mec13055-sup-0001-AppendixS1
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APPENDIX S1 Case studies reviewed to describe trends in ecological transcriptomic studies in the last 10 years. The table gives for each of the 575 studies the species, which question categories, whether conducted in the field or lab and whether microarray or RNAseq were included in the study. Question categories: 1 corresponds to studies that investigated the extent of natural variation, 2 corresponds to studies that investigated organismal response to stimulus, and 3 corresponds to studies that investigated the effect of differential gene expression on phenotype. Paper Subject Question Type Field/Lab Technology Abu-Abied et al. 2012 Eucalyptus grandis 1 lab Microarray Aguilar et al. 2010 Anopheles gambiae 1 both Microarray Anderson et al. 2006 Phlebotomus spp. 1 lab Microarray Andersson et al. 2013 multiple 1 field RNAseq Andrés et al. 2013 Gryllus spp. 1 field RNAseq Aranda et al. 2011 Montastraea faveolata 2 lab Microarray Arcà et al. 2005 Anopheles gambiae 1 lab Microarray Arfi et al. 2013 Pycnoporus coccineus 2 lab RNAseq Arnaiz et al. 2010 Paramecium tetraurelia 1 lab Microarray Aubin-Horth et al. 2009 1 field Microarray Avarre et al. 2014 Salmo salar Sarotherodon melanotheron heudelotii 1 lab RNAseq Babik et al. 2010 Myodes glareolus 1 lab RNAseq Bachmann et al. 2012 Lactococcus lactis 2, 3 lab Microarray Bachvaroff et al. 2014 multiple 1 lab RNAseq Badisco et al. 2011 Schistocerca gregaria 1 lab Microarray Badouin et al. 2013 Formica exsecta 1 field RNAseq Bai et al. 2010 Aphis glycines 1 lab RNAseq Bai et al. 2013 Hyriopsis cumingii 1 lab RNAseq Bajgain et al. 2011 Artemisia tridentata 1 lab RNAseq Balakrishnan et al. 2013 Uraeginthus granatina 1 lab RNAseq Baldo et al. 2011 multiple 1 lab RNAseq Ballerini et al. 2013 Iris fulva 1 lab RNAseq Banni et al. 2011 Mytilus galloprovincialis 1 lab Microarray 1 Bao et al. 2012 Nilaparvata lugens 1 lab RNAseq Bao et al. 2013 Nilaparvata lugens 2 lab RNAseq Bar-Yaacov et al. 2013 Chamaeleo chamaeleon 1 field RNAseq Barah et al. 2013 Arabidopsis thaliana 2 lab Microarray Bardil et al. 2011 Coffee arabica 1, 2 lab Microarray Barreto et al. 2011 Tigriopus californicus 1 lab RNAseq Barshis et al. 2013 Acropora hyacinthus 1, 2 lab RNAseq Bass et al. 2012 Nilaparvata lugens 1 lab RNAseq Bassene et al. 2010 1 field Microarray Baumgarten et al. 2013 Citrus spp. Symbiodinium microadriaticum 2 lab RNAseq Bay et al. 2009 Acropora millepora 1 lab Microarray Bay et al. 2009b Acropora millepora 1 lab Microarray Bayne et al. 2006 Oncorhynchus mykiss 2 lab Microarray Bazinet et al. 2013 multiple 1 lab RNAseq Becks et al. 2012 multiple 1, 2 lab Microarray Beemster et al. 2005 Arabidopsis thaliana 1 lab Microarray Belgard et al. 2013 multiple 1 lab RNAseq Bermingham et al. 2009 Buchnera aphidicola 1 lab Microarray Bernatchez et al. 2011 Anguilla spp. 1 field Microarray Bettencourt et al. 2010 Bathymodiuolus azoricus 1 field RNAseq Bilyk and Cheng 2013 Pagothenia borchgrevinki 1 lab RNAseq Boltana et al. 2013 Danio rerio 2, 3 lab Microarray Bonneau et al. 2013 Medicago truncatula 2, 3 lab Microarray