SUPPLEMENTARY INFORMATION Todd, Black and Gemmell. The power and promise of RNA-seq in ecology and evolution. Appendix S1 References reviewed Details of references reviewed in order to evaluate trends in biological replicate usage by ecoevolutionary studies utilising RNA-seq data for differential expression analysis (2008-2014) (Box 1). For each of 158 studies reporting statistical differential expression analysis from RNA-seq data, the table below gives the focal organism, sequencing platform, and details of the experimental design, including the number of treatment groups, whether or not multiple samples were pooled for library preparation, and the number of biological replicates used (as the number of replicate library preparations per treatment group). 3 Pooled/separate library preparation Pooled Biological replicates 2 Illumina 2 Pooled 1 454 Illumina Illumina 2 4 4 Pooled Separate Separate 1 4, 5 or 6 4 to 6 Illumina 9 Separate 1 Illumina 54 Separate 2 Acyrthosiphon pisum Illumina 2 Pooled 2 Microplitis demolitor Illumina 4 Pooled 1 Saccharomyces spp. Ceratitis capitata Aphis glycines Illumina Illumina Illumina 4 6 6 Separate Pooled Pooled 2 3 4 Polygonia c-album Illumina 4 Pooled 2 Illumina Illumina 454 2 12 2 Separate Pooled Pooled 10 1 1 SOLiD 2 Separate 1 Illumina 6 Separate 6 to 10 Illumina 8 Pooled 1 or 2 Illumina 3 Separate 2, 3 or 4 Paper Year Subject Platform Conditions Arfi et al. 2013 2013 Pycnoporus coccineus Sarotherodon melanotheron heudelotii Hyriopsis cumingii Acropora hyacinthus Symbiodinium spp. Symbiodinium microadriaticum multiple Illumina Avarre et al. 2014 Bai et al. 2013 Barshis et al. 2013 Barshis et al. 2014 Baumgarten et al. 2013 Brawand et al. 2011 Burke and Moran 2011 Burke and Strand 2014 Busby et al. 2011 Calla et al. 2014 Cassone et al. 2014 Celorio-Mancera et al. 2013 Chapman et al. 2013 Chen et al. 2010 Chen et al. 2011 2014 2013 2013 2014 2013 2011 2011 2014 2011 2014 2014 2013 2013 2010 Chu et al. 2014 2014 Senecio spp. Locusta migratoria Balanus amphitrite Methanolobus psychrophilus R15 Peromyscus maniculatus Brugia malayi, Aedes aegypti Nucella lapillus Coate et al. 2013 2013 Glycine dolichocarpa Illumina 12 Pooled 3 2013 multiple Amphimedon queenslandica Illumina 4 Pooled 1 SOLiD 4 Pooled 1 Trichoderma harzianum Illumina 3 Separate 1 Separate 3 Chen et al. 2012 Cheviron et al. 2014 Choi et al. 2014 Colombo et al. 2013 Conaco et al. 2012 2011 2012 2014 2014 2012 Crivelente Horta et al. 2014 Czesny et al. 2012 2014 2012 Alosa pseudoharengus 454 2 Daniels et al. 2014 2014 Junonia coenia Illumina 8 Pooled 2 Darby et al. 2014 2014 Wolbachia Illumina 2 Separate 3 de Groot et al. 2014 Denekamp et al. 2011 Dion-Cote et al. 2014 Dirks et al. 2014 2014 Deinococcus deserti Illumina 2 Separate 1 Brachionus plicatilis Illumina 13 Pooled 1 lake whitefish Illumina 5 Pooled 4 or 5 Anguilla anguilla Illumina 4 Separate 3 or 4 2011 2014 2014 Dong et al. 2014 2014 Bactrocera minax Illumina 4 Dou et al. 2013 Separate 1 2013 Liposcelis bostrychophila Illumina 3 Pooled 1 Dowen et al. 2012 2012 Arabidopsis thaliana Illumina 4 Separate 2 Duncan et al. 2014 2014 multiple Illumina 2 Pooled 1 Dunning et al. 2013 2013 Micrarchus nov. sp. 2 454 2 Separate 2 Dunning et al. 2014 2014 Micrarchus spp. Illumina 6 Separate 3 or 6 Ekblom et al. 2012 2012 Philomachus pugnax 454 6 Separate 3 to 6 Ekblom et al. 2014 2014 Passer domesticus Illumina 3 separate 1 Elran et al. 2014 Esponosa et al. 2014 Etebari et al. 2011 Eves-van den Akker et al. 2014 Fan et al. 2013 2014 Nematostella vectensis Illumina 5 Pooled 3 or 4 Perkinsus marinus Illumina 2 Separate 3 Plutella xylostella Illumina 2 Pooled 1 Nacobbus aberrans Illumina 3 Pooled 3 2013 Salicornia europaea Illumina 12 Pooled 1 Fang et al. 2013 Feldmeyer et al. 2014 Ferreira et al. 2013 2013 Caulobacter crescentus Temnothorax longispinosus Polistes canadensis SOLiD 5 Separate 3 Illumina 4 Pooled 1 Forconi et al. 2014 Franssen et al. 2014 2014 2011 2014 2014 2013 2014 2014 Fraser et al. 2014 Garcia-Vedrenne et al. 2013 Gerdol et al. 2014 2014 Grumaz et al. 2013 2013 2014 illumina 4 Separate 2 to 6 Latimeria spp. Zostera marina, Nanozostera noltii Poecilia latipinna Illumina 3 separate 1 Illumina 8 Pooled 1 Illumina 4 Separate 2 or 3 Quahog Parasite Unknown Illumina 2 Pooled 1 Mytilus galloprovincialis Illumina 4 Pooled 1 2013 Candida spp. Illumina 4 Separate 1 or 3 Gunter et al. 2013 2013 Astatoreochromis alluaudi Illumina 2 Separate 5 Hanson et al. 2013 2013 Brachionus calyciflorus Illumina 2 Pooled 2 Harr et al. 2010 2010 Mus spp. Illumina 4 Separate 2 Henning et al. 2013 Hershkovitz et al. 2013 Hook et al. 2014a 2013 Amphilophus citrinellus illumina 3 Separate 6 Metschnikowia fructicola Illumina 4 Pooled 1 2014 Ceratoneis closterium 454 4 Pooled 1 Hook et al. 2014b 2014 Melita plumulosa 454 4 Pooled 1 Huth and Place 2013 Ibarra-Laclette et al. 2011 Ignatov et al. 2010 2013 Trematomus bernacchii 454 6 Pooled 1 Utricularia gibba 454 4 Pooled 1 2010 Mycobacterium avium 454 2 Pooled 1 Jeukens et al. 2010 2013 2011 2010 Coregonus clupeaformis 454 2 Pooled 1 Kanter et al. 2013 2013 Ambrosia artemisiifolia 454 2 Pooled 1 Kao et al. 2013 2013 Schmidtea mediterranea SOLiD 12 Pooled 2 Kelley et al. 2012 2012 Poecilia mexicana Illumina 2 Separate 3 Kersten et al. 2013 2013 Quercus rober L. Illumina 4 Pooled 1 Kim et al. 2013 2013 Pseudomonas putida Illumina 4 Separate 1 Kimura et al. 2011 Kobayashi et al. 2013 Kodama et al. 2014 2011 Dokdonia sp. MED134 454 3 Separate 1 Shorea beccariana 454 4 Separate 1 Paramecium bursaria Illumina 2 Separate 3 Kumaran et al. 2014 2013 2014 2014 Bactrocera tryoni Illumina 2 Separate 1 Lee et al. 2013 2013 Laodelphax striatellus 454 2 Pooled 1 Lei, Y. et al. 2014 2014 Plutella xylostella Illumina 3 Separate 1 Lei, B. et al. 2014 2014 Nicotiana tabacum Illumina 10 Pooled 1 Li et al. 2013 2013 Chrysopa pallens Illumina 10 Pooled 1 Li et al. 2012 2012 Cnaphalocrocis medinalis Illumina 5 Pooled 1 Liu et al. 2014 2014 Ostrinia furnacalis Illumina 2 Pooled 1 2013 Vicia sativa Illumina 8 Pooled 1 Fagopyrum spp. 454 2 Pooled 1 Oxyrrhis marina Pyganodon grandis, Uniomerus tetralasmus Portunus trituberculatus 454 2 Pooled 1 Illumina 4 Pooled 3 Illumina 3 Pooled 1 Amphilophus citrinellus Illumina 6 Separate 4, 5 or 6 Liu et al. 2013 Logacheva et al. 2011 Lowe et al. 2011 Luo et al. 2014 2011 2011 2014 Lv et al. 2013 Manousaki et al. 2013 Marra et al. 2014 2013 2014 multiple Illumina 3 Separate 4 Mayfield et al. 2014 McDonnell et al. 2013 Meng et al. 2013 2014 Pocillopora damicornis Illumina 4 Separate 3 Apis mellifera Illumina 3 Pooled 2 2013 Sinocyclocheilus spp. Illumina 4 Pooled 1 Meyer et al. 2011 Moyers and Rieseberg 2013 Newton et al. 2013 2011 Acropora millepora 454 6 Pooled 1 Helianthus annuus Illumina 2 Separate 6 2013 Lates calcarifer Illumina 4 Pooled 1 Ng et al. 2014 2014 Illumina 5 Pooled 1 Illumina 2 Pooled 4 2013 2013 2013 2014 Gallus gallus Nothobranchius furzeri, N. kadleci Salvelinus alpinus Illumina 4 Separate 3 Novo et al. 2013 