1996) Expression monitoring by hybridization to high-density oligonucleotide arrays. Nat Biotechnol 14:1675–1680. Scholar
  110. Losada L, Barker BM, Pakala S et al (2014) Large-Scale Transcriptional Response to Hypoxia in Aspergillus fumigatus Observed Using RNAseq Identifies a Novel Hypoxia Regulated ncRNA. Mycopathologia 178:331–339. Scholar
  111. Love MI, Huber W, Anders S (2014) Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol 15:550. Scholar
  112. Lowe R, Shirley N, Bleackley M et al (2017) Transcriptomics technologies. PLOS Comput Biol 13:e1005457. Scholar
  113. Lu H, Giordano F, Ning Z (2016) Oxford Nanopore MinION Sequencing and Genome Assembly. Genomics, Proteomics BioinformaGoogle Scholar
  114. Luthra R, Chen H, Roy-Chowdhuri S, Singh RR (2015) Next-generation sequencing in clinical molecular diagnostics of cancer: advantages and challenges. Cancers (Basel)Google Scholar
  115. Marioni JC, Mason CE, Mane SM et al (2008) RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays. Genome Res 18:1509–1517. Scholar
  116. Martin R, Albrecht-Eckardt D, Brunke S et al (2013) A Core Filamentation Response Network in Candida albicans Is Restricted to Eight Genes. PLoS One 8.
  117. May RC, Stone NRH, Wiesner DL et al (2016) Cryptococcus: from environmental saprophyte to global pathogen. Nat Rev Microbiol 14:106–117Google Scholar
  118. McCoy RC, Taylor RW, Blauwkamp TA et al (2014) Illumina TruSeq synthetic long-reads empower de novo assembly and resolve complex, highly-repetitive transposable elements. PLoS ONE. Scholar
  119. Metpally RPR, Nasser S, Courtright A et al (2013) Comparison of analysis tools for miRNA high throughput sequencing using nerve crush as a model. Front Genet. Scholar
  120. Mitrovich QM, Tuch BB, Guthrie C, Johnson AD (2007) Computational and experimental approaches double the number of known introns in the pathogenic yeast Candida albicans. Genome Res 17:492–502. Scholar
  121. Mitsuhashi S, Kryukov K, Nakagawa S et al (2017) A portable system for metagenomic analyses using nanopore-based sequencer and laptop computers can realize rapid on-site determination of bacterial compositions. bioRxiv.
  122. Mixão V, Gabaldón T (2017) Hybridization and emergence of virulence in opportunistic human yeast pathogens. Yeast. Scholar
  123. Morrissy AS, Morin RD, Delaney A et al (2009) Next-generation tag sequencing for cancer gene expression profiling. Genome Res 19:1825–1835. Scholar
  124. Moyes DL, Richardson JP, Naglik JR (2014). From: Human Pathogenic Fungi: Molecular Biology and Pathogenic Mechanisms. In: Sullivan DJ, Moran GP (eds). Caister Academic Press, U.KGoogle Scholar
  125. Moyes DL, Wilson D, Richardson JP et al (2016) Candidalysin is a fungal peptide toxin critical for mucosal infection. Nature 532:64–68. Scholar
  126. Naglik JR, Challacombe SJ, Hube B (2003) Candida albicans Secreted Aspartyl Proteinases in Virulence and Pathogenesis. Microbiol Mol Biol Rev 67:400–428. Scholar