Bonneaud et al. 2011 Carpodacus mexicanus 1, 2 lab Microarray Bougas et al. 2010 Salvelinus fontinalis 1 lab Microarray Bougas et al. 2013 Salvelinus fontinalis 1 lab Microarray Boulet et al. 2012 Salvelinus fontinalis 1, 3 lab Microarray Brady et al. 2011 Acropora millepora 1 lab RNAseq Brawand et al. 2011 multiple 1, 3 lab RNAseq Briscoe et al. 2013 Broekgaarden et al. 2008 Broekgaarden et al. 2011 Heliconius melpomene 1 lab RNAseq Brassica oleracea 2 lab Microarray Brassica nigra 2 lab Microarray Bruce et al. 2008 Arabidopsis thaliana 2, 3 lab Microarray Bryk et al. 2013 Mus musculus 1 lab Microarray Buckley et al. 2006 Gillichthys mirabilis 2 lab Microarray 2 Burke and Moran 2011 Acyrthosiphon pisum 1, 2 lab RNAseq Burke and Strand 2014 Microplitis demolitor 3 lab RNAseq Burki et al. 2013 Mikrocytos mackini 1 lab RNAseq Burns et al. 2012 Amphiura filiformis 2, 3 field Microarray Burns et al. 2013 Ophionotus victoriae 1, 2 lab RNAseq Busby et al. 2011 Saccharomyces spp. 1 lab RNAseq Calla et al. 2014 Ceratitis capitata 2 both RNAseq Campanero et al. 2005 Photobacterium profundum 1 lab Microarray Cardoen et al. 2011 Apis mellifera carnica 3 lab Microarray Carvalhais et al. 2013 Bacillus amyloliquefaciens 2 lab Microarray Cassone et al. 2011 Anopheles gambiae 2 lab Microarray Castilho et al. 2009 Thunnus orientalis 2 lab Microarray Castoe et al. 2013 Celorio-Mancera et al. 2013 Python molurus bivittatus 1 lab RNAseq Polygonia c-album 2 lab RNAseq Chan et al. 2012 Chaney and Gracey 2011 Arabidopsis thaliana 2, 3 lab Microarray Crassostrea gigas 2 lab Microarray Chapman et al. 2009 Crassostrea virginica 2 field Microarray Chapman et al. 2011 Crassostrea virginica 2 field Microarray Chapman et al. 2013 Senecio spp. 1 lab RNAseq Chaudhary et al. 2008 Gossypium barbadense 2 lab Microarray Chelaifa et al. 2010 Spartina spp. 1 lab Microarray Chelaifa et al. 2010b Spartina spp. 1 lab Microarray Chen et al. 2010 Locusta migratoria 1 lab RNAseq Chen et al. 2011 Balanus amphitrite 1 lab RNAseq Chen et al. 2013 Vitis vinifera 1 lab Microarray Chen, M. et al. 2012 1 lab RNAseq Chen, Z. et al. 2012 multiple Methanolobus psychrophilus R15 2 lab RNAseq Cheviron et al. 2008 Zonotrichia capensis 1, 2 field Microarray Cheviron et al. 2014 Peromyscus maniculatus 1, 3 both RNAseq Chiari et al. 2012 1 lab RNAseq Chu et al. 2012 multiple Paradoxornis webbianus bulomachus 1 field RNAseq Chun et al. 2008 Euprymna scolopes 2 field Microarray Clark et al. 2010 Laternula elliptica 2 lab Microarray Clark et al. 2012 Desulfovibrio vulgaris 1, 3 lab Microarray Coate and Doyle 2010 Glycine dolichocarpa 1 lab Microarray 3 Coate et al. 2013 Glycine dolichocarpa 1, 3 lab RNAseq Cohen et al. 2007 multiple 1 lab Microarray Collén et al. 2007 Chondrus crispus 2 lab Microarray Colombo et al. 2013 multiple 1, 3 field RNAseq Comeault et al. 2012 Timema cristinae 1 field RNAseq Conaco et al. 2012 Conant and Wagner 2004 Connor and Gracey 2011 Amphimedon queenslandica 1 field RNAseq Caenorhabditis elegans 3 lab Microarray Mytilus californianus 1 both Microarray Cook et al. 2011 Dolerus spp. 1 field RNAseq Coppe et al. 2010 Corredor-Adámez et al. 2005 