2013 multiple Illumina 3 Separate 1 Nowack et al. 2011 2011 Paulinella chomatophora Illumina 2 Separate 1 2012 multiple 454 4 Pooled 1 Palumbi et al. 2014 2014 Acropora hyacinthus Illumina 2 Separate 6 Parikh et al. 2010 Pereira Lima Teixeria et al. 2014 Perry et al. 2014 2010 Dictyostelium spp. Illumina 2 Separate 2 Theobroma cacao Illumina 2 Separate 5 Ng'oma et al. 2014 Norman et al. 2014 Ozawa et al. 2012 2014 2014 2014 Drosophila melanogaster Illumina 6 Pooled 3 Pinosio et al. 2014 2014 Pinus halepensis Illumina 2 Separate 1 Poelchau et al. 2011 2011 Aedes albopictus 454 2 Pooled 1 Poelchau et al. 2013 2013 Aedes albopictus Illumina 6 Pooled 2 or 3 Poelchau et al. 2014 Prasopdee et al. 2014 Pravosudov et al. 2013 Reinhardt et al. 2014 Rendón-Anaya et al. 2012 Rinker et al. 2013 Sarropoulou et al. 2014 Schoville et al. 2012 2014 Aedes albopictus Bithynia siamensis goniomphalos Illumina 4 Pooled 3 Illumina 2 Pooled 1 Poecile atricapillus Illumina 2 Pooled 5 Teleopsis dalmanni Centruroides noxius Hoffmann Anopheles spp. Illumina 2 Pooled 2 454 2 Pooled 1 Illumina 2 Pooled 1 Sarda sarda Illumina 5 Pooled 1 2014 2013 2014 2012 2013 2014 2012 Tigriopus californicus Illumina 4 Pooled 1 Schunter et al. 2014 Schwarzenberger et al. 2014 Seto and Tamura 2013 Shelomi et al. 2014 2014 Tripterygion delaisi Illumina 3 Separate 5 Daphnia Illumina 3 Pooled 3 Drosophila spp. 454 4 Pooled 1 2014 Peruphasma schultei Illumina 2 Pooled 3 Shiao et al. 2012 2014 2013 2012 Mus musculus Illumina 2 Pooled 1 Sikhakolli et al. 2012 2012 Fusarium spp. Illumina 12 Separate 1 Sloan et al. 2014a 2014 Pachypsylla venusta Illumina 2 Pooled 3 Small et al. 2013 2013 Smith, G. et al. 2014 Syngnathus spp. 454 4 Pooled 1 2014 Manduca sexta Illumina 2 Pooled 4 Smith, G. et al. 2013 2013 Drosophila mojavensis SOLiD 4 Pooled 4 Smith, S. et al. 2013 Somervou et al. 2014 Szoevenyi et al. 2011 Szoevenyi et al. 2013 Traeger et al. 2013 2013 Melanotaenia duboulayi Illumina 2 Separate 6 Melitaea cinxia Illumina 4 Separate 15 Funaria hygrometrica 454 2 Separate 1 Funaria hygrometrica Illumina 6 Pooled 1 2013 multiple Illumina 3 Pooled 2 2013 Ficedula albicollis Illumina 16 Separate 5 Artemia franciscana 454 2 Pooled 1 Gluconacetobacter diazotrophicus Illumina 8 Pooled 1 Gryllus firmus Illumina 3 Pooled 3 Pocillopora damicornis Illumina 4 Pooled 1 2014 soybean SOLiD 11 Pooled 1 Illumina Uebbing et al. 2013 Valenzuela-Miranda et al. 2014 Vargas et al. 2014 Vellichirammal et al. 2014 Vidal-Dupiol et al. 2013 Wang, L. et al. 2014 Wang, X. et al. 2014 2014 2011 2013 2014 2014 2014 2013 2014 Locusta migratoria 10 Pooled 1 Wang, Z. et al. 2014 2014 Lupinus albus Illumina 3 Pooled 1 Wei et al. 2013 2013 Barbarea vulgaris Illumina 7 Pooled 1 2013 Acropora millepora Illumina 3 Separate 4 Scaptomyza flava Illumina 4 Pooled 2 454 2 Separate 6 Illumina 7 Pooled 3 Weiss et al. 2013 Whiteman et al. 2012 Wolf et al. 2010 2012 Xiang et al. 2010 2010 Corvus corone Heliocidaris erythrogramma Lateolabrax japonicus Illumina 2 Pooled 1 Xie et al. 2014 2014 Bemisia tabaci Illumina 8 Pooled 1 Xu et al. 2012 2012 Sogatella furcifera Illumina 2 Pooled 1 Xu et al. 2013 2013 Leuciscus waleckii Illumina 6 Pooled 1 Xu et al. 2014 2014 Oryza sativa Illumina 5 Pooled 1 Xue et al. 2010 2010 Nilaparvata lugens Illumina 6 Pooled 1 Wygoda et al. 2014 2010 2014 Yang et al. 2014 2014 Phalaenopsis Illumina 2 Separate 1 Yeaman et al. 2014 2014 multiple Illumina 14 Separate 3 to 8 Yek et al. 2013 2013 Acromyrmex echinatior Illumina 5 Pooled 3 Yoshida et al. 2014 2014 Loligo bleekeri Illumina 2 Pooled 1 Zhai et al. 2013 2013 Nilaparvata lugens Illumina 4 Pooled 1 Zhang et al. 2011 2011 Xiphophorus maculatus 454 2 Pooled 1 Zhao et al. 2013 2013 Helicoverpa armigera Illumina 2 Pooled 1 Zheng et al. 2012 2012 Bactrocera dorsalis 454 3 Pooled 1 Zheng et al. 2013 2013 Nannochloropsis spp. Illumina 2 Separate 1 2014 Apostichopus japonicus Illumina 4 Pooled 1 2014 Solanum lycopersicum Illumina 2 Pooled 2 Zhou et al. 2014 Zouari et al. 2014 References Arfi, Y., Levasseur, A., & Record, E. (2013). Differential gene expression in Pycnoporus coccineus during interspecific mycelial interactions with different competitors. Applied and Environmental Microbiology, 79(21), 6626-6636. doi: 10.1128/aem.02316-13. Avarre, J. C., Dugue, R., Alonso, P., Diombokho, A., Joffrois, C., Faivre, N., . . . Durand, J. D. (2014). Analysis of the black-chinned tilapia Sarotherodon melanotheron heudelotii reproducing under a wide range of salinities: from RNA-seq to candidate genes. Molecular Ecology Resources, 14(1), 139-149. doi: 10.1111/1755-0998.12148. Bai, Z., Zheng, H., Lin, J., Wang, G., & Li, J. (2013). Comparative analysis of the transcriptome in tissues secreting purple and white nacre in the pearl mussel Hyriopsis cumingii. PloS one, 8(1), e53617. Barshis, D. J., Ladner, J. T., Oliver, T. A., Seneca, F. O., Traylor-Knowles, N., & Palumbi, S. R. (2013). Genomic basis for coral resilience to climate change. Proc Natl Acad Sci USA, 110(4), 1387-1392. doi: 10.1073/pnas.1210224110. Barshis, D. J., Ladner, J. T., Oliver, T. A., & Palumbi, S. R. (2014). Lineage-specific transcriptional profiles of Symbiodinium spp. unaltered by heat stress in a coral host. Molecular Biology and Evolution, 31(6), 1343-1352. doi: 10.1093/molbev/msu107. Baumgarten, S., Bayer, T., Aranda, M., Liew, Y. J., Carr, A., Micklem, G., & Voolstra, C. R. (2013). Integrating microRNA and mRNA expression profiling in Symbiodinium microadriaticum, a dinoflagellate symbiont of reef-building corals. BMC Genomics, 14, 1-18. Brawand, D., Soumillon, M., Necsulea, A., Julien, P., Csárdi, G., Harrigan, P., . . . Kircher, M. (2011). The evolution of gene expression levels in mammalian organs. Nature, 478(7369), 343-348. Burke, G. R., & Moran, N. A. (2011). Responses of the pea aphid transcriptome to infection by facultative symbionts. Insect Molecular Biology, 20(3), 357-365. doi: 10.1111/j.13652583.2011.01070. Burke, G. R. & Strand, M. R. (2014). Systematic analysis of a wasp parasitism arsenal. Molecular Ecology, 23(4), 890-901. doi: 10.1111/mec.12648. Busby, M. A., Gray, J. M., Costa, A. M., Stewart, C., Stromberg, M. P., Barnett, D., . . . Marth, G. T. (2011). Expression divergence measured by transcriptome sequencing of four yeast species. BMC Genomics, 12. doi: 10.1186/1471-2164-12-635. Calla, B., Hall, B., Hou, S., & Geib, S. M. (2014). A genomic perspective to assessing quality of mass-reared sit flies used in mediterranean fruit fly (Ceratitis capitata) eradication in california. BMC Genomics, 15. doi: 10.1186/1471-2164-15-98. Cassone, B. J., Michel, A. P., Stewart, L. R., Bansal, R., Mian, M. A. R., & Redinbaugh, M. G. (2014). Reduction in fecundity and shifts in cellular processes by a native virus on an invasive insect. Genome Biology and Evolution, 6(4), 873-885. doi: 10.1093/gbe/evu057. Celorio-Mancera, M. d. l. P., Wheat, C. W., Vogel, H., Soderlind, L., Janz, N., & Nylin, S. (2013). Mechanisms of macroevolution: polyphagous plasticity in butterfly larvae revealed by RNA-Seq. Molecular Ecology, 22(19), 4884-4895. doi: 10.1111/mec.12440. Chapman, M. A., Hiscock, S. J., & Filatov, D. A. (2013). Genomic divergence during speciation driven by adaptation to altitude. Molecular Biology and Evolution, 30(12), 2553-2567. doi: 10.1093/molbev/mst168. Chen, S., Yang, P., Jiang, F., Wei, Y., Ma, Z., & Kang, L. (2010). De novo analysis of transcriptome dynamics in the migratory locust during the development of phase traits. PLoS ONE, 5(12). doi: 10.1371/journal.pone.0015633. Chen, Z.