  127. Nature Microbiology Editorial (2017) Stop neglecting fungi. Nat. Microbiol. 2:17120.
  128. Niemiec MJ, Grumaz C, Ermert D et al (2017) Dual transcriptome of the immediate neutrophil and Candida albicans interplay. BMC Genom 18:696. Scholar
  129. Ning G, Cheng X, Luo P et al (2017) Hybrid sequencing and map finding (HySeMaFi): optional strategies for extensively deciphering gene splicing and expression in organisms without reference genome. Sci Rep. Scholar
  130. Nobile CJ, Nett JE, Andes DR, Mitchell AP (2006) Function of Candida albicans adhesin hwp1 in biofilm formation. Eukaryot Cell 5:1604–1610. Scholar
  131. Nuss AM, Beckstette M, Pimenova M et al (2017) Tissue dual RNA-seq allows fast discovery of infection-specific functions and riboregulators shaping host–pathogen transcriptomes. Proc Natl Acad Sci 114:E791–E800. Scholar
  132. O’Brien HE, Parrent JL, Jackson JA et al (2005) Fungal Community Analysis by Large-Scale Sequencing of Environmental Samples. Appl Environ Microbiol 71:5544–5550. Scholar
  133. O’Keeffe G, Hammel S, Owens RA et al (2014) RNA-seq reveals the pan-transcriptomic impact of attenuating the gliotoxin self-protection mechanism in Aspergillus fumigatus. BMC Genomics 15.
  134. O’Meara TR, Holmer SM, Selvig K et al (2013) Cryptococcus neoformans Rim101 is associated with cell wall remodeling and evasion of the host immune responses. MBio. Scholar
  135. O’Meara TR, Norton D, Price MS et al (2010) Interaction of Cryptococcus neoformans Rim101 and protein kinase a regulates capsule. PLoS Pathog. Scholar
  136. O’Neil D, Glowatz H, Schlumpberger M (2013) Ribosomal RNA Depletion for Efficient Use of RNA-Seq Capacity. In: Current Protocols in Molecular Biology. Wiley, Hoboken, NJ, USA, p Unit 4.19Google Scholar
  137. Oren I, Paul M (2014) Up to date epidemiology, diagnosis and management of invasive fungal infections. Clin Microbiol Infect 20:1–4Google Scholar
  138. Otto C, Stadler PF, Hoffmann S (2014) Lacking alignments? The next-generation sequencing mapper segemehl revisited. Bioinformatics 30:1837–1843. Scholar
  139. Ouyang J, Hu J, Chen JL (2016) lncRNAs regulate the innate immune response to viral infection. Wiley Interdiscip Rev RNA 7:129–143. Scholar
  140. Papon N, Courdavault V, Clastre M, Bennett RJ (2013) Emerging and Emerged Pathogenic Candida Species: Beyond the Candida albicans Paradigm. PLoS Pathog 9.
  141. Park BJ, Wannemuehler KA, Marston BJ et al (2009) Estimation of the current global burden of cryptococcal meningitis among persons living with HIV/AIDS. AIDS. Scholar
  142. Parkhomchuk D, Borodina T, Amstislavskiy V et al (2009) Transcriptome analysis by strand-specific sequencing of complementary DNA. Nucleic Acids Res 37:e123–e123. Scholar
  143. Patel RK, Jain M (2012) NGS QC toolkit: a toolkit for quality control of next generation sequencing data. PLoS ONE 7:e30619. Scholar
  144. Paterson RRM, Lima N (2017) Filamentous Fungal Human Pathogens from Food Emphasising Aspergillus. Fusarium Mucor Microorganisms 5:44. Scholar
  145. Patro R, Duggal G, Love MI et al (2017) Salmon provides fast and bias-aware quantification of transcript expression. Nat Methods 14:417–419. Scholar
  146. Pel HJ, De Winde JH, Archer DB et al (2007) Genome sequencing and analysis of the versatile cell factory Aspergillus niger CBS 513.88. Nat Biotechnol 25:221–231. Scholar
  147. Perfect JR, Cox GM, Lee JY et al (2001) The impact of culture isolation of Aspergillus species: a hospital-based survey of aspergillosis. Clin Infect Dis 33:1824–1833.