Anguilla anguilla 1 field RNAseq Danio rerio 1 lab Microarray Cseke et al. 2009 Populus tremuloides 1 field Microarray Cui et al. 2013 multiple 1 lab RNAseq Cullingham et al. 2013 Pinus spp. 1 field RNAseq Czesny et al. 2012 Alosa pseudoharengus 1 field RNAseq Czypionka et al. 2012 Cottus spp. 1 lab Microarray Davidson et al. 2012 multiple 1 lab RNAseq de Boer et al. 2011 Folsomia candida 2 field Microarray de Carvalho et al. 2013 De Wit and Palumbi 2013 Spartina spp. 1 lab RNAseq Haliotis rufescens 1 field RNAseq Debes et al. 2012 Salmo salar 1, 2 lab Microarray Denekamp et al. 2011 Brachionus plicatilis 1 lab RNAseq Denver et al. 2005 Caenorhabditis elegans 1 lab Microarray Der et al. 2011 Derome and Bernatchez 2006 Pteridium aquilinum 1 lab RNAseq Coregonus artedi 1 field Microarray Derome et al. 2006 Coregonus clupeaformis 1 field Microarray Derome et al. 2008 Coregonus spp. 1, 3 lab Microarray Des Marais et al. 2012 Arabidopsis thaliana 1, 2 lab Microarray DeSalvo et al. 2008 Montastraea faveolata 2 lab Microarray DeSalvo et al. 2010 Acropora palmata 2 field Microarray DeSalvo et al. 2010b Montastraea faveolata 1, 2 lab Microarray Dhar et al. 2011 Domazet-Loso and Tautz, et al. 2010 Saccharomyces cerevisiae 2, 3 lab Microarray Danio rerio 1 lab Microarray Doroszuk et al. 2012 Drosophila melanogaster 1, 3 lab Microarray 4 dos Santos Ferreira et al. 2007 Euglena gracilis 2 lab Microarray Dou et al. 2013 Liposcelis bostrychophila 1 lab RNAseq Douglas et al. 2011 Buchnera aphidicola 2 lab Microarray Dowen et al. 2012 Arabidopsis thaliana 2, 3 lab RNAseq Drew et al. 2012 Danio rerio 1, 3 lab Microarray Dudycha et al. 2012 Daphnia spp. 1 lab Microarray Dunning et al. 2013 Micrarchus nov. sp. 2 2 lab RNAseq Durban et al. 2011 multiple 1 lab RNAseq Dworkin et al. 2009 Drosophila melanogaster 1 lab Microarray Ekblom et al. 2012 Philomachus pugnax 1, 3 lab RNAseq Elmer et al. 2010 Amphilophus spp. 1 lab RNAseq Etebari et al. 2011 Plutella xylostella 2 lab RNAseq Evans et al. 2008 Gillichthys mirabilis 2 lab Microarray Evans et al. 2011 1, 2 field Microarray Evans et al. 2013 Ewen-Campen et al. 2011 Oncorhynchus nerka Strongylocentrotus purpuratus 2 lab Microarray Oncopeltus fasciatus 1 lab RNAseq Fabro et al. 2008 Arabidopsis thaliana 2 lab Microarray Fan et al. 2012 Bacillus amyloliquefaciens 2 lab Microarray Fan et al. 2013 Salicornia europaea 2 lab RNAseq Fang et al. 2013 Caulobacter crescentus 1 lab RNAseq Fehsenfeld et al. 2011 Carcinus maenas 2 lab Microarray Feldmeyer et al. 2014 Temnothorax longispinosus 1, 3 lab RNAseq Ferreira et al. 2013 Polistes canadensis 1, 3 field RNAseq Filteau et al. 2013 Coregonus cupleaformis 1 lab Microarray Fonsesca et al. 2011 Pseudomonas putida 2 lab Microarray Frangipani et al. 2014 Pseudomonas aeruginosa 3 lab Microarray Freitak et al. 2012 Tribolium castaneum 1, 2 lab Microarray Friedrich et al. 2011 Ptomaphagus hirtus 1 lab RNAseq Fu and He 2012 Hypophthalmichthus molitrix 1 field RNAseq Gallagher et al. 2008 Oncorhynchus kisutch 1 lab Microarray Galletti et al. 2013 Rickettsia rickettsii 2 lab Microarray Ganot et al. 2011 Anemonia viridis 1 lab Microarray Garcia et al. 2012 