-F., Matsumura, K., Wang, H., Arellano, S. M., Yan, X., Alam, I., . . . Qian, P.-Y. (2011). Toward an understanding of the molecular mechanisms of barnacle larval settlement: a comparative transcriptomic approach. PLoS ONE, 6(7). doi: 10.1371/journal.pone.0022913. Chen, Z., Yu, H., Li, L., Hu, S., & Dong, X. (2012). The genome and transcriptome of a newly described psychrophilic archaeon, Methanolobus psychrophilus R15, reveal its cold adaptive characteristics. Environmental Microbiology Reports, 4(6), 633-641. doi: 10.1111/j.1758-2229.2012.00389. Cheviron, Z. A., Connaty, A. D., McClelland, G. B., & Storz, J. F. (2014). Functional genomics of adaptation to hypoxic cold-stress in high-altitude deer mice: transcriptomic plasticity and thermogenic performance. Evolution, 68(1), 48-62. doi: 10.1111/evo.12257. Choi, Y.-J., Aliota, M. T., Mayhew, G. F., Erickson, S. M., & Christensen, B. M. (2014). Dual RNA-seq of parasite and host reveals gene expression dynamics during filarial worm-mosquito interactions. PLoS Neglected Tropical Diseases, 8(5). doi: 10.1371/journal.pntd.0002905. Chu, N. D., Miller, L. P., Kaluziak, S. T., Trussell, G. C., & Vollmer, S. V. (2014). Thermal stress and predation risk trigger distinct transcriptomic responses in the intertidal snail Nucella lapillus. Molecular Ecology, 23(24), 6104-6113. doi: 10.1111/mec.12994. Coate, J. E., Powell, A. F., Owens, T. G., & Doyle, J. J. (2013). Transgressive physiological and transcriptomic responses to light stress in allopolyploid Glycine dolichocarpa (Leguminosae). Heredity, 110(2), 160-170. doi: 10.1038/hdy.2012.77. Colombo, M., Diepeveen, E. T., Muschick, M., Santos, M. E., Indermaur, A., Boileau, N., . . . Salzburger, W. (2013). The ecological and genetic basis of convergent thick-lipped phenotypes in cichlid fishes. Molecular Ecology, 22(3), 670-684. doi: 10.1111/mec.12029. Conaco, C., Neveu, P., Zhou, H., Arcila, M. L., Degnan, S. M., Degnan, B. M., & Kosik, K. S. (2012). Transcriptome profiling of the demosponge Amphimedon queenslandica reveals genome-wide events that accompany major life cycle transitions. BMC Genomics, 13. doi: 10.1186/1471-2164-13-209. Crivelente Horta, M. A., Vicentini, R., Delabona, P. d. S., Laborda, P., Crucello, A., Freitas, S., . . . Souza, A. P. (2014). Transcriptome profile of Trichoderma harzianum ioc-3844 induced by sugarcane bagasse. PLoS ONE, 9(2). doi: 10.1371/journal.pone.0088689. Czesny, S., Epifanio, J., & Michalak, P. (2012). Genetic divergence between freshwater and marine morphs of alewife (Alosa pseudoharengus): a 'Next-Generation' sequencing analysis. PLoS ONE, 7(3). doi: 10.1371/journal.pone.0031803. Daniels, E. V., Murad, R., Mortazavi, A., & Reed, R. D. (2014). Extensive transcriptional response associated with seasonal plasticity of butterfly wing patterns. Molecular Ecology, 23(24), 6123-6134. doi: 10.1111/mec.12988. Darby, A. C., Gill, A. C., Armstrong, S. D., Hartley, C. S., Xia, D., Wastling, J. M., & Makepeace, B. L. (2014). Integrated transcriptomic and proteomic analysis of the global response of Wolbachia to doxycycline-induced stress. ISME Journal, 8(4), 925-937. doi: 10.1038/ismej.2013.192. de Groot, A., Roche, D., Fernandez, B., Ludanyi, M., Cruveiller, S., Pignol, D., . . . Blanchard, L. (2014). RNA sequencing and proteogenomics reveal the importance of leaderless mRNAs in the radiation-tolerant bacterium Deinococcus deserti. Genome Biology and Evolution, 6(4), 932-948. doi: 10.1093/gbe/evu069. Denekamp, N. Y., Reinhardt, R., Albrecht, M. W., Drungowski, M., Kube, M., & Lubzens, E. (2011). The expression pattern of dormancy-associated genes in multiple life-history stages in the rotifer Brachionus plicatilis. Hydrobiologia, 662(1), 51-63. doi: 10.1007/s10750-010-0518-y. Dion-Cote, A.-M., Renaut, S., Normandeau, E., & Bernatchez, L. (2014). RNA-seq reveals transcriptomic shock involving transposable elements reactivation in hybrids of young lake whitefish species. Molecular Biology and Evolution, 31(5), 1188-1199. doi: 10.1093/molbev/msu069. Dirks, R. P., Burgerhout, E., Brittijn, S. A., de Wijze, D. L., Ozupek, H., Tuinhof-Koelma, N., . . . van den Thillart, G. E. E. J. M. (2014). Identification of molecular markers in pectoral fin to predict artificial maturation of female european eels (Anguilla anguilla). General and Comparative Endocrinology, 204267-276. doi: 10.1016/j.ygcen.2014.06.023. Dong, Y., Desneux, N., Lei, C., & Niu, C. (2014). Transcriptome characterization analysis of bactrocera minax and new insights into its pupal diapause development with gene expression analysis. International Journal of Biological Sciences, 10(9), 1051-1063. doi: 10.7150/ijbs.9438. Dou, W., Shen, G.-M., Niu, J.-Z., Ding, T.-B., Wei, D.-D., & Wang, J.-J. (2013). Mining genes involved in insecticide resistance of Liposcelis bostrychophila Badonnel by transcriptome and expression profile analysis. PLoS ONE, 8(11). doi: 10.1371/journal.pone.0079878. Dowen, R. H., Pelizzola, M., Schmitz, R. J., Lister, R., Dowen, J. M., Nery, J. R., . . . Ecker, J. R. (2012). Widespread dynamic DNA methylation in response to biotic stress. Proc Natl Acad Sci USA, 109(32), E2183-E2191. Duncan, R. P., Husnik, F., Van Leuven, J. T., Gilbert, D. G., Davalos, L. M., McCutcheon, J. P., & Wilson, A. C. C. (2014). Dynamic recruitment of amino acid transporters to the insect/symbiont interface. Molecular Ecology, 23(6), 1608-1623. doi: 10.1111/mec.12627. Dunning, L. T., Dennis, A. B., Park, D., Sinclair, B. J., Newcomb, R. D., & Buckley, T. R. (2013). Identification of cold-responsive genes in a New Zealand alpine stick insect using RNA-Seq. Comparative Biochemistry and Physiology D-Genomics & Proteomics, 8(1), 24-31. doi: 10.1016/j.cbd.2012.10.005. Dunning, L. T., Dennis, A. B., Sinclair, B. J., Newcomb, R. D., & Buckley, T. R. (2014). Divergent transcriptional responses to low temperature among populations of alpine and lowland species of New Zealand stick insects (Micrarchus). Molecular Ecology, 23(11), 2712-2726. doi: 10.1111/mec.12767. Ekblom, R., Farrell, L. L., Lank, D. B., & Burke, T. (2012). Gene expression divergence and nucleotide differentiation between males of different color morphs and mating strategies in the ruff. Ecology and Evolution, 2(10), 2485-2500. doi: 10.1002/ece3.370 Ekblom, R., Wennekes, P., Horsburgh, G. J., & Burke, T. (2014). Characterization of the house sparrow (Passer domesticus) transcriptome: a resource for molecular ecology and immunogenetics. Molecular Ecology Resources, 14(3), 636-646. doi: 