Current analysis of host–parasite interactions with a focus on next generation sequencing data

Zoology

Volumn 119, Issue 4, 2016, Pages 298-306

  Greenwood, Jenny M ^a   Ezquerra, Alberto López ^a   Behrens, Sarah ^a   Branca, Antoine ^a,b   Mallet, Ludovic ^a  

^a UNIVERSITY OF MÜNSTER   (Germany)

^b UNIVERSITÉ PARIS SUD   (France)

Author keywords

Genomics; Host parasite interaction; Next generation sequencing; Transcriptomics

Indexed keywords

ANIMAL; BIOLOGICAL MODEL; COMPUTER SIMULATION; EVOLUTION; GENE EXPRESSION REGULATION; GENETICS; HOST PARASITE INTERACTION; IMMUNOLOGY; NUCLEIC ACID AMPLIFICATION; PROCEDURES;

ANIMALS; BIOLOGICAL EVOLUTION; COMPUTER SIMULATION; GENE EXPRESSION REGULATION; HOST-PARASITE INTERACTIONS; MODELS, IMMUNOLOGICAL; NUCLEIC ACID AMPLIFICATION TECHNIQUES;

EID: 84989837562     PISSN: 09442006     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.zool.2016.06.010     Document Type: Review

References (134)

1. Agrawal, A.A., Laforsch, C., Tollrian, R., Transgenerational induction of defence in animals and plants. Nature 401 (1999), 60–63.
2. Altmann, A., Weber, P., Quast, C., Rex-Haffner, M., Binder, E.B., Müller-Myhsok, B., vipR: variant identification in pooled DNA using R. Bioinformatics 27 (2011), i77–i84.
3. Anders, S., Huber, W., Differential expression analysis for sequence count data. Genome Biol., 11, 2010, R106.
4. Anders, S., Reyes, A., Huber, W., Detecting differential usage of exons from RNA-seq data. Genome Res. 22 (2012), 2008–2017.
5. Anders, S., McCarthy, D., Chen, Y., Okoniewski, M., Smyth, G., Huber, W., Robinson, M., Count-based differential expression analysis of RNA sequencing data using R and Bioconductor. Nat. Protoc. 8 (2013), 1765–1786.
6. Asgari, S., MicroRNA functions in insects. Insect Biochem. Mol. Biol. 43 (2013), 388–397.
7. Auer, P.L., Doerge, R.W., Statistical design and analysis of RNA sequencing data. Genetics 185 (2010), 405–416.
8. Bansal, V., Harismendy, O., Tewhey, R., Murray, S.S., Schork, N.J., Topol, E.J., Frazer, K.A., Accurate detection and genotyping of SNPs utilizing population sequencing data. Genome Res. 20 (2010), 537–545.
9. Bartel, D.P., MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116 (2004), 281–297.
10. Becq, J., Churlaud, C., Deschavanne, P., A benchmark of parametric methods for horizontal transfers detection. PLoS ONE, 5, 2010, e9989.
11. Behrens, S., Peuß, R., Milutinović, B., Eggert, H., Esser, D., Rosenstiel, P., Schulenburg, H., Bornberg-Bauer, E., Kurtz, J., Infection routes matter in population-specific responses of the red flour beetle to the entomopathogen Bacillus thuringiensis. BMC Genomics, 15, 2014, 445.
12. Bézier, A., Annaheim, M., Herbinière, J., Wetterwald, C., Gyapay, G., Bernard-Samain, S., Wincker, P., Roditi, I., Heller, M., Belghazi, M., Pfister-Wilhem, R., Periquet, G., Dupuy, C., Huguet, E., Volkoff, A., Lanzrein, B., Drezen, J.M., Polydnaviruses of braconid wasps derive from an ancestral nudivirus. Science 323 (2009), 926–930.
13. Boothroyd, J.C., Blader, I., Cleary, M., Singh, U., DNA microarrays in parasitology: strengths and limitations. Trends Parasitol. 19 (2003), 470–476.
14. Bose, J., Kloesener, M.H., Schulte, R.D., Multiple-genotype infections and their complex effect on virulence. Zoology 119 (2016), 339–349.
15. Buck, A.H., Coakley, G., Simbari, F., McSorley, H.J., Quintana, J.F., Le Bihan, T., Kumar, S., Abreu-Goodger, C., Lear, M., Harcus, Y., Ceroni, A., Babayan, S.A., Blaxter, M., Ivens, A., Maizels, R.M., Exosomes secreted by nematode parasites transfer small RNAs to mammalian cells and modulate innate immunity. Nat. Commun., 5, 2014, 5488.