Garcia-Vedrenne et al. 2013 Drosophila melanogaster 2, 3 lab Microarray Quahog Parasite Unknown 2 lab RNAseq Genissel et al. 2008 Drosophila melanogaster 1 lab Microarray 5 Geraldes et al. 2011 Populus trichocarpa 1 lab RNAseq Gierga et al. 2012 Synechoccus spp. 1, 2 lab Microarray Giger et al. 2008 Salmo spp. 1 field Microarray Gioti et al. 2012 Drosophila melanogaster 1, 3 lab Microarray Gioti et al. 2013 Neurospora spp. 1 lab RNAseq Goetz et al. 2010 Salvelinus namaycush 1, 3 lab RNAseq Goltsev et al. 2009 Anopheles gambiae 1 lab Microarray Gomulski et al. 2012 Ceratitis capitata 1 lab Microarray Gracey et al. 2004 Cyprinus carpio 2 lab Microarray Gracey et al. 2008 Granados-Cifuentes et al. 2013 Mytilus californianus 2 field Microarray Acropora millepora 1 lab Microarray Gross, J. et al. 2013 Astyanax mexicanus 1 lab RNAseq Gross, S. et al. 2013 Grostern and AlvarezCohen 2013 Agave spp. Pseudonocardia dioxanivorans 1 field RNAseq 2 lab Microarray Grumaz et al. 2013 Candida spp. 1 lab RNAseq Gu et al. 2013 Aphis gossypii 1, 2, 3 lab RNAseq Guggisberg et al. 2013 Cirsium arvense L. 1, 2 lab Microarray Gui et al. 2013 Sousa chinensis 1 field RNAseq Gunter et al. 2013 Astatoreochromis alluaudi 1, 2 lab RNAseq Guo et al. 2013 Pungitius pungitius 1 lab RNAseq Hall et al. 2013 Pinus spp. 1 field RNAseq Hanson et al. 2013 Brachionus calyciflorus 1 lab RNAseq Harms et al. 2013 Hyas araneus 1 lab RNAseq Harr et al. 2010 Mus spp. 1 lab RNAseq Harris et al. 2013 Peromyscus leucopus 1 field RNAseq He et al. 2010 Desulfovibrio vulgaris 2, 3 lab Microarray Healy et al. 2010 Fundulus heteroclitus 2 field Microarray Heath et al. 2012 Medicago truncatula 1 lab Microarray Hegarty et al. 2005 Senecio spp. 1 lab Microarray Hegarty et al. 2009 Senecio spp. 1, 2 lab Microarray Henning et al. 2013 Amphilophus citrinellus 1, 3 lab RNAseq Herranz et al. 2013 Drosopihila melanogaster 2 lab Microarray Hershkovitz et al. 2013 Metschnikowia fructicola 1, 2 lab RNAseq Hewson et al. 2009 Crocosphaera watsonii 1 field RNAseq Hines et al. 2012 Heliconius erato 1, 3 lab Microarray Hocher et al. 2011 multiple 1 lab Microarray 6 Hodgins et al. 2014 Ambrosia artemisiifolia 1, 2 field Microarray Hoffman et al. 2011 Arctocephalus gazella 1 field RNAseq Hohnjec et al. 2005 Medicago truncatula 1, 2 lab Microarray Holliday et al. 2008 Picea sitchensis 1, 2 lab Microarray Hori et al. 2013 Gadus morhua 2 lab Microarray Horvarth et al. 2005 Euphorbia esula 2 lab Microarray Hou et al. 2012 Loxodonta africana 1 lab Microarray Hoy et al. 2013 Metaseiulus occidentalis 1 lab RNAseq Hull et al. 2013 Lygus hesperus 1 lab RNAseq Hüning et al. 2013 Mytilus edulis 2 lab RNAseq Huth and Place 2013 Trematomus bernacchii 2 lab RNAseq Hwang et al. 2008 Ibarra-Laclette et al. 2011 Oncorhynchus kisutch 2 lab Microarray Utricularia gibba 1 field RNAseq Ignatov et al. 2010 Immonen and Ritchie 2012 Mycobacterium avium 1 lab RNAseq 2 lab Microarray Isanapong et al. 2013 Drosophila melanogaster Diplosphaera colotermitum TAV2 1 lab Microarray Jammes et al. 2005 Arabidopsis thaliana 2 lab Microarray Jansen et al. 2013 Daphnia magna 2 lab Microarray Janz et al. 2010 Populus spp. 