  148. Pfaller MA, Diekema DJ (2007) Epidemiology of invasive candidiasis: a persistent public health problem. Clin Microbiol Rev 20:133–163Google Scholar
  149. Pfaller MA, Diekema DJ (2010) Epidemiology of Invasive Mycoses in North America. Crit Rev Microbiol 36:1–53. Scholar
  150. Pfaller MA, Messer SA, Hollis RJ et al (2009) Variation in susceptibility of bloodstream isolates of Candida glabrata to fluconazole according to patient age and geographic location in the United States in 2001 to 2007. J Clin Microbiol 47:3185–3190. Scholar
  151. Pruitt KD, Tatusova T, Maglott DR (2007) NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res 35:D61–D65. Scholar
  152. Pryszcz LP, Németh T, Gácser A, Gabaldón T (2014) Genome comparison of candida orthopsilosis clinical strains reveals the existence of hybrids between two distinct subspecies. Genome Biol Evol 6:1069–1078. Scholar
  153. Pryszcz LP, Németh T, Saus E et al (2015) The Genomic Aftermath of Hybridization in the Opportunistic Pathogen Candida metapsilosis. PLoS Genet 11.
  154. Quick J, Ashton P, Calus S et al (2015) Rapid draft sequencing and real-time nanopore sequencing in a hospital outbreak of Salmonella. Genome Biol. Scholar
  155. Rapaport F, Khanin R, Liang Y et al (2013) Comprehensive evaluation of differential gene expression analysis methods for RNA-seq data. Genome Biol 14:R95. Scholar
  156. Rappolee D A, Mark D, Banda MJ, Werb Z (1988) Wound macrophages express TGF-alpha and other growth factors in vivo: analysis by mRNA phenotyping. Science (80-) 241:708–12.
  157. Rasheed M, Battu A, Kaur R (2018) Aspartyl proteases in Candida glabrata are required for suppression of the host innate immune response. J Biol Chem jbc.M117.813741.
  158. Reuter S, Ellington MJ, Cartwright EJP et al (2013) Rapid bacterial whole-genome sequencing to enhance diagnostic and public health microbiology. JAMA Intern Med. Scholar
  159. Rhoads A, Au KF (2015) PacBio Sequencing and Its Applications. Genomics, Proteomics BioinformaGoogle Scholar
  160. Rhodes J, Desjardins CA, Sykes SM et al (2017) Tracing genetic exchange and biogeography of cryptococcus neoformans var. Grubii at the global population level. Genetics 207:327–346. Scholar
  161. Ritchie ME, Phipson B, Wu D et al (2015) limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res 43:e47–e47. Scholar
  162. Rizzetto L, Giovannini G, Bromley M et al (2013) Strain Dependent Variation of Immune Responses to A. fumigatus: Definition of Pathogenic Species. PLoS One 8.
  163. Robinson MD, McCarthy DJ, Smyth GK (2010) edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26:139–140. Scholar
  164. Rosenbach A, Dignard D, Pierce JV et al (2010) Adaptations of Candida albicans for growth in the mammalian intestinal tract. Eukaryot Cell 9:1075–1086. Scholar
  165. Rosenberg AB, Roco CM, Muscat RA et al (2018) Single-cell profiling of the developing mouse brain and spinal cord with split-pool barcoding. Science (80-).
  166. Rosenthal K, Oehling V, Dusny C, Schmid A (2017) Beyond the bulk: Disclosing the life of single microbial cells. FEMS Microbiol, RevGoogle Scholar
  167. Saliba AE, Li L, Westermann AJ et al (2016) Single-cell RNA-seq ties macrophage polarization to growth rate of intracellular Salmonella. Nat Microbiol. Scholar
  168. Samson RA, Visagie CM, Houbraken J, Hong S-B, Hubka V, Klaassen CHW, Perrones G, Seifert KA, Susca A, Tanney JB, Varga J, Kocsube S, Szigeti G, Yaguchi T, Frisvad JC (2014) Phylogeny, identification and nomenclature of the genus Aspergillus. Stud Mycol 78:343–371. Scholar
  169. Sanger F, Nicklen S, Coulson AR (1977) DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A 74:5463–5467Google Scholar