10.1111/17550998.12213. Elran, R., Raam, M., Kraus, R., Brekhman, V., Sher, N., Plaschkes, I., . . . Lotan, T. (2014). Early and late response of Nematostella vectensis transcriptome to heavy metals. Molecular Ecology, 23(19), 4722-4736. doi: 10.1111/mec.12891. Espinosa, E. P., Corre, E., & Allam, B. (2014). Pallial mucus of the oyster Crassostrea virginica regulates the expression of putative virulence genes of its pathogen Perkinsus marinus. International Journal for Parasitology, 44(5), 305-317. doi: 10.1016/j.ijpara.2014.01.006. Etebari, K., Palfreyman, R. W., Schlipalius, D., Nielsen, L. K., Glatz, R. V., & Asgari, S. (2011). Deep sequencing-based transcriptome analysis of Plutella xylostella larvae parasitized by Diadegma semiclausum. BMC Genomics, 12. doi: 10.1186/1471-2164-12446. Eves-van den Akker, S., Lilley, C. J., Danchin, E. G. J., Rancurel, C., Cock, P. J. A., Urwin, P. E., & Jones, J. T. (2014). The transcriptome of Nacobbus aberrans reveals insights into the evolution of sedentary endoparasitism in plant-parasitic nematodes. Genome Biology and Evolution, 6(9), 2181-2194. doi: 10.1093/gbe/evu171. Fan, P., Nie, L., Jiang, P., Feng, J., Lv, S., Chen, X., . . . Li, Y. (2013). Transcriptome analysis of Salicornia europaea under saline conditions revealed the adaptive primary metabolic pathways as early events to facilitate salt adaptation. PLoS ONE, 8(11). doi: 10.1371/journal.pone.0080595. Fang, G., Passalacqua, K. D., Hocking, J., Llopis, P. M., Gerstein, M., Bergman, N. H., & Jacobs-Wagner, C. (2013). Transcriptomic and phylogenetic analysis of a bacterial cell cycle reveals strong associations between gene co-expression and evolution. BMC Genomics, 14. doi: 10.1186/1471-2164-14-450. Feldmeyer, B., Elsner, D., & Foitzik, S. (2014). Gene expression patterns associated with caste and reproductive status in ants: worker-specific genes are more derived than queenspecific ones. Molecular Ecology, 23(1), 151-161. doi: 10.1111/mec.12490. Ferreira, P. G., Patalano, S., Chauhan, R., Ffrench-Constant, R., Gabaldon, T., Guigo, R., & Sumner, S. (2013). Transcriptome analyses of primitively eusocial wasps reveal novel insights into the evolution of sociality and the origin of alternative phenotypes. Genome Biology, 14(2), 1-14. Forconi, M., Chalopin, D., Barucca, M., Biscotti, M. A., De Moro, G., Galiana, D., . . . Volff, J.-N. (2014). Transcriptional activity of transposable elements in coelacanth. Journal of Experimental Zoology Part B-Molecular and Developmental Evolution, 322(6), 379-389. doi: 10.1002/jez.b.22527. Franssen, S. U., Gu, J., Winters, G., Huylmans, A.-K., Wienpahl, I., Sparwel, M., . . . Bornberg-Bauer, E. (2014). Genome-wide transcriptomic responses of the seagrasses Zostera marina and Nanozostera noltii under a simulated heatwave confirm functional types. Marine Genomics, 1565-73. doi: 10.1016/j.margen.2014.03.004. Fraser, B. A., Janowitz, I., Thairu, M., Travis, J., & Hughes, K. A. (2014). Phenotypic and genomic plasticity of alternative male reproductive tactics in sailfin mollies. Proceedings of the Royal Society B-Biological Sciences, 281(1781), 7. doi: 10.1098/rspb.2013.2310. Garcia-Vedrenne, A. E., Groner, M., Page-Karjian, A., Siegmund, G.-F., Singhal, S., Sziklay, J., & Roberts, S. (2013). Development of genomic resources for a Thraustochytrid pathogen and investigation of temperature influences on gene expression. PLoS ONE, 8(9), 1-10. Gerdol, M., De Moro, G., Manfrin, C., Milandri, A., Riccardi, E., Beran, A., . . . Pallavicini, A. (2014). RNA sequencing and de novo assembly of the digestive gland transcriptome in Mytilus galloprovincialis fed with toxinogenic and non-toxic strains of Alexandrium minutum. BMC Research Notes, 7722-722. Grumaz, C., Lorenz, S., Stevens, P., Lindemann, E., Schoeck, U., Retey, J., . . . Sohn, K. (2013). Species and condition specific adaptation of the transcriptional landscapes in Candida albicans and Candida dubliniensis. BMC Genomics, 14. doi: 10.1186/14712164-14-212. Gunter, H. M., Fan, S., Xiong, F., Franchini, P., Fruciano, C., & Meyer, A. (2013). Shaping development through mechanical strain: the transcriptional basis of diet-induced phenotypic plasticity in a cichlid fish. Molecular Ecology, 22(17), 4516-4531. doi: 10.1111/mec.12417. Hanson, S. J., Stelzer, C.-P., Welch, D. B. M., & Logsdon, J. M., Jr. (2013). Comparative transcriptome analysis of obligately asexual and cyclically sexual rotifers reveals genes with putative functions in sexual reproduction, dormancy, and asexual egg production. BMC Genomics, 14, 1-17. Harr, B., & Turner, L. M. (2010). Genome-wide analysis of alternative splicing evolution among Mus subspecies. Molecular Ecology, 19, 228-239. doi: 10.1111/j.1365294X.2009.04490. Henning, F., Jones, J. C., Franchini, P., & Meyer, A. (2013). Transcriptomics of morphological color change in polychromatic Midas cichlids. BMC Genomics, 14. doi: 10.1186/1471-2164-14-171. Hershkovitz, V., Sela, N., Taha-Salaime, L., Liu, J., Rafael, G., Kessler, C., . . . Droby, S. (2013). De novo assembly and characterization of the transcriptome of Metschnikowia fructicola reveals differences in gene expression following interaction with Penicillium digitatum and grapefruit peel. BMC Genomics, 14. doi: 10.1186/1471-2164-14-168. Hook, S. E., Osborn, H. L., Gissi, F., Moncuquet, P., Twine, N. A., Wilkins, M. R., & Adams, M. S. (2014a). RNA-seq analysis of the toxicant-induced transcriptome of the marine diatom, Ceratoneis closterium. Marine Genomics, 16, 45-53. doi: 10.1016/j.margen.2013.12.004. Hook, S. E., Twine, N. A., Simpson, S. L., Spadaro, D. A., Moncuquet, P., & Wilkins, M. R. (2014b). 454 pyrosequencing-based analysis of gene expression profiles in the amphipod Melita plumulosa: transcriptome assembly and toxicant induced changes. Aquatic Toxicology, 15373-88. doi: 10.1016/j.aquatox.2013.11.022. Huth, T. J., & Place, S. P. (2013). De novo assembly and characterization of tissue specific transcriptomes in the emerald notothen, Trematomus bernacchii. BMC Genomics, 14, 113. Ibarra-Laclette, E., Albert, V. A., Perez-Torres, C. A., Zamudio-Hernandez, F., OrtegaEstrada, M. d. J., Herrera-Estrella, A., & Herrera-Estrella, L. (2011). Transcriptomics and molecular evolutionary rate analysis of the bladderwort (Utricularia), a carnivorous plant with a minimal genome. BMC Plant Biology, 11. doi: 10.1186/1471-2229-11-101. Ignatov, D. V., Skvortsov, T. A., Majorov, K. B., Apt, A. S., & Azhikina, T. L. (2010). Adaptive changes in Mycobacterium avium gene expression profile following infection of genetically susceptible and resistant mice. Acta Naturae, 2(3), 78-84. Jeukens, J., Renaut, S., St-Cyr, J., Nolte, A. W., & Bernatchez, L. (2010). The transcriptomics of sympatric dwarf and normal lake whitefish (Coregonus clupeaformis spp., Salmonidae) divergence as revealed by next-generation sequencing. Molecular Ecology, 19(24), 5389-5403. doi: 10.1111/j.1365-294X.2010.04934. Kanter, U., Heller, W., Durner, J., Winkler, J. B., Engel, M., Behrendt, H., . . . Ernst, D. (2013). Molecular and immunological characterization of ragweed (Ambrosia artemisiifolia L.) pollen after exposure of the plants to elevated ozone over a whole growing season. PLoS ONE, 8(4). doi: 10.1371/journal.pone.0061518. Kao, D., Felix, D., & Aboobaker, A. (2013). The planarian regeneration transcriptome reveals a shared but temporally shifted regulatory program between opposing head and tail scenarios. BMC Genomics, 14. doi: 10.1186/1471-2164-14-797. Kelley, J. L., Passow, C. N., Plath, M., Arias Rodriguez, L., Yee, M.