2, 3 lab Microarray Jeffries et al. 2012 Oncorhynchus nerka 2 lab Microarray Jeffries et al. 2014 Oncorhyncus spp. 1, 2 lab RNAseq Jeukens et al. 2010 Coregonus clupeaformis 1 field RNAseq Jeyasingh et al. 2011 Daphnia pulex 2, 3 lab Microarray Jiang et al. 2009 Jiménez-Guri et al. 2013 Johansson, F. et al. 2013 Johansson, H. et al. 2013 Drosophila spp. 1 lab Microarray multiple 1 lab RNAseq Rana temporaria 2, 3 lab Microarray Formica exsecta 1 lab RNAseq Johnson et al. 2012 Karenia brevis 1, 2 lab Microarray Jouaux et al. 2013 Crassostrea gigas 1, 2 field Microarray Kaakoush et al. 2009 multiple 2 lab Microarray Kadam et al. 2008 Myxococcus xanthus 1, 3 lab Microarray Kalyuzhnaya et al. 2010 Methylotenera mobilis 1 lab Microarray Kanter et al. 2013 Ambrosia artemisiifolia 2, 3 lab RNAseq Kao et al. 2008 Saccharomyces cerevisiae 1, 3 lab Microarray 7 Kao et al. 2013 Schmidtea mediterranea 1 lab RNAseq Kaplinsky et al. 2013 Trachemys scripta 1 lab RNAseq Karkiuki et al. 2010 Brugia spp 1 lab Microarray Kassahn et al. 2007 Pomecentrus moluccensis 2 lab Microarray Katoh et al. 2004 Anabaena 2 lab Microarray Kawanabe et al. 2012 Arabidopsis spp. 1 lab Microarray Keeling et al. 2012 Dendoctonus ponderosae 1 field RNAseq Kegel et al. 2013 Emiliania huxleyi 1, 3 lab Microarray Kelley et al. 2012 Poecilia mexicana 1 field RNAseq Kempema et al. 2007 Arabidopsis thaliana 2 lab Microarray Kersten et al. 2013 2 lab RNAseq Khaitovich et al. 2005 Quercus rober L. Pan troglodytes, Homo sapiens 1 lab Microarray Kijimoto et al. 2009 Onthophagus taurus 1 lab Microarray Kim et al. 2010 Dunaliella salina 2 lab Microarray Kim et al. 2013 Pseudomonas putida 2 lab RNAseq Kimura et al. 2011 Dokdonia sp. MED134 2 lab RNAseq Kitano et al. 2011 Gasterosteus aculeatus 1, 3 lab Microarray Kobayashi et al. 2013 Shorea beccariana 2, 3 field RNAseq Konotchick et al. 2013 Macrocystis pyrifera 1 field RNAseq Kozak et al. 2014 Lucania spp. 1, 3 lab RNAseq Kunster et al. 2010 multiple 1 lab RNAseq Kusnierczyk et al. 2008 2, 3 lab Microarray Küster et al. 2007 Arabidopsis thaliana Medicago truncatula, Glomus intraradices, Amanita muscaria 1 lab Microarray Kvist et al. 2013 Meliteaea cinxia 1, 2 lab Microarray Lai et al. 2008 Helianthus annus 1, 2 lab Microarray Lang et al. 2009 Crassostrea gigas 1, 2 lab Microarray Latta et al. 2012 Daphnia pulex 2 lab Microarray Le Trionnaire et al. 2009 Acyrthosiphon pisum 1, 3 lab Microarray Le Trionnaire et al. 2012 Acyrthosiphon pisum 1 lab Microarray Leakey et al. 2009 Glycine max 1, 3 field Microarray Lee et al. 2011 Dehalococcoides spp. 3 lab Microarray Lee et al. 2013 Laodelphax striatellus 1 lab RNAseq Lehnert et al. 2012 Aiptasia pallida 1 lab RNAseq Lei et al. 2014 Plutella xylostella 2 lab RNAseq Lemay et al. 2013 Oncorhynchus nerka 1 field RNAseq 8 Lemay et al. 2013b Lemmetyinen et al. 2013 Lewandowska-Sabat et al. 2012 Ochotona princeps 1 field RNAseq Salmo salar 1 lab Microarray Arabidopsis thaliana 1 field Microarray Li and Brouwer 2013 Palaemonetes pugio 2, 3 field Microarray Li et al. 2013 Chrysopa pallens 1 lab RNAseq Li, A. et al. 2012 Larix spp. 1 field Microarray Li, BW et al. 2012 Brugia malayi 