16. Canchaya, C., Fournous, G., Chibani-Chennoufi, S., Dillmann, M.-L., Brüssow, H., Phage as agents of lateral gene transfer. Curr. Opin. Microbiol. 6 (2003), 417–424.
17. Castillo, J.C., Creasy, T., Kumari, P., Shetty, A., Shokal, U., Tallon, L.J., Eleftherianos, I., Drosophila anti-nematode and antibacterial immune regulators revealed by RNA-Seq. BMC Genomics, 16, 2015, 519.
18. Chang, Z., Li, G., Liu, J., Zhang, Y., Ashby, C., Liu, D., Cramer, C.L., Huang, X., Bridger: a new framework for de novo transcriptome assembly using RNA-seq data. Genome Biol. 16 (2015), 1–10.
19. Chiapello, H., Mallet, L., Guérin, C., Aguileta, G., Amselem, J., Kroj, T., Ortega-Abboud, E., Lebrun, M.-H., Henrissat, B., Gendrault, A., Rodolphe, F., Tharreau, D., Fournier, E., Deciphering genome content and evolutionary relationships of isolates from the fungus magnaporthe oryzae attacking different host plants. Genome Biol. Evol. 7 (2015), 2896–2912.
20. Chin, C.-S., Alexander, D.H., Marks, P., Klammer, A.A., Drake, J., Heiner, C., Clum, A., Copeland, A., Huddleston, J., Eichler, E.E., Turner, S.W., Korlach, J., Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat. Methods 10 (2013), 563–569.
21. Choi, Y.J., Aliota, M.T., Mayhew, G.F., Erickson, S.M., Christensen, B.M., Dual RNA-seq of parasite and host reveals gene expression dynamics during filarial worm–mosquito interactions. PLoS Negl. Trop. Dis., 8, 2014, e2905.
22. Chopra, R., Burow, G., Farmer, A., Mudge, J., Simpson, C.E., Burow, M.D., Comparisons of de novo transcriptome assemblers in diploid and polyploid species using peanut (Arachis spp.) RNA-Seq data. PLOS ONE, 9, 2014, e115055.
23. Clark, P.M., Loher, P., Quann, K., Brody, J., Londin, E.R., Rigoutsos, I., Argonaute CLIP-Seq reveals miRNA targetome diversity across tissue types. Sci. Rep., 4, 2014, 5947.
24. Cutler, D.J., Jensen, J.D., To pool, or not to pool?. Genetics 186 (2010), 41–43.
25. de Vienne, D.M., Ollier, S., Aguileta, G., Phylo-MCOA: a fast and efficient method to detect outlier genes and species in phylogenomics using multiple co-inertia analysis. Mol. Biol. Evol. 29 (2012), 1587–1598.
26. Dobin, A., Davis, C.A., Schlesinger, F., Drenkow, J., Zaleski, C., Jha, S., Batut, P., Chaisson, M., Gingeras, T.R., STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29 (2013), 15–21.
27. Durand, D., Halldórsson, B.V., Vernot, B., A hybrid micro-macroevolutionary approach to gene tree reconstruction. J. Computat. Biol. 13 (2006), 320–335.
28. Dutton, L.C., Paszkiewicz, K.H., Silverman, R.J., Splatt, P.R., Shaw, S., Nobbs, A.H., Lamont, R.J., Jenkinson, H.F., Ramsdale, M., Transcriptional landscape of trans-kingdom communication between Candida albicans and Streptococcus gordonii. Mol. Oral Microbiol. 31 (2016), 136–161.
29. Eggert, H., Kurtz, J., Diddens-de Buhr, M.F., Different effects of paternal trans-generational immune priming on survival and immunity in step and genetic offspring. Proc. R. Soc. B, 281, 2014, 20142089.
30. Engström, P.G., Steijger, T., Sipos, B., Grant, G.R., Kahles, A., Alioto, T., Behr, J., Bertone, P., Bohnert, R., Campagna, D., Davis, C.A., Dobin, A., Gingeras, T.R., Goldman, N., Guigó, R., Harrow, J., Hubbard, T.J., Jean, G., Kosarev, P., Li, S., Liu, J., Mason, C.E., Molodtsov, V., Ning, Z., Ponstingl, H., Prins, J.F., Rätsch, G., Ribeca, P., Seledtsov, I., Solovyev, V., Valle, G., Vitulo, N., Wang, K., Wu, T.D., Zeller, G., Systematic evaluation of spliced alignment programs for RNA-seq data. Nat. Methods 10 (2013), 1185–1191.