-C., & Tobler, M. (2012). Genomic resources for a model in adaptation and speciation research: characterization of the Poecilia mexicana transcriptome. BMC Genomics, 13, 1-13. Kersten, B., Ghirardo, A., Schnitzler, J.-P., Kanawati, B., Schmitt-Kopplin, P., Fladung, M., & Schroeder, H. (2013). Integrated transcriptomics and metabolomics decipher differences in the resistance of pedunculate oak to the herbivore Tortrix viridana L. BMC Genomics, 14. doi: 10.1186/1471-2164-14-737. Kim, J., Carlos Oliveros, J., Nikel, P. I., de Lorenzo, V., & Silva-Rocha, R. (2013). Transcriptomic fingerprinting of Pseudomonas putida under alternative physiological regimes. Environmental Microbiology Reports, 5(6), 883-891. doi: 10.1111/17582229.12090. Kimura, H., Young, C. R., Martinez, A., & DeLong, E. F. (2011). Light-induced transcriptional responses associated with proteorhodopsin-enhanced growth in a marine flavobacterium. ISME Journal, 5(10), 1641-1651. doi: 10.1038/ismej.2011.36. Kobayashi, M. J., Takeuchi, Y., Kenta, T., Kume, T., Diway, B., & Shimizu, K. K. (2013). Mass flowering of the tropical tree Shorea beccariana was preceded by expression changes in flowering and drought-responsive genes. Molecular Ecology, 22(18), 47674782. doi: 10.1111/mec.12344. Kodama, Y., Suzuki, H., Dohra, H., Sugii, M., Kitazume, T., Yamaguchi, K., . . . Fujishima, M. (2014). Comparison of gene expression of paramecium bursaria with and without Chlorella variabilis symbionts. BMC Genomics, 15. doi: 10.1186/1471-2164-15-183. Kumaran, N., Prentis, P. J., Mangalam, K. P., Schutze, M. K., & Clarke, A. R. (2014). Sexual selection in true fruit flies (Diptera: Tephritidae): transcriptome and experimental evidences for phytochemicals increasing male competitive ability. Molecular Ecology, 23(18), 4645-4657. doi: 10.1111/mec.12880. Lee, J. H., Choi, J. Y., Tao, X. Y., Kim, J. S., Kim, W., & Je, Y. H. (2013). Transcriptome analysis of the small brown planthopper, Laodelphax striatellus carrying rice stripe virus. Plant Pathology Journal, 29(3), 330-337. doi: 10.5423/ppj.nt.01.2013.0001. Lei, B., Lu, K., Ding, F., Zhang, K., Chen, Y., Zhao, H., . . . Pan, W. (2014). RNA sequencing analysis reveals transcriptomic variations in tobacco (Nicotiana tabacum) leaves affected by climate, soil, and tillage factors. International Journal of Molecular Sciences, 15(4), 6137-6160. doi: 10.3390/ijms15046137. Lei, Y., Zhu, X., Xie, W., Wu, Q., Wang, S., Guo, Z., . . . Zhang, Y. (2014). Midgut transcriptome response to a Cry toxin in the diamondback moth, Plutella xylostella (Lepidoptera: Plutellidae). Gene, 533(1), 180-187. doi: 10.1016/j.gene.2013.09.091. Li, S.-W., Yang, H., Liu, Y.-F., Liao, Q.-R., Du, J., & Jin, D.-C. (2012). Transcriptome and gene expression analysis of the rice leaf folder, Cnaphalocrosis medinalis. PLoS ONE, 7(11). doi: 10.1371/journal.pone.0047401. Li, Z-Q., Zhang, S., Ma, Y., Luo, J-Y., Wang, C-Y., Lv, L-M., . . . Cui, J-J. (2013). First transcriptome and digital gene expression analysis in neuroptera with an emphasis on chemoreception genes in Chrysopa pallens (Rambur). PLoS ONE, 8(6): e67151. doi: 10.1371/journal.pone.0067151. Liu, Y., Shen, D., Zhou, F., Wang, G., & An, C. (2014). Identification of immunity-related genes in Ostrinia furnacalis against entomopathogenic fungi by RNA-seq analysis. PLoS ONE, 9(1), e86436-e86436. Liu, Z., Ma, L., Nan, Z., & Wang, Y. (2013). Comparative transcriptional profiling provides insights into the evolution and development of the zygomorphic flower of Vicia sativa (Papilionoideae). PLoS ONE, 8(2). doi: 10.1371/journal.pone.0057338. Logacheva, M. D., Kasianov, A. S., Vinogradov, D. V., Samigullin, T. H., Gelfand, M. S., Makeev, V. J., & Penin, A. A. (2011). De novo sequencing and characterization of floral transcriptome in two species of buckwheat (Fagopyrum). BMC Genomics, 12. doi: 10.1186/1471-2164-12-30. Lowe, C. D., Mello, L. V., Samatar, N., Martin, L. E., Montagnes, D. J. S., & Watts, P. C. (2011). The transcriptome of the novel dinoflagellate Oxyrrhis marina (Alveolata: Dinophyceae): response to salinity examined by 454 sequencing. BMC Genomics, 12. doi: 10.1186/1471-2164-12-519. Luo, Y., Li, C., Landis, A. G., Wang, G., Stoeckel, J., & Peatman, E. (2014). Transcriptomic profiling of differential responses to drought in two freshwater mussel species, the giant floater Pyganodon grandis and the pondhorn uniomerus tetralasmus. PLoS ONE, 9(2). doi: 10.1371/journal.pone.0089481. Lv, J., Liu, P., Wang, Y., Gao, B., Chen, P., & Li, J. (2013). Transcriptome analysis of Portunus trituberculatus in response to salinity stress provides insights into the molecular basis of osmoregulation. PLoS ONE, 8(12). doi: 10.1371/journal.pone.0082155. Manousaki, T., Hull, P. M., Kusche, H., Machado-Schiaffino, G., Franchini, P., Harrod, C., . . . Meyer, A. (2013). Parsing parallel evolution: ecological divergence and differential gene expression in the adaptive radiations of thick-lipped Midas cichlid fishes from Nicaragua. Molecular Ecology, 22(3), 650-669. doi: 10.1111/mec.12034. Marra, N. J., Romero, A., & DeWoody, J. A. (2014). Natural selection and the genetic basis of osmoregulation in heteromyid rodents as revealed by RNA-seq. Molecular Ecology, 23(11), 2699-2711. doi: 10.1111/mec.12764. Mayfield, A. B., Wang, Y.-B., Chen, C.-S., Lin, C.-Y., & Chen, S.-H. (2014). Compartmentspecific transcriptomics in a reef-building coral exposed to elevated temperatures. Molecular Ecology, 23(23), 5816-5830. doi: 10.1111/mec.12982. McDonnell, C. M., Alaux, C., Parrinello, H., Desvignes, J.-P., Crauser, D., Durbesson, E., . . . Le Conte, Y. (2013). Ecto- and endoparasite induce similar chemical and brain neurogenomic responses in the honey bee (Apis mellifera). BMC Ecology, 13. doi: 10.1186/1472-6785-13-25. Meng, F., Braasch, I., Phillips, J. B., Lin, X., Titus, T., Zhang, C., & Postlethwait, J. H. (2013). Evolution of the eye transcriptome under constant darkness in Sinocyclocheilus cavefish. Molecular Biology and Evolution, 30(7), 1527-1543. doi: 10.1093/molbev/mst079. Meyer, E., Aglyamova, G. V., & Matz, M. V. (2011). Profiling gene expression responses of coral larvae (Acropora millepora) to elevated temperature and settlement inducers using a novel RNA-Seq procedure. Molecular Ecology, 20(17), 3599-3616. doi: 10.1111/j.1365294X.2011.05205. Moyers, B. T., & Rieseberg, L. H. (2013). Divergence in gene expression is uncoupled from divergence in coding sequence in a secondarily woody sunflower. International Journal of Plant Sciences, 174(7), 1079-1089. doi: 10.1086/671197. Newton, J. R., Zenger, K. R., & Jerry, D. R. (2013). Next-generation transcriptome profiling reveals insights into genetic factors contributing to growth differences and temperature adaptation in Australian populations of barramundi (Lates calcarifer). Marine Genomics, 11, 45-52. doi: 10.1016/j.margen.2013.07.002. Ng, C. S., Wu, P., Fan, W.