1 lab Microarray Li, J. et al. 2012 Helicoverpa armigera 1 lab RNAseq Li, S. et al. 2012 Cnaphalocrocis medinalis 1 lab RNAseq Lin et al. 2014 Tetraclita japonica formosana 1, 3 field RNAseq Liu et al. 2012 Aphis glycines 1 lab RNAseq Liu, G. et al. 2013 multiple 1 lab RNAseq Liu, Z. et al. 2013 Lockwood and Somero 2011 Vicia sativa 1 lab RNAseq Mytilus spp. 1, 2 lab Microarray Lockwood et al. 2010 Mytilus spp. 1, 2 lab Microarray Logacheva et al. 2011 Fagopyrum spp. 1 lab RNAseq Lorenz et al. 2010 Pinus taeda 2 lab Microarray Lowe et al. 2011 2 lab RNAseq Ludeman et al. 2014 Oxyrrhis marina Ephydatia muelleri, Spongilla lacustris 3 lab RNAseq Lundberg et al. 2013 Phylloscopus trochilus 1 field RNAseq Lv et al. 2013 Portunus trituberculatus 2 lab RNAseq Maaty et al. 2009 Sulfolobus solfataricus 2, 3 lab Microarray Malenke et al. 2013 Neotoma lepida 1, 2 lab Microarray Malone et al. 2006 Xenopus spp. 1 both Microarray Mancia et al. 2008 Tursiops truncatus 2 field Microarray Mancia et al. 2010 Tursiops truncatus 1 field Microarray Mancia et al. 2012 Zalophus californianus 2, 3 field Microarray Mane et al. 2007 Arabidopsis thaliana 2 lab Microarray Manfredini et al. 2014 Solenopsis invicta 1, 2 lab Microarray Manousaki et al. 2013 Amphilophus citrinellus 1, 3 field RNAseq Margres et al. 2013 Micrurus fulvius 1 lab RNAseq Marinković et al. 2012 Chironomus riparius 1 lab RNAseq Marques et al. 2008 Martens-Uzunova et al. 2008 Danio rerio 2, 3 lab Microarray Aspergillus niger 1, 3 lab Microarray 9 Martin et al. 2006 Salmo salar 2 lab Microarray Martinez et al. 2009 Postia placenta 3 lab Microarray Mattila et al. 2012 Stegodyphus spp. 1 lab RNAseq Matz et al. 2008 Pseudomonas aeruginosa 2 field Microarray Matzkin 2012 Drosophila mojavensis 1 lab Microarray Maughan et al. 2009 Bacillus subtilis 3 lab Microarray Mauter et al. 2013 Escherichia coli 2 lab Microarray Mavarez et al. 2009 Salvelinus fontinalis 1 lab Microarray McCoy et al. 2014 Euphydryas gillettii 1 field RNAseq McDonnell et al. 2013 Apis mellifera 2 lab RNAseq McKain et al. 2012 multiple 1 lab RNAseq Meier et al. 2014 Salmo trutta 3 field Microarray Mela et al. 2011 multiple 2, 3 lab Microarray Meng et al. 2013 Sinocyclocheilus spp. 1 lab RNAseq Meyer et al. 2011 Acropora millepora 2 lab RNAseq Mezey et al. 2008 Drosophila spp. 1 lab Microarray Michely et al. 2013 Ostreococcus tauri 1 lab Microarray Milan et al. 2011 Ruditapes phillippinarum 1, 2 lab RNAseq Milan et al. 2013 Ruditapes phillippinarum 1, 2 field Microarray Miller et al. 2012 Sphenodon punctatus 1 lab RNAseq Mittapalli et al. 2010 Agrilus planipennis 1 field RNAseq Mok et al. 2007 Plasmodium falciparum 1 lab Microarray Moreno-Paz et al. 2010 Leptospirillum spp. 1 field Microarray Moriwaki et al. 2010 Arabidopsis thaliana 2 lab Microarray Moya et al. 2012 Moyers and Rieseberg 2013 Mukhopadhyay et al. 2006 Anemonia viridis 2 lab Microarray Helianthus annuus 1, 3 field RNAseq Desulfovibrio vulgaris 2 lab Microarray Nagano et al. 2012 Oryza sativa 1, 2 field Microarray Natt et al. 2012 Gallus gallus 1 lab Microarray Navarro et al. 2013 Dreissena polymorpha 1, 2, 3 field Microarray Newton et al. 