31. Esteve-Codina, A., Paudel, Y., Ferretti, L., Raineri, E., Megens, H.-J., Silio, L., Rodriguez, M., Groenen, M., Ramos-Onsins, S., Perez-Enciso, M., Dissecting structural and nucleotide genome-wide variation in inbred Iberian pigs. BMC Genomics, 14, 2013, 148.
32. Etebari, K., Furlong, M.J., Asgari, S., Genome wide discovery of long intergenic non-coding RNAs in diamondback moth (Plutella xylostella) and their expression in insecticide resistant strains. Sci. Rep., 5, 2015, 14642.
33. Fay, J.C., Wu, C.-I., Hitchhiking under positive Darwinian selection. Genetics 155 (2000), 1405–1413.
34. Foth, B.J., Tsai, I.J., Reid, A.J., Bancroft, A.J., Nichol, S., Tracey, A., Holroyd, N., Cotton, J.A., Stanley, E.J., Zarowiecki, M., Liu, J.Z., Huckvale, T., Cooper, P.J., Grencis, R.K., Berriman, M., Whipworm genome and dual-species transcriptome analyses provide molecular insights into an intimate host–parasite interaction. Nat. Genet. 46 (2014), 693–700.
35. Friesen, T.L., Stukenbrock, E.H., Liu, Z., Meinhardt, S., Ling, H., Faris, J.D., Rasmussen, J.B., Solomon, P.S., McDonald, B.A., Oliver, R.P., Emergence of a new disease as a result of interspecific virulence gene transfer. Nat. Genet. 38 (2006), 953–956.
36. Gasmi, L., Boulain, H., Gauthier, J., Hua-Van, A., Musset, K., Jakubowska, A.K., Aury, J.-M., Volkoff, A.-N., Huguet, E., Herrero, S., Drezen, J.M., Recurrent domestication by Lepidoptera of genes from their parasites mediated by bracoviruses. PLoS Genet., 11, 2015, e1005470.
37. Gnerre, S., MacCallum, I., Przybylski, D., Ribeiro, F.J., Burton, J.N., Walker, B.J., Sharpe, T., Hall, G., Shea, T.P., Sykes, S., Berlin, A.M., Aird, D., Costello, M., Daza, R., Williams, L., Nicol, R., Gnirke, A., Nusbaum, C., Lander, E.S., Jaffe, D.B., High-quality draft assemblies of mammalian genomes from massively parallel sequence data. Proc. Natl. Acad. Sci. U. S. A. 108 (2011), 1513–1518.
38. Grabherr, M.G., Haas, B.J., Yassour, M., Levin, J.Z., Thompson, D.A., Amit, I., Adiconis, X., Fan, L., Raychowdhury, R., Zeng, Q., Chen, Z., Mauceli, E., Hacohen, N., Gnirke, A., Rhind, N., di Palma, F., Birren, B.W., Nusbaum, C., Lindblad-Toh, K., Friedman, N., Regev, A., Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat. Biotechnol. 29 (2011), 644–652.
39. Grant, G.R., Farkas, M.H., Pizarro, A., Lahens, N., Schug, J., Brunk, B., Stoeckert, C.J., Hogenesch, J.B., Pierce, E.A., Comparative analysis of RNA-seq alignment algorithms and the RNA-seq unified mapper (RUM). Bioinformatics 27 (2011), 2518–2528.
40. Guo, H., Ingolia, N.T., Weissman, J.S., Bartel, D.P., Mammalian microRNAs predominantly act to decrease target mRNA levels. Nature 466 (2010), 835–840.
41. Haas, B.J., Delcher, A.L., Mount, S.M., Wortman, J.R., Smith, R.K. Jr., Hannick, L.I., Maiti, R., Ronning, C.M., Rusch, D.B., Town, C.D., Salzberg, S.L., White, O., Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies. Nucleic Acids Res. 31 (2003), 5654–5666.
42. Haas, B.J., Papanicolaou, A., Yassour, M., Grabherr, M., Blood, P.D., Bowden, J., Couger, M.B., Eccles, D., Li, B., Lieber, M., MacManes, M.D., Ott, M., Orvis, J., Pochet, N., Strozzi, F., Weeks, N., Westerman, R., William, T., Dewey, C.N., Henschel, R., LeDuc, R.D., Friedman, N., Regev, A., De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. Nat. Protoc. 8 (2013), 1494–1512.