-L., Yan, J., Chen, C.-K., Lai, Y.-T., . . . Li, W.-H. (2014). Genomic organization, transcriptomic analysis, and functional characterization of avian alpha- and beta-keratins in diverse feather forms. Genome Biology and Evolution, 6(9), 2258-2273. doi: 10.1093/gbe/evu181. Ng'oma, E., Groth, M., Ripa, R., Platzer, M., & Cellerino, A. (2014). Transcriptome profiling of natural dichromatism in the annual fishes Nothobranchius furzeri and Nothobranchius kadleci. BMC Genomics, 15. doi: 10.1186/1471-2164-15-754. Norman, J. D., Ferguson, M. M., & Danzmann, R. G. (2014). Transcriptomics of salinity tolerance capacity in Arctic charr (Salvelinus alpinus): a comparison of gene expression profiles between divergent QTL genotypes. Physiological Genomics, 46(4), 123-137. doi: 10.1152/physiolgenomics.00105.2013. Novo, M., Riesgo, A., Fernández-Guerra, A., & Giribet, G. (2013). Pheromone evolution, reproductive genes, and comparative transcriptomics in Mediterranean earthworms (Annelida, Oligochaeta, Hormogastridae). Molecular Biology and Evolution, 30(7):161429. doi: 10.1093/molbev/mst074. Nowack, E. C. M., Vogel, H., Groth, M., Grossman, A. R., Melkonian, M., & Gloeckner, G. (2011). Endosymbiotic gene transfer and transcriptional regulation of transferred genes in Paulinella chromatophora. Molecular Biology and Evolution, 28(1), 407-422. doi: 10.1093/molbev/msq209. Ozawa, R., Nishimura, O., Yazawa, S., Muroi, A., Takabayashi, J., & Arimura, G-I. (2012). Temperature-dependent, behavioural, and transcriptional variability of a tritrophic interaction consisting of bean, herbivorous mite, and predator. Molecular Ecology, 21(22), 5624-5635. doi: 10.1111/mec.12052. Palumbi, S. R., Barshis, D. J., Traylor-Knowles, N., & Bay, R. A. (2014). Mechanisms of reef coral resistance to future climate change. Science, 344(6186), 895-898. Parikh, A., Miranda, E. R., Katoh-Kurasawa, M., Fuller, D., Rot, G., Zagar, L., . . . Shaulsky, G. (2010). Conserved developmental transcriptomes in evolutionarily divergent species. Genome Biology, 11(3). doi: 10.1186/gb-2010-11-3-r35. Pereira Lima Teixeira, P. J., de Toledo Thomazella, D. P., Reis, O., Vital do Prado, P. F., Scatolin do Rio, M. C., Fiorin, G. L., . . . Guimaraes Pereira, G. A. (2014). Highresolution transcript profiling of the atypical biotrophic interaction between Theobroma cacao and the fungal pathogen Moniliophthora perniciosa. Plant Cell, 26(11), 42454269. doi: 10.1105/tpc.114.130807. Perry, J. C., Harrison, P. W., & Mank, J. E. (2014). The ontogeny and evolution of sex-biased gene expression in Drosophila melanogaster. Molecular Biology and Evolution, 31(5), 1206-1219. doi: 10.1093/molbev/msu072. Pinosio, S., Gonzalez-Martinez, S. C., Bagnoli, F., Cattonaro, F., Grivet, D., Marroni, F., . . . Vendramin, G. G. (2014). First insights into the transcriptome and development of new genomic tools of a widespread circum-mediterranean tree species, Pinus halepensis Mill. Molecular Ecology Resources, 14(4), 846-856. doi: 10.1111/1755-0998.12232. Poelchau, M. F., Reynolds, J. A., Denlinger, D. L., Elsik, C. G., & Armbruster, P. A. (2011). A de novo transcriptome of the Asian tiger mosquito, Aedes albopictus, to identify candidate transcripts for diapause preparation. BMC Genomics, 12. doi: 10.1186/14712164-12-619. Poelchau, M. F., Reynolds, J. A., Elsik, C. G., Denlinger, D. L., & Armbruster, P. A. (2013). RNA-Seq reveals early distinctions and late convergence of gene expression between diapause and quiescence in the Asian tiger mosquito, Aedes albopictus. Journal of Experimental Biology, 216(21), 4082-4090. doi: 10.1242/jeb.089508. Poelchau, M. F., Reynolds, J. A., Elsik, C. G., Denlinger, D. L., & Armbruster, P. A. (2013) Deep sequencing reveals complex mechanisms of diapause preparation in the invasive mosquito, Aedes albopictus. Proceedings of the Royal Society B-Biological Sciences, 280. Prasopdee, S., Sotillo, J., Tesana, S., Laha, T., Kulsantiwong, J., Nolan, M. J., . . . Cantacessi, C. (2014). RNA-seq reveals infection-induced gene expression changes in the snail intermediate host of the carcinogenic liver fluke, Opisthorchis viverrini. PLoS Neglected Tropical Diseases, 8(3). doi: 10.1371/journal.pntd.0002765. Pravosudov, V. V., Roth, T. C., II, Forister, M. L., Ladage, L. D., Kramer, R., Schilkey, F., & Van Der Linden, A. M. (2013). Differential hippocampal gene expression is associated with climate-related natural variation in memory and the hippocampus in food-caching chickadees. Molecular Ecology, 22(2), 397-408. doi: 10.1111/mec.12146. Reinhardt, J. A., Brand, C. L., Paczolt, K. A., Johns, P. M., Baker, R. H., & Wilkinson, G. S. (2014). Meiotic drive impacts expression and evolution of x-linked genes in stalk-eyed flies. PLoS Genetics, 10(5). doi: 10.1371/journal.pgen.1004362. Rendon-Anaya, M., Delaye, L., Possani, L. D., & Herrera-Estrella, A. (2012). Global transcriptome analysis of the scorpion Centruroides noxius: new toxin families and evolutionary insights from an ancestral scorpion species. PLoS ONE, 7(8). doi: 10.1371/journal.pone.0043331. Ribeiro, J. M. C., Labruna, M. B., Mans, B. J., Maruyama, S. R., Francischetti, I. M. B., Barizon, G. C., & de Miranda Santos, I. K. F. (2012). The sialotranscriptome of Antricola delacruzi female ticks is compatible with non-hematophagous behavior and an alternative source of food. Insect Biochemistry and Molecular Biology, 42(5), 332-342. doi: 10.1016/j.ibmb.2012.01.003. Rinker, D. C., Zhou, X., Pitts, R. J., Rokas, A., & Zwiebel, L. J. (2013). Antennal transcriptome profiles of anopheline mosquitoes reveal human host olfactory specialization in Anopheles gambiae. BMC Genomics, 14, 1-14. Sarropoulou, E., Moghadam, H. K., Papandroulakis, N., De la Gandara, F., Ortega Garcia, A., & Makridis, P. (2014). The atlantic bonito (Sarda sarda, Bloch 1793) transcriptome and detection of differential expression during larvae development. PLoS ONE, 9(2). doi: 10.1371/journal.pone.0087744. Schoville, S. D., Barreto, F. S., Moy, G. W., Wolff, A., & Burton, R. S. (2012). Investigating the molecular basis of local adaptation to thermal stress: population differences in gene expression across the transcriptome of the copepod Tigriopus californicus. BMC Evolutionary Biology, 12. doi: 10.1186/1471-2148-12-170. Schunter, C., Vollmer, S. V., Macpherson, E., & Pascual, M. (2014). Transcriptome analyses and differential gene expression in a non-model fish species with alternative mating tactics. BMC Genomics, 15. doi: 10.1186/1471-2164-15-167. Schwarzenberger, A., Sadler, T., Motameny, S., Ben-Khalifa, K., Frommolt, P., Altmueller, J., . . . von Elert, E. (2014). Deciphering the genetic basis of microcystin tolerance. BMC Genomics, 15. doi: 10.1186/1471-2164-15-776. Seto, Y., & Tamura, K. (2013). Extensive differences in antifungal immune response in two Drosophila species revealed by comparative transcriptome analysis. International Journal of Genomics. doi: 10.1155/2013/542139. Shelomi, M., Jasper, W. C., Atallah, J., Kimsey, L. S., & Johnson, B. R. (2014). Differential expression of endogenous plant cell wall degrading enzyme genes in the stick insect (Phasmatodea) midgut. BMC Genomics, 15. doi: 10.1186/1471-2164-15-917. Shiao, M.