  170. Sanglard D (2016) Emerging Threats in Antifungal-Resistant Fungal Pathogens. Front Med 3.
  171. Sarma S, Upadhyay S (2017) Current perspective on emergence, diagnosis and drug resistance in Candida auris. Infect Drug Resist 10:155–165Google Scholar
  172. Satoh K, Makimura K, Hasumi Y et al (2009) Candida auris sp. nov., a novel ascomycetous yeast isolated from the external ear canal of an inpatient in a Japanese hospital. Microbiol Immunol 53:41–44. Scholar
  173. Saus E, Willis JR, Pryszcz LP et al (2018) nextPARS: parallel probing of RNA structures in Illumina. RNA 24:609–619. Scholar
  174. Schena M, Shalon D, Davis RW, Brown PO (1995) Quantitative Monitoring of Gene Expression Patterns with a Complementary DNA Microarray. Science (80-) 270:467–470.
  175. Schmidt K, Mwaigwisya S, Crossman LC et al (2017) Identification of bacterial pathogens and antimicrobial resistance directly from clinical urines by nanopore-based metagenomic sequencing. J Antimicrob Chemother. Scholar
  176. Schröder MS, Martinez de San Vicente K, Prandini THR et al (2016) Multiple Origins of the Pathogenic Yeast Candida orthopsilosis by Separate Hybridizations between Two Parental Species. PLoS Genet 12.
  177. Schulze S, Henkel SG, Driesch D et al (2015) Computational prediction of molecular pathogen-host interactions based on dual transcriptome data. Front Microbiol. Scholar
  178. Schulze S, Schleicher J, Guthke R, Linde J (2016) How to predict molecular interactions between species?. Front, MicrobiolGoogle Scholar
  179. Schurch NJ, Schofield P, Gierliński M et al (2016) How many biological replicates are needed in an RNA-seq experiment and which differential expression tool should you use? RNA 22:839–851. Scholar
  180. Seqc/Maqc-Iii Consortium (2014) A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium. Nat Biotechnol 32:903–914. Scholar
  181. Seyednasrollah F, Laiho A, Elo LL (2015) Comparison of software packages for detecting differential expression in RNA-seq studies. Brief Bioinform 16:59–70. Scholar
  182. Shankar J, Cerqueira GC, Wortman JR et al (2018) RNA-Seq Profile Reveals Th-1 and Th-17-Type of Immune Responses in Mice Infected Systemically with Aspergillus fumigatus. Mycopathologia. Scholar
  183. Sharon D, Tilgner H, Grubert F, Snyder M (2013) A single-molecule long-read survey of the human transcriptome. Nat Biotechnol. Scholar
  184. Shaw WH, Lin Q, Muhammad ZZBR et al (2016) Identification of HIV mutation as diagnostic biomarker through next generation sequencing. J Clin Diagnostic Res. Scholar
  185. Sherry NL, Porter JL, Seemann T et al (2013) Outbreak investigation using high-throughput genome sequencing within a diagnostic microbiology laboratory. J Clin Microbiol. Scholar
  186. Short DP, O’Donnell K, Geiser DM (2014) Clonality, recombination, and hybridization in the plumbing-inhabiting human pathogen Fusarium keratoplasticum inferred from multilocus sequence typing. BMC Evol Biol 14:91. Scholar
  187. Smeekens SP, van de Veerdonk FL, Netea MG (2016) An Omics Perspective on Candida Infections: toward Next-Generation Diagnosis and Therapy. Front Microbiol 7:154. Scholar
  188. Soneson C (2013) Delorenzi M (2013) A comparison of methods for differential expression analysis of RNA-seq data. BMC Bioinforma 141(14):91. Scholar
  189. Soneson C, Love MI, Robinson MD (2015) Differential analyses for RNA-seq: transcript-level estimates improve gene-level inferences. F1000Research 4:1521.