43. Haase, D., Rieger, J.K., Witten, A., Stoll, M., Bornberg-Bauer, E., Kalbe, M., Reusch, T.B.H., Specific gene expression responses to parasite genotypes reveal redundancy of innate immunity in vertebrates. PLOS ONE, 9, 2014, e108001.
44. Hamilton, W.D., Sex versus non-sex versus parasite. Oikos 35 (1980), 282–290.
45. Harris, J.F., Micheva-Viteva, S., Li, N., Hong-Geller, E., Small RNA-mediated regulation of host–pathogen interactions. Virulence 4 (2013), 785–795.
46. Hess, A.M., Prasad, A.N., Ptitsyn, A., Ebel, G.D., Olson, K.E., Barbacioru, C., Monighetti, C., Campbell, C.L., Small RNA profiling of dengue virus–mosquito interactions implicates the PIWI RNA pathway in anti-viral defense. BMC Microbiol., 11, 2011, 45.
47. Hussain, M., Frentiu, F.D., Moreira, L.A., O'Neill, S.L., Asgari, S., Wolbachia uses host microRNAs to manipulate host gene expression and facilitate colonization of the dengue vector Aedes aegypti. Proc. Natl. Acad. Sci. U. S. A. 108 (2011), 9250–9255.
48. Jaenike, J., A hypothesis to account for the maintenance of sex within populations. Evol. Theory 3 (1978), 191–194.
49. Jayakodi, M., Jung, J.W., Park, D., Ahn, Y.J., Lee, S.C., Shin, S.Y., Shin, C., Yang, T.J., Kwon, H.W., Genome-wide characterization of long intergenic non-coding RNAs (lincRNAs) provides new insight into viral diseases in honey bees Apis cerana and Apis mellifera. BMC Genomics, 16, 2015, 680.
50. John, B., Enright, A.J., Aravin, A., Tuschl, T., Sander, C., Marks, D.S., Human microRNA targets. PLoS Biol., 2, 2004, e363.
51. Kim, D., Pertea, G., Trapnell, C., Pimentel, H., Kelley, R., Salzberg, S.L., TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol., 14, 2013, R36.
52. Kim, Y., Stephan, W., Detecting a local signature of genetic hitchhiking along a recombining chromosome. Genetics 160 (2002), 765–777.
53. Kingman, J.F., On the genealogy of large populations. J. Appl. Probab. 19A (1982), 27–43.
54. Koboldt, D.C., Chen, K., Wylie, T., Larson, D.E., McLellan, M.D., Mardis, E.R., Weinstock, G.M., Wilson, R.K., Ding, L., VarScan: variant detection in massively parallel sequencing of individual and pooled samples. Bioinformatics 25 (2009), 2283–2285.
55. Kofler, R., Orozco-terWengel, P., De Maio, N., Pandey, R.V., Nolte, V., Futschik, A., Kosiol, C., Schlötterer, C., PoPoolation: a toolbox for population genetic analysis of next generation sequencing data from pooled individuals. PLoS ONE, 6, 2011, e15925.
56. Kofler, R., Pandey, R.V., Schlötterer, C., PoPoolation2: identifying differentiation between populations using sequencing of pooled DNA samples (Pool-Seq). Bioinformatics 27 (2011), 3435–3436.
57. Krek, A., Grun, D., Poy, M.N., Wolf, R., Rosenberg, L., Epstein, E.J., MacMenamin, P., da Piedade, I., Gunsalus, K.C., Stoffel, M., Rajewsky, N., Combinatorial microRNA target predictions. Nat. Genet. 37 (2005), 495–500.
58. Kurtz, J., Franz, K., Evidence for memory in invertebrate immunity. Nature 425 (2003), 37–38.
59. Lee, Y.S., Nakahara, K., Pham, J.W., Kim, K., He, Z., Sontheimer, E.J., Carthew, R.W., Distinct roles for Drosophila Dicer-1 and Dicer-2 in the siRNA/miRNA silencing pathways. Cell 117 (2004), 69–81.
60. Leggett, R.M., MacLean, D., Reference-free SNP detection: dealing with the data deluge. BMC Genomics, 15, 2014, S10.
61. Leng, N., Dawson, J.A., Thomson, J.A., Ruotti, V., Rissman, A.I., Smits, B.M.G., Haag, J.D., Gould, M.N., Stewart, R.M., Kendziorski, C., EBSeq: an empirical Bayes hierarchical model for inference in RNA-seq experiments. Bioinformatics 29 (2013), 1035–1043.