2013 Lates calcarifer 1, 2, 3 lab RNAseq Nguyen et al. 2012 Helicoverpa zea 1 lab RNAseq Nikinmaa et al. 2013 Nipitwattanaphon et al. 2013 Gasterosteus aculeatus 3 lab Microarray Solenopsis invicta 1 lab Microarray Niu, D. et al. 2013 Sinonovacula constricta 1 field RNAseq 10 Niu, S. et al. 2013 Pinus tabuliformis 1 lab RNAseq Norman et al. 2014 Salvelinus alpinus 1, 2, 3 lab RNAseq Nota et al. 2010 Folsomia candida 2 lab Microarray Novo et al. 2013 multiple 1 field RNAseq Nowack et al. 2011 Paulinella chomatophora 1 lab RNAseq Nyberg et al.2012 Pristina leidyi 1 lab RNAseq Nygren et al. 2012 1 lab Microarray O'Donnell et al. 2010 Neurospora intermedia Strongylocentrotus purpuratus 2 lab Microarray Ometto et al. 2012 Solenopsis spp. 1 lab Microarray Ometto et al. 2013 Drosophila suzukii 1 lab RNAseq Osada et al. 2006 Drosophila melanogaster 1 lab Microarray Overgaard et al. 2010 Drosophila melanogaster 2 lab Microarray Ozawa et al. 2012 Padilla-Gamiño et al. 2013 multiple Strongylocentrotus purpuratus. 2, 3 lab RNAseq 2, 3 lab Microarray Pagarete et al. 2011 multiple 2 field Microarray Page et al. 2013 Ambystoma spp. 1 lab Microarray Pallavicini et al. 2013 Latimeria menadoensis 1 lab RNAseq Palumbi et al. 2014 Acropora hyacinthus 1, 2 both RNAseq Pandey et al. 2008 Nicotiana attenuata 2, 3 lab RNAseq Parikh et al. 2010 Dictyostelium spp. 1 lab RNAseq Park et al. 2008 Populus deltoides 1 lab Microarray Patell et al. 2010 Pseudomonas aeruginosa 1 lab Microarray Patzelt et al. 2013 Dinoroseobacter shibae 3 lab Microarray Pauchet et al. 2009 Chrysomela tremulae 1 lab RNAseq Pavey et al. 2011 Oncorhynchus nerka 1 field Microarray Pellino et al. 2013 Ranunculus auricomus spp. 1 field RNAseq Pellizzari et al. 2013 Sparus aurata 2 lab Microarray Peng et al. 2011 Nilaparvata lugens 1 lab RNAseq Perdiguero et al. 2013 Pinus pinaster 2 lab Microarray Perez-Porro et al. 2013 Crella elegans 1 field RNAseq Philipp et al. 2012 2 lab RNAseq Philippe et al. 2010 Mytilus edulis Populus trichocarpa x deltoides 2, 3 lab Microarray Pierce et al. 2012 Elysia chlorotica 1 lab RNAseq Pina et al. 2005 Arabidopsis thaliana 1 lab Microarray Piveteau et al. 2011 Listeria monocytogenes 1, 2 lab Microarray 11 Place et al. 2012 Mytilus californianus 1, 2 field Microarray Plett et al. 2010 Populus trumula x alba 1 lab Microarray Poelchau et al. 2011 Aedes albopictus 1 lab RNAseq Poelchau et al. 2013 Aedes albopictus 1, 2 lab RNAseq Polato et al. 2010 Montastraea faveolata 2 lab Microarray Polato et al. 2011 Acropora palmata 1, 2 lab RNAseq Polato et al. 2013 Acropora palmata 1, 2 field Microarray Pontes et al. 2008 Sodalis glossinidius 1 lab Microarray Porcelli et al. 2013 Campylobacter jejuni 1 lab RNAseq Portune et al. 2010 Acropora palmata 1, 2 lab Microarray Pravosudov et al. 2013 Poecile atricapillus 1, 3 lab RNAseq Prince et al. 2010 Tribolium castaneum 1 lab Microarray Prosdocimi et al. 2011 multiple 1 field RNAseq Provost et al. 2011 Spodoptera frugiperda 2, 3 lab Microarray Qiao et al. 2013 Odorrana margaretae 1 field RNAseq Rajpurohit et al. 2013 Renaut and Bernatchez 2011 Drosophila mojavensis 1, 2 lab Microarray Coregonus spp. 1, 3 