  190. Stajich JE, Harris T, Brunk BP et al (2012) FungiDB: an integrated functional genomics database for fungi. Nucleic Acids Res 40:D675–D681. Scholar
  191. Stegle O, Teichmann SA, Marioni JC (2015) Computational and analytical challenges in single-cell transcriptomics. Nat. Rev, GenetGoogle Scholar
  192. Stoesser N, Batty EM, Eyre DW et al (2013) Predicting antimicrobial susceptibilities for Escherichia coli and Klebsiella pneumoniae isolates using whole genomic sequence data. J Antimicrob Chemother. Scholar
  193. Subramanian A, Tamayo P, Mootha VK et al (2005) Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci. Scholar
  194. Sudbery P, Gow N, Berman J (2004) The distinct morphogenic states of Candida albicans. Trends Microbiol 12:317–324Google Scholar
  195. Sutcliffe JG, Milner RJ, Bloom FE, Lerner RA (1982) Common 82-nucleotide sequence unique to brain RNA. Proc Natl Acad Sci U S A 79:4942–4946. Scholar
  196. Tarazona S, García-Alcalde F, Dopazo J et al (2011) Differential expression in RNA-seq: a matter of depth. Genome Res 21:2213–2223. Scholar
  197. Thänert R, Goldmann O, Beineke A, Medina E (2017) Host-inherent variability influences the transcriptional response of Staphylococcus aureus during in vivo infection. Nat Commun 8.
  198. The Gene Ontology Consortium (2017) Expansion of the Gene Ontology knowledgebase and resources. Nucleic Acids Res. Scholar
  199. Thewes S, Kretschmar M, Park H et al (2007) In vivo and ex vivo comparative transcriptional profiling of invasive and non-invasive Candida albicans isolates identifies genes associated with tissue invasion. Mol Microbiol 63:1606–1628. Scholar
  200. Tierney L, Linde J, Müller S et al (2012) An Interspecies Regulatory Network Inferred from Simultaneous RNA-seq of Candida albicans Invading Innate Immune Cells. Front Microbiol 3:85. Scholar
  201. Tóth R, Cabral V, Thuer E et al (2018) Investigation of Candida parapsilosis virulence regulatory factors during host-pathogen interaction. Sci Rep 8:1–14. Scholar
  202. Turabelidze G, Lawrence SJ, Gao H et al (2013) Precise dissection of an escherichia coli o157:H7 outbreak by single nucleotide polymorphism analysis. J Clin Microbiol. Scholar
  203. Turner SA, Butler G (2014) The Candida pathogenic species complex. Cold Spring Harb Perspect Med 4.
  204. Velculescu VE, Zhang L, Vogelstein B, Kinzler KW (1995) Serial Analysis of Gene Expression. Science (80-) 270:484–487.
  205. Wain J, Mavrogiorgou E (2013) Next-generation sequencing in clinical microbiology. Expert Rev. Mol, DiagnGoogle Scholar
  206. Wan Y, Qu K, Ouyang Z, Chang HY (2013) Genome-wide mapping of RNA structure using nuclease digestion and high-throughput sequencing. Nat Protoc 8:849–869. Scholar
  207. Wang J, Chen L, Chen Z, Zhang W (2015a) RNA-seq based transcriptomic analysis of single bacterial cells. Integr Biol (United Kingdom). Scholar
  208. Wang Z, Gerstein M, Snyder M (2009) RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 10:57–63Google Scholar
  209. Wang B, Regulski M, Tseng E et al (2018) A comparative transcriptional landscape of maize and sorghum obtained by single-molecule sequencing. Genome Res. Scholar
  210. Wang K, Zhang Z, Chen X et al (2015b) Transcription factor ADS-4 regulates adaptive responses and resistance to antifungal azole stress. Antimicrob Agents Chemother 59:5396–5404. Scholar
  211. Warner JR (1999) The economics of ribosome biosynthesis in yeast. Trends Biochem Sci 24:437–440Google Scholar
  212. Watkins TN, Liu H, Chung M et al (2018) Comparative transcriptomics of Aspergillus fumigatus strains upon exposure to human airway epithelial cells. Microb Genomics 1–9.