62. Lenz, T.L., Eizaguirre, C., Rotter, B., Kalbe, M., Milinski, M., Exploring local immunological adaptation of two stickleback ecotypes by experimental infection and transcriptome-wide digital gene expression analysis. Mol. Ecol. 22 (2013), 774–786.
63. Lewis, B.P., Burge, C.B., Bartel, D.P., Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 120 (2005), 15–20.
64. Li, H., A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. Bioinformatics 27 (2011), 2987–2993.
65. Lindner, R., Friedel, C.C., A comprehensive evaluation of alignment algorithms in the context of RNA-Seq. PLoS ONE, 7, 2012, e52403.
66. Liu, C.G., Calin, G.A., Volinia, S., Croce, C.M., MicroRNA expression profiling using microarrays. Nat. Protoc. 3 (2008), 563–578.
67. Liu, F., Lu, J., Hu, W., Wang, S.Y., Cui, S.J., Chi, M., Yan, Q., Wang, X.R., Song, H.D., Xu, X.N., Wang, J.J., Zhang, X.L., Zhang, X., Wang, Z.Q., Xue, C.L., Brindley, P.J., McManus, D.P., Yang, P.Y., Feng, Z., Chen, Z., Han, Z.G., New perspectives on host–parasite interplay by comparative transcriptomic and proteomic analyses of Schistosoma japonicum. PLoS Pathog., 2, 2006, e29.
68. Liu, Y., Zhou, J., White, K.P., RNA-seq differential expression studies: more sequence, or more replication?. Bioinformatics 30 (2014), 301–304.
69. Mackay, T.F.C., The genetic architecture of quantitative traits. Annu. Rev. Genet. 35 (2001), 303–339.
70. Magoc, T., Wood, D., Salzberg, S.L., EDGE-pro: estimated degree of gene expression in prokaryotic genomes. Evol. Bioinform. Online 9 (2013), 127–136.
71. Mallon, E.B., Loosli, R., Schmid-Hempel, P., Specific versus nonspecific immune defense in the bumblebee, Bombus terrestris L. Evolution 57 (2003), 1444–1447.
72. Marioni, J.C., Mason, C.E., Mane, S.M., Stephens, M., Gilad, Y., RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays. Genome Res. 18 (2008), 1509–1517.
73. Martins, N.E., Faria, V.G., Teixeira, L., Magalhães, S., Sucena, É., Host adaptation is contingent upon the infection route taken by pathogens. PLoS Pathog., 9, 2013, e1003601.
74. Masri, L., Branca, A., Sheppard, A.E., Papkou, A., Laehnemann, D., Guenther, P.S., Prahl, S., Saebelfeld, M., Hollensteiner, J., Liesegang, H., Brzuszkiewicz, E., Daniel, R., Michiels, N.K., Schulte, R.D., Kurtz, J., Rosenstiel, P., Telschow, A., Bornberg-Bauer, E., Schulenburg, H., Host–pathogen coevolution: the selective advantage of Bacillus thuringiensis virulence and its cry toxin genes. PLoS Biol., 13, 2015, e1002169.
75. McDonald, J.H., Kreitman, M., Adaptive protein evolution at the Adh locus in Drosophila. Nature 351 (1991), 652–654.
76. McKenna, A., Hanna, M., Banks, E., Sivachenko, A., Cibulskis, K., Kernytsky, A., Garimella, K., Altshuler, D., Gabriel, S., Daly, M., DePristo, M.A., The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20 (2010), 1297–1303.
77. Morris, K.V., Mattick, J.S., The rise of regulatory RNA. Nat. Rev. Genet. 15 (2014), 423–437.
78. Mortazavi, A., Williams, B.A., McCue, K., Schaeffer, L., Wold, B., Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat. Methods 5 (2008), 621–628.
79. Mukherjee, K., Vilcinskas, A., Development and immunity-related microRNAs of the lepidopteran model host Galleria mellonella. BMC Genomics, 15, 2014, 705.
80. Mundry, M., Bornberg-Bauer, E., Sammeth, M., Feulner, P.G.D., Evaluating characteristics of de novo assembly software on 454 transcriptome data: a simulation approach. PLoS ONE, 7, 2012, e31410.