-S., Chang, A. Y.-F., Liao, B.-Y., Ching, Y.-H., Lu, M.-Y. J., Chen, S. M., & Li, W.-H. (2012). Transcriptomes of mouse olfactory epithelium reveal sexual differences in odorant detection. Genome Biology and Evolution, 4(5), 703-712. doi: 10.1093/gbe/evs039. Sikhakolli, U. R., Lopez-Giraldez, F., Li, N., Common, R., Townsend, J. P., & Trail, F. (2012). Transcriptome analyses during fruiting body formation in Fusarium graminearum and Fusarium verticillioides reflect species life history and ecology. Fungal Genetics and Biology, 49(8), 663-673. doi: 10.1016/j.fgb.2012.05.009. Sloan, D. B., Nakabachi, A., Richards, S., Qu, J., Murali, S. C., Gibbs, R. A., & Moran, N. A. (2014). Parallel histories of horizontal gene transfer facilitated extreme reduction of endosymbiont genomes in sap-feeding insects. Molecular Biology and Evolution, 31(4), 857-871. doi: 10.1093/molbev/msu004. Small, C. M., Harlin-Cognato, A. D., & Jones, A. G. (2013). Functional similarity and molecular divergence of a novel reproductive transcriptome in two male-pregnant Syngnathus pipefish species. Ecology and Evolution, 3(12), 4092-4108. doi: 10.1002/ece3.763. Smith, G., Fang, Y., Liu, X., Kenny, J., Cossins, A. R., de Oliveira, C. C., . . . Ritchie, M. G. (2013). Transcriptome-wide expression variation associated with environmental plasticity and mating success in cactophilic Drosophila mojavensis. Evolution, 67(7), 1950-1963. doi: 10.1111/evo.12082. Smith, G., Chen, Y.-R., Blissard, G. W., & Briscoe, A. D. (2014). Complete dosage compensation and sex-biased gene expression in the moth Manduca sexta. Genome Biology and Evolution, 6(3), 526-537. doi: 10.1093/gbe/evu035. Smith, S., Bernatchez, L., & Beheregaray, L. B. (2013). RNA-seq analysis reveals extensive transcriptional plasticity to temperature stress in a freshwater fish species. BMC Genomics, 14, 1-12. Somervuo, P., Kvist, J., Ikonen, S., Auvinen, P., Paulin, L., Koskinen, P., . . . Hanski, I. (2014). Transcriptome analysis reveals signature of adaptation to landscape fragmentation. PLoS ONE, 9(7). doi: 10.1371/journal.pone.0101467. Szoevenyi, P., Rensing, S. A., Lang, D., Wray, G. A., & Shaw, A. J. (2011). Generationbiased gene expression in a bryophyte model system. Molecular Biology and Evolution, 28(1), 803-812. doi: 10.1093/molbev/msq254. Szoevenyi, P., Ricca, M., Hock, Z., Shaw, J. A., Shimizu, K. K., & Wagner, A. (2013). Selection is no more efficient in haploid than in diploid life stages of an angiosperm and a moss. Molecular Biology and Evolution, 30(8), 1929-1939. doi: 10.1093/molbev/mst095. Traeger, S., Altegoer, F., Freitag, M., Gabaldon, T., Kempken, F., Kumar, A., . . . Nowrousian, M. (2013). The genome and development-dependent transcriptomes of Pyronema confluens: a window into fungal evolution. PLoS Genetics, 9(9). doi: 10.1371/journal.pgen.1003820. Uebbing, S., Kunstner, A., Makinen, H., & Ellegren, H. (2013). Transcriptome sequencing reveals the character of incomplete dosage compensation across multiple tissues in flycatchers. Genome Biology and Evolution, 5(8), 1555-1566. doi: 10.1093/gbe/evt114. Valenzuela-Miranda, D., Gallardo-Escarate, C., Valenzuela-Munoz, V., Farlora, R., & Gajardo, G. (2014). Sex-dependent transcriptome analysis and single nucleotide polymorphism (SNP) discovery in the brine shrimp Artemia franciscana. Marine Genomics, 18, 151-154. doi: 10.1016/j.margen.2014.10.007. Vargas, L., Santa Brigida, A. B., Mota Filho, J. P., de Carvalho, T. G., Rojas, C. A., Vaneechoutte, D., . . . Hemerly, A. S. (2014). Drought tolerance conferred to sugarcane by association with Gluconacetobacter diazotrophicus: a transcriptomic view of hormone pathways. PLoS ONE, 9(12). doi: 10.1371/journal.pone.0114744. Vellichirammal, N. N., Zera, A. J., Schilder, R. J., Wehrkamp, C., Riethoven, J.-J. M., & Brisson, J. A. (2014). De novo transcriptome assembly from fat body and flight muscles transcripts to identify morph-specific gene expression profiles in Gryllus firmus. PLoS ONE, 9(1). doi: 10.1371/journal.pone.0082129. Vidal-Dupiol, J., Zoccola, D., Tambutte, E., Grunau, C., Cosseau, C., Smith, K. M., . . . Tambutte, S. (2013). Genes related to ion-transport and energy production are upregulated in response to CO2-driven pH decrease in corals: new insights from transcriptome analysis. PLoS ONE, 8(3). doi: 10.1371/journal.pone.0058652. Wang, L., Cao, C., Ma, Q., Zeng, Q., Wang, H., Cheng, Z., . . . Wang, Y. (2014). RNA-seq analyses of multiple meristems of soybean: novel and alternative transcripts, evolutionary and functional implications. BMC Plant Biology, 14. doi: 10.1186/1471-2229-14-169. Wang, X., Fang, X., Yang, P., Jiang, X., Jiang, F., Zhao, D., . . . Kang, L. (2014). The locust genome provides insight into swarm formation and long-distance flight. Nature Communications, 5, 1-9. doi: 10.1038/ncomms3957. Wang, Z., Straub, D., Yang, H., Kania, A., Shen, J., Ludewig, U., & Neumann, G. (2014). The regulatory network of cluster-root function and development in phosphate-deficient white lupin (Lupinus albus) identified by transcriptome sequencing. Physiologia Plantarum, 151(3), 323-338. doi: 10.1111/ppl.12187. Wei, X., Zhang, X., Shen, D., Wang, H., Wu, Q., Lu, P., . . . Li, X. (2013). Transcriptome analysis of Barbarea vulgaris infested with diamondback moth (Plutella xylostella) larvae. PLoS ONE, 8(5). doi: 10.1371/journal.pone.0064481. Weiss, Y., Foret, S., Hayward, D. C., Ainsworth, T., King, R., Ball, E. E., & Miller, D. J. (2013). The acute transcriptional response of the coral Acropora millepora to immune challenge: expression of GiMAP/IAN genes links the innate immune responses of corals with those of mammals and plants. BMC Genomics, 14, 1-13. Whiteman, N. K., Gloss, A. D., Sackton, T. B., Groen, S. C., Humphrey, P. T., Lapoint, R. T., . . . Pierce, N. E. (2012). Genes involved in the evolution of herbivory by a leaf-mining, drosophilid fly. Genome Biology and Evolution, 4(9), 900-916. doi: 10.1093/gbe/evs063. Wolf, J. B., Bayer, T., Haubold, B., Schilhabel, M., Rosenstiel, P., & Tautz, D. (2010). Nucleotide divergence vs. gene expression differentiation: comparative transcriptome sequencing in natural isolates from the carrion crow and its hybrid zone with the hooded crow. Molecular Ecology, 19(s1), 162-175. Wygoda, J. A., Yang, Y., Byrne, M., & Wray, G. A. (2014). Transcriptomic analysis of the highly derived radial body plan of a sea urchin. Genome Biology and Evolution, 6(4), 964-973. doi: 10.1093/gbe/evu070. Xiang, L.