  213. Weinreb C, Wolock S, Tusi BK et al (2018) Fundamental limits on dynamic inference from single-cell snapshots. Proc Natl Acad Sci. Scholar
  214. Westermann AJ, Barquist L, Vogel J (2017) Resolving host–pathogen interactions by dual RNA-seq. PLoS Pathog 13:e1006033. Scholar
  215. Westermann AJ, Gorski SA, Vogel J (2012) Dual RNA-seq of pathogen and host. Nat Rev Microbiol 10:618–630. Scholar
  216. Whaley SG, Caudle KE, Simonicova L et al (2018) Jjj1 Is a Negative Regulator of Pdr1-Mediated Fluconazole Resistance in Candida glabrata. mSphere 3:1–11.
  217. Williams CR, Baccarella A, Parrish JZ, Kim CC (2016) Trimming of sequence reads alters RNA-Seq gene expression estimates. BMC Bioinformatics 17:103. Scholar
  218. Wilson D, Hube B (2014). From: Human Pathogenic Fungi: Molecular Biology and Pathogenic Mechanisms. Sullivan DJ, Moran GP (eds). Caister Academic Press, U.KGoogle Scholar
  219. Wolf T, Kämmer P, Brunke S, Linde J (2018) Two’s company: studying interspecies relationships with dual RNA-seq. Curr Opin Microbiol 42:7–12. Scholar
  220. Wu Y, Li Y, Yu S et al (2016) A Genome-Wide Transcriptional Analysis of Yeast-Hyphal Transition in Candida tropicalis by RNA-Seq. PLoS ONE 11:e0166645. Scholar
  221. Wu G, Zhao H, Li C et al (2015) Genus-Wide Comparative Genomics of Malassezia Delineates Its Phylogeny, Physiology, and Niche Adaptation on Human Skin. PLoS Genet 11.
  222. Xie Y, Wu G, Tang J et al (2014) SOAPdenovo-Trans: de novo transcriptome assembly with short RNA-Seq reads. Bioinformatics 30:1660–1666. Scholar
  223. Yang Q, Gao L, Tao M et al (2016) Transcriptomics Analysis of Candida albicans Treated with Huanglian Jiedu Decoction Using RNA-seq. Evidence-based Complement Altern Med 2016.
  224. Yang X, Liu D, Liu F et al (2013) HTQC: a fast quality control toolkit for Illumina sequencing data. BMC Bioinformatics 14:33. Scholar
  225. Yu L, Fernandez S, Brock G (2017) Power analysis for RNA-Seq differential expression studies. BMC Bioinformatics 18:234. Scholar
  226. Zhang N, Park YD, Williamson PR (2014) New technology and resources for cryptococcal research. Fungal Genet Biol. Scholar
  227. Zhao W, He X, Hoadley KA et al (2014) Comparison of RNA-Seq by poly (A) capture, ribosomal RNA depletion, and DNA microarray for expression profiling. BMC Genom 15:419. Scholar
  228. Zhao S, Zhang Y, Gordon W et al (2015) Comparison of stranded and non-stranded RNA-seq transcriptome profiling and investigation of gene overlap. BMC Genom 16:675. Scholar
  229. Zheng GXY, Terry JM, Belgrader P et al (2017) Massively parallel digital transcriptional profiling of single cells. Nat Commun. Scholar
  230. Zhu YY, Machleder EM, Chenchik A et al (2001) Reverse transcriptase template switching: a SMART approach for full-length cDNA library construction. Biotechniques 30:892–897Google Scholar
  231. Zoll J, Snelders E, Verweij PE, Melchers WJG (2016) Next-Generation Sequencing in the Mycology Lab. Curr Fungal Infect Rep 10:37–42. Scholar

Copyright information

© Springer Nature Switzerland AG 2018

Authors and Affiliations

  1. 1.Centre for Genomic Regulation, The Barcelona Institute of Science and TechnologyBarcelonaSpain
  2. 2.Universitat Pompeu FabraBarcelonaSpain
  3. 3.Institució Catalana de Recerca i Estudis AvançatsBarcelonaSpain

Personalised recommendations