81. Myers, E.W., Sutton, G.G., Delcher, A.L., Dew, I.M., Fasulo, D.P., Flanigan, M.J., Kravitz, S.A., Mobarry, C.M., Reinert, K.H.J., Remington, K.A., Anson, E.L., Bolanos, R.A., Chou, H.-H., Jordan, C.M., Halpern, A.L., Lonardi, S., Beasley, E.M., Brandon, R.C., Chen, L., Dunn, P.J., Lai, Z., Liang, Y., Nusskern, D.R., Zhan, M., Zhang, Q., Zheng, X., Rubin, G.M., Adams, M.D., Venter, J.C., A whole-genome assembly of Drosophila. Science 287 (2000), 2196–2204.
82. Neupane, S., Finlay, R.D., Alström, S., Elfstrand, M., Högberg, N., Transcriptional responses of the bacterial antagonist Serratia plymuthica to the fungal phytopathogen Rhizoctonia solani. Environ. Microbiol. Rep. 7 (2015), 123–127.
83. Ngwa, C.J., Scheuermayer, M., Mair, G.R., Kern, S., Brügl, T., Wirth, C.C., Aminake, M.N., Wiesner, J., Fischer, R., Vilcinskas, A., Pradel, G., Changes in the transcriptome of the malaria parasite Plasmodium falciparum during the initial phase of transmission from the human to the mosquito. BMC Genomics, 14, 2013, 256.
84. Nielsen, R., Molecular signatures of natural selection. Annu. Rev. Genet. 39 (2005), 197–218.
85. Nookaew, I., Papini, M., Pornputtapong, N., Scalcinati, G., Fagerberg, L., Uhlén, M., Nielsen, J., A comprehensive comparison of RNA-Seq-based transcriptome analysis from reads to differential gene expression and cross-comparison with microarrays: a case study in Saccharomyces cerevisiae. Nucleic Acids Res. 40 (2012), 10084–10097.
86. Ochman, H., Lawrence, J.G., Groisman, E.A., Lateral gene transfer and the nature of bacterial innovation. Nature 405 (2000), 299–304.
87. Ouyang, S., Zhu, W., Hamilton, J., Lin, H., Campbell, M., Childs, K., Thibaud-Nissen, F., Malek, R.L., Lee, Y., Zheng, L., Orvis, J., Haas, B., Wortman, J., Buell, C.R., The TIGR rice genome annotation resource: improvements and new features. Nucleic Acids Res. 35 (2007), D883–D887.
88. Pabinger, S., Dander, A., Fischer, M., Snajder, R., Sperk, M., Efremova, M., Krabichler, B., Speicher, M.R., Zschocke, J., Trajanoski, Z., A survey of tools for variant analysis of next-generation genome sequencing data. Brief. Bioinform. 15 (2014), 256–278.
89. Pavlidis, P., Živković, D., Stamatakis, A., Alachiotis, N., Sweed: likelihood-based detection of selective sweeps in thousands of genomes. Mol. Biol. Evol. 30 (2013), 2224–2234.
90. Perlin, M.H., Amselem, J., Fontanillas, E., Toh, S.S., Chen, Z., Goldberg, J., Duplessis, S., Henrissat, B., Young, S., Zeng, Q., Aguileta, G., Petit, E., Badouin, H., Andrews, J., Razeeq, D., Gabaldón, T., Quesneville, H., Giraud, T., Hood, M.E., Schultz, D.J., Cuomo, C.A., Sex and parasites: genomic and transcriptomic analysis of Microbotryum lychnidis-dioicae, the biotrophic and plant-castrating anther smut fungus. BMC Genomics, 16, 2015, 461.
91. Pittman, K.J., Aliota, M.T., Knoll, L.J., Dual transcriptional profiling of mice and Toxoplasma gondii during acute and chronic infection. BMC Genomics, 15, 2014, 806.
92. Pride, D.T., Blaser, M.J., Identification of horizontally acquired genetic elements in Helicobacter pylori and other prokaryotes using oligonucleotide difference analysis. Genome Lett. 1 (2002), 2–15.
93. Raineri, E., Ferretti, L., Esteve-Codina, A., Nevado, B., Heath, S., Pérez-Enciso, M., SNP calling by sequencing pooled samples. BMC Bioinform., 13, 2012, 239.
94. Rapaport, F., Khanin, R., Liang, Y., Pirun, M., Krek, A., Zumbo, P., Mason, C.E., Socci, N.D., Betel, D., Comprehensive evaluation of differential gene expression analysis methods for RNA-seq data. Genome Biol., 14, 2013, R95.