-X., He, D., Dong, W.-R., Zhang, Y.-W., & Shao, J.-Z. (2010). Deep sequencingbased transcriptome profiling analysis of bacteria-challenged Lateolabrax japonicus reveals insight into the immune-relevant genes in marine fish. BMC Genomics, 11. doi: 10.1186/1471-2164-11-472. Xie, W., Guo, L., Jiao, X., Yang, N., Yang, X., Wu, Q., . . . Zhang, Y. (2014). Transcriptomic dissection of sexual differences in Bemisia tabaci, an invasive agricultural pest worldwide. Scientific Reports, 4. doi: 10.1038/srep04088. Xu, C., Bai, Y., Lin, X., Zhao, N., Hu, L., Gong, Z., . . . Liu, B. (2014). Genome-wide disruption of gene expression in allopolyploids but not hybrids of rice subspecies. Molecular Biology and Evolution, 31(5), 1066-1076. doi: 10.1093/molbev/msu085. Xu, J., Li, Q., Xu, L., Wang, S., Jiang, Y., Zhao, Z., . . . Xu, P. (2013). Gene expression changes leading extreme alkaline tolerance in Amur ide (Leuciscus waleckii) inhabiting soda lake. BMC Genomics, 14(1), 682. Xu, Y., Zhou, W., Zhou, Y., Wu, J., & Zhou, X. (2012). Transcriptome and comparative gene expression analysis of Sogatella furcifera (Horvath) in response to southern rice blackstreaked dwarf virus. PLoS ONE, 7(4). doi: 10.1371/journal.pone.0036238. Xue, J., Bao, Y.-Y., Li, B.-l., Cheng, Y.-B., Peng, Z.-Y., Liu, H., . . . Zhang, C.-X. (2010). Transcriptome analysis of the brown planthopper Nilaparvata lugens. PLoS ONE, 5(12). doi: 10.1371/journal.pone.0014233. Yang, Y., Wang, J., Ma, Z., Sun, G., & Zhang, C. (2014). De novo sequencing and comparative transcriptome analysis of white petals and red labella in Phalaenopsis for discovery of genes related to flower color and floral differentation. Acta Societatis Botanicorum Poloniae, 83(3), 191-199. doi: 10.5586/asbp.2014.023. Yeaman, S., Hodgins, K. A., Suren, H., Nurkowski, K. A., Rieseberg, L. H., Holliday, J. A., & Aitken, S. N. (2014). Conservation and divergence of gene expression plasticity following c. 140million years of evolution in lodgepole pine (Pinus contorta) and interior spruce (Picea glaucaxpicea engelmannii). New Phytologist, 203(2), 578-591. doi: 10.1111/nph.12819. Yek, S. H., Boomsma, J. J., & Schiott, M. (2013). Differential gene expression in Acromyrmex leaf-cutting ants after challenges with two fungal pathogens. Molecular Ecology, 22(8), 2173-2187. doi: 10.1111/mec.12255. Yoshida, M.-a., Yamada, L., Ochi, H., Iwata, Y., Tamura-Nakano, M., Sawada, H., . . . Hirohashi, N. (2014). Integrative omics analysis reveals differentially distributed proteins in dimorphic euspermatozoa of the squid, Loligo bleekeri. Biochemical and Biophysical Research Communications, 450(3), 1218-1224. doi: 10.1016/j.bbrc.2014.04.076. Zhai, Y., Zhang, J., Sun, Z., Dong, X., He, Y., Kang, K., . . . Zhang, W. (2013). Proteomic and transcriptomic analyses of fecundity in the brown planthopper Nilaparvata lugens (Stal). Journal of Proteome Research, 12(11), 5199-5212. doi: 10.1021/pr400561c. Zhang, Z., Wang, Y., Wang, S., Liu, J., Warren, W., Mitreva, M., & Walter, R. B. (2011). Transcriptome analysis of female and male Xiphophorus maculatus Jp 163 A. PLoS ONE, 6(4), e18379. Zhao, Z., Wu, G., Wang, J., Liu, C., & Qiu, L. (2013). Next-Generation sequencing-based transcriptome analysis of Helicoverpa armigera larvae immune-primed with Photorhabdus luminescens TT01. PLoS ONE, 8(11). doi: 10.1371/journal.pone.0080146. Zheng, M., Tian, J., Yang, G., Zheng, L., Chen, G., Chen, J., & Wang, B. (2013). Transcriptome sequencing, annotation and expression analysis of Nannochloropsis sp. at different growth phases. Gene, 523(2), 117-121. doi: 10.1016/j.gene.2013.04.005. Zheng, W., Peng, T., He, W., & Zhang, H. (2012). High-throughput sequencing to reveal genes involved in reproduction and development in Bactrocera dorsalis (Diptera: Tephritidae). PLoS ONE, 7(5). doi: 10.1371/journal.pone.0036463. Zhou, Z. C., Dong, Y., Sun, H. J., Yang, A. F., Chen, Z., Gao, S., . . . Wang, B. (2014). Transcriptome sequencing of sea cucumber (Apostichopus japonicus) and the identification of gene-associated markers. Molecular Ecology Resources, 14(1), 127138. doi: 10.1111/1755-0998.12147. Zouari, I., Salvioli, A., Chialva, M., Novero, M., Miozzi, L., Tenore, G. C., . . . Bonfante, P. (2014). From root to fruit: RNA-seq analysis shows that arbuscular mycorrhizal symbiosis may affect tomato fruit metabolism. BMC Genomics, 15. doi: 10.1186/1471-2164-15-221. Appendix S2 R code used for power analysis R code and parameters used to perform power simulations on pilot RNAseq data from bluehead wrasse (Box 3). Simulations were performed using the R/Bioconductor package PROPER (Wu et al. 2015), with dispersion and baseline expression estimated from pilot data via the DSS package (Wu et al. 2013). Pilot data consisted of two separate experiments examining sex-biased gene expression in the gonad and forebrain of bluehead wrasse, each experiment consisting of three biological replicates per sex (3 female, 3 male). Gonad and forebrain experiments were analysed separately using identical simulation parameters, except for the proportion of simulated differential expression. This was 25% for gonad, and 1% for brain, chosen to reflect observations in real 3x3 comparisons for these tissues (Liu et al. in review). Using the same value for this parameter did not alter the interpretation. ##Load counts table and define treatment groups. wrasse<-read.table('rawcounts_table.tsv',header=T) groups = c(rep("F",3), rep("M",3)) ##Filter transcripts with fewer than 10 counts across all samples. ##Use DSS package to estimate dispersion and baseline expression. library(DSS) library(edgeR) counts = as.matrix(wrasse) counts<-counts[apply(counts,1,sum)>9,] design = data.frame(gender=groups) X = model.matrix(~gender, data=design) rownames(X)<-colnames(counts) seqData = newSeqCountSet(counts, as.data.frame(X)) seqData = estNormFactors(seqData) seqData = estDispersion(seqData) dispersion = dispersion(seqData) fit.edgeR<-glmFit(counts, X, lib.size=normalizationFactor(seqData), dispersion=dispersion(seqData)) lrt.edgeR<-glmLRT(fit.edgeR, coef=2) ##Simulate counts using PROPER package: 50,000 transcripts (‘ngenes’), 25% DE in gonad OR 1% DE in brain (‘p.DE’). ##Simulate for 2, 3, 5, 7 and 10 replicates per condition (‘Nreps’), test DE with DESeq (‘DEmethod’), over 100 iterations (‘nsims’). library(PROPER) library(DESeq) sz = 50000 zz = sample(1:nrow(counts),sz) sim.opts.wrasse = RNAseq.SimOptions.2grp( ngenes = sz, p.DE=0.01, lOD = log(dispersion(seqData))[zz], lBaselineExpr = apply(log(counts+0.5),1,mean)[zz], lfc = lrt.edgeR$table$logFC[zz], sim.seed = 11111) simres = runSims(Nreps = c(2, 3, 5, 7, 10), sim.opts=sim.opts.wrasse, DEmethod="DESeq", nsims=100) ##From simulated data, calculate power at FDR 0.05, for a 1.5 fold-change (equiv. 0.585 log2 fold-change) (‘delta’). powers = comparePower(simres, alpha.type="fdr", alpha.nominal=0.05, stratify.by="expr", delta=0.585) summaryPower(powers) ##Plot result plotPower(powers, main="Forebrain", lty=1,1:ncol(powers$power))