95. Riddell, C.E., Lobaton Garces, J.D., Adams, S., Barribeau, S.M., Twell, D., Mallon, E.B., Differential gene expression and alternative splicing in insect immune specificity. BMC Genomics, 15, 2014, 1031.
96. Robinson, M.D., McCarthy, D.J., Smyth, G.K., edgeR: a bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26 (2010), 139–140.
97. Roth, O., Sadd, B.M., Schmid-Hempel, P., Kurtz, J., Strain-specific priming of resistance in the red flour beetle, Tribolium castaneum. Proc. Natl. Acad. Sci. U. S. A. 276 (2009), 145–151.
98. Roth, O., Joop, G., Eggert, H., Hilbert, J., Daniel, J., Schmid-Hempel, P., Kurtz, J., Paternally derived immune priming for offspring in the red flour beetle, Tribolium castaneum. J. Anim. Ecol. 79 (2010), 403–413.
99. Sadd, B.M., Schmid-Hempel, P., Insect immunity shows specificity in protection upon secondary pathogen exposure. Curr. Biol. 16 (2006), 1206–1210.
100. Scaria, V., Pasha, A., Long non-coding RNAs in infection biology. Front. Genet., 3, 2012, 308.
101. Schlotterer, C., Tobler, R., Kofler, R., Nolte, V., Sequencing pools of individuals – mining genome-wide polymorphism data without big funding. Nat. Rev. Genet. 15 (2014), 749–763.
102. Schnettler, E., Donald, C.L., Human, S., Watson, M., Siu, R.W., McFarlane, M., Fazakerley, J.K., Kohl, A., Fragkoudis, R., Knockdown of piRNA pathway proteins results in enhanced Semliki Forest virus production in mosquito cells. J. Genet. Virol. 94 (2013), 1680–1689.
103. Schrider, D.R., Begun, D.J., Hahn, M.W., Detecting highly differentiated copy-number variants from pooled population sequencing. Pac. Symp. Biocomput. 18 (2013), 344–355.
104. Schulenburg, H., Ewbank, J.J., Diversity and specificity in the interaction between Caenorhabditis elegans and the pathogen Serratia marcescens. BMC Evol. Biol., 4, 2004, 49.
105. Schulze, S., Henkel, S.G., Driesch, D., Guthke, R., Linde, J., Computational prediction of molecular pathogen–host interactions based on dual transcriptome data. Front. Microbiol., 6, 2015, 65.
106. Shimodaira, H., An approximately unbiased test of phylogenetic tree selection. Syst. Biol. 51 (2002), 492–508.
107. Skalsky, R.L., Cullen, B.R., Viruses, microRNAs, and host interactions. Annu. Rev. Microbiol. 64 (2010), 123–141.
108. Soneson, C., Delorenzi, M., A comparison of methods for differential expression analysis of RNA-seq data. BMC Bioinform., 14, 2013, 91.
109. Sonnhammer, E.L., Koonin, E.V., Orthology, paralogy and proposed classification for paralog subtypes. Trends Genet. 18 (2002), 619–620.
110. Stead, L.F., Sutton, K.M., Taylor, G.R., Quirke, P., Rabbitts, P., Accurately identifying low-allelic fraction variants in single samples with next-generation sequencing: applications in tumor subclone resolution. Hum. Mutat. 34 (2013), 1432–1438.
111. Steijger, T., Abril, J.F., Engström, P.G., Kokocinski, F., RGASP Consortium, Hubbard, T.J., Guigó, R., Harrow, J., Bertone, P., Akerman, M., Alioto, T., Ambrosini, G., Antonarakis, S.E., Behr, J., Bertone, P., Assessment of transcript reconstruction methods for RNA-seq. Nat. Methods 10 (2013), 1177–1184.
112. Stolzer, M., Lai, H., Xu, M., Sathaye, D., Vernot, B., Durand, D., Inferring duplications, losses, transfers and incomplete lineage sorting with nonbinary species trees. Bioinformatics 28 (2012), i409–i415.
113. Syvanen, M., Horizontal gene transfer: evidence and possible consequences. Annu. Rev. Genet. 28 (1994), 237–261.
114. Tajima, F., Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123 (1989), 585–595.
115. Tierney, L., Linde, J., Müller, S., Brunke, S., Molina, J.C., Hube, B., Schöck, U., Guthke, R., Kuchler, K., An interspecies regulatory network inferred from simultaneous RNA-seq of Candida albicans invading innate immune cells. Front. Microbiol., 3, 2012, 85.
116. Torres-Cortés, G., Ghignone, S., Bonfante, P., Schüßler, A., Mosaic genome of endobacteria in arbuscular mycorrhizal fungi: transkingdom gene transfer in an ancient mycoplasma–fungus association. Proc. Natl. Acad. Sci. U. S. A. 112 (2015), 7785–7790.
117. Trapnell, C., Roberts, A., Goff, L., Pertea, G., Kim, D., Kelley, D.R., Pimentel, H., Salzberg, S.L., Rinn, J.L., Pachter, L., Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat. Protoc. 7 (2012), 562–578.
118. Trapnell, C., Hendrickson, D.G., Sauvageau, M., Goff, L., Rinn, J.L., Pachter, L., Differential analysis of gene regulation at transcript resolution with RNA-seq. Nat. Biotechnol. 31 (2013), 46–53.
119. Ule, J., Jensen, K.B., Ruggiu, M., Mele, A., Ule, A., Darnell, R.B., CLIP identifies Nova-regulated RNA networks in the brain. Science 302 (2003), 1212–1215.
120. Ulitsky, I., Bartel, D.P., lincRNAs: genomics, evolution, and mechanisms. Cell 154 (2013), 26–46.
121. Uricaru, R., Rizk, G., Lacroix, V., Quillery, E., Plantard, O., Chikhi, R., Lemaitre, C., Peterlongo, P., Reference-free detection of isolated SNPs. Nucleic Acids Res., 43, 2015, e11.
122. Vallania, F.L., Druley, T.E., Ramos, E., Wang, J., Borecki, I., Province, M., Mitra, R.D., High-throughput discovery of rare insertions and deletions in large cohorts. Genome Res. 20 (2010), 1711–1718.
123. Vernot, B., Stolzer, M., Goldman, A., Durand, D., Reconciliation with non-binary species trees. J. Comput. Biol. 15 (2008), 981–1006.
124. Vizoso, D.B., Ebert, D., Phenotypic plasticity of host–parasite interactions in response to the route of infection. J. Evol. Biol. 18 (2005), 911–921.
125. Wang, K., Singh, D., Zeng, Z., Coleman, S.J., Huang, Y., Savich, G.L., He, X., Mieczkowski, P., Grimm, S.A., Perou, C.M., MacLeod, J.N., Chiang, D.Y., Prins, J.F., Liu, J., MapSplice: accurate mapping of RNA-seq reads for splice junction discovery. Nucleic Acids Res., 38, 2010, e178.
126. Wayne, M.L., McIntyre, L.M., Combining mapping and arraying: an approach to candidate gene identification. Proc. Natl. Acad. Sci. U. S. A. 99 (2002), 14903–14906.
127. Wei, Z., Wang, W., Hu, P., Lyon, G.J., Hakonarson, H., SNVer: a statistical tool for variant calling in analysis of pooled or individual next-generation sequencing data. Nucleic Acids Res., 39, 2011, e132.
128. Westermann, A.J., Gorski, S.A., Vogel, J., Dual RNA-seq of pathogen and host. Nat. Rev. Microbiol. 10 (2012), 618–630.
129. Wu, T.D., Nacu, S., Fast and SNP-tolerant detection of complex variants and splicing in short reads. Bioinformatics 26 (2010), 873–881.
130. Yang, G., Yang, L., Zhao, Z., Wang, J., Zhang, X., Signature miRNAs involved in the innate immunity of invertebrates. PLoS ONE, 7, 2012, e39015.
131. Yang, Z., Paml 4: phylogenetic analysis by maximum likelihood. Mol. Biol. Evol. 24 (2007), 1586–1591.
132. Zhang, C., Darnell, R.B., Mapping in vivo protein-RNA interactions at single-nucleotide resolution from HITS-CLIP data. Nat. Biotechnol. 29 (2011), 607–614.
133. Zhang, G., Hussain, M., Asgari, S., Regulation of arginine methyltransferase 3 by a Wolbachia-induced microRNA in Aedes aegypti and its effect on Wolbachia and dengue virus replication. Insect Biochem. Mol. Biol. 53 (2014), 81–88.
134. Zheng, H., Fu, R., Wang, J.T., Liu, Q., Chen, H., Jiang, S.W., Advances in the techniques for the prediction of microRNA targets. Int. J. Mol. Sci. 14 (2013), 8179–8187.