lab Microarray Renaut et al. 2009 Coregonus cupleaformis 1 lab Microarray Renaut et al. 2010 Coregonus spp. 1 lab RNAseq Renaut et al. 2011 Coregonus clupeaformis 1 field RNAseq Renaut et al. 2014 Rendón-Anaya et al. 2012 Helianthus spp. Centruroides noxius Hoffmann 1 lab RNAseq 1 lab RNAseq Rensink et al. 2005 Solanacae family 1 lab Microarray Rey et al. 2013 Danio rerio 1, 3 lab Microarray Ribeiro et al. 2012 Antricola delacruzi 1 field RNAseq Richards et al. 2012 Arabidopsis thaliana 1, 2 field Microarray Richier et al. 2008 Anthopleura elegantissima 2 lab Microarray Riley et al. 2014 Rhizophagus spp. 1 lab RNAseq Rinker et al. 2013 Anopheles spp. 3 lab RNAseq Roberge et al. 2007 Salmo salar 1 lab Microarray Roberge et al. 2008 Salmo salar Lithobates clamitans, Pseudacris regilla 2 lab Microarray 1 lab RNAseq Populus trichocarpa 1 field Microarray Anthopleura elegantissima 2 lab Microarray Robertson et al. 2014 Rodgers-Melnick et al. 2012 Rodriguez-Lanetty et al. 2006 12 Roeding et al. 2009 Pandinus imperator 1 lab RNAseq Rokitta et al. 2011 Emiliana huxleyi 1 lab Microarray Ronges et al. 2012 Petrolisthes cinctipes 2, 3 lab Microarray Rosenblum et al. 2012 Rana spp. 2 lab Microarray Salcedo et al. 2012 Heterocapsa circularisquama 1 lab RNAseq Salem et al. 2006 Oncorhynchus mykiss 1 lab Microarray Samils et al. 2013 Neurospora tetrasperma 1 lab Microarray Sanogo et al. 2011 Gasterosteus aculeatus 2 lab Microarray Sanogo et al. 2012 Gasterosteus aculeatus 1, 2 lab Microarray Santos et al. 2008 Danio rerio 1 lab Microarray Sass et al. 2013 Burkholderia cenocepacia 2, 3 lab Microarray Sauvage et al. 2010 Salvelinus fontinalis 2 lab Microarray Schmidt et al. 2013 Schnitzler and Weis 2010 Chironomus spp. 1 lab RNAseq Fungia scutaria 1, 2 lab Microarray Schoville et al. 2012 Tigriopus californicus 1 lab RNAseq Schramm et al. 2006 Arabidopsis thaliana 2 lab Microarray Schwartz, J. et al. 2010 Elysia chlorotica 1 lab RNAseq Schwartz, T. et al. 2010 Thamnophis elegans 1 both RNAseq Schweizer et al. 2013 Arabidopsis thaliana 2 lab Microarray Scully et al. 2013 Anoplophora glabripennis 1 lab RNAseq Seeb et al. 2011 Sellin Jeffries et al. 2012 Oncorhynchus keta 1 field RNAseq Pimephales promelas 2 field Microarray Sen et al. 2013 Reticulitermes flavipes 2 lab Microarray Seo et al. 2012 multiple 2 lab Microarray Seto and Tamura 2013 Drosophila spp. 1, 2 lab RNAseq Shaw et al. 2012 Artibeus jamaicensis 1 lab RNAseq Shi et al. 2013 Reaumuria soongorica 1 field RNAseq Shiao et al. 2012 Mus musculus 1 lab RNAseq Shin et al. 2012 multiple 1 lab RNAseq Sikhakolli et al. 2012 Fusarium spp. 1 lab RNAseq Sinha et al. 2012 multiple 1 lab Microarray Sloan et al. 2012 Silene vulgaris 1 lab RNAseq Small et al. 2009 Danio rerio 1 lab Microarray Small et al. 2013 Syngnathus spp. 1 lab RNAseq Smith, G. et al. 2013 Drosophila mojavensis 2, 3 lab RNAseq Smith, S. et al. 2013 Melanotaenia duboulayi 1, 2 lab RNAseq 13 Sneddon et al. 2005 Oncorhynchus mykiss 1 lab Microarray Snell-Rood et al. 2010 Onthophagus taurus 1 lab Microarray Soós et al. 2012 Lactuca sativa 2, 3 lab Microarray Spiess et al. 2012 Quercus robur 2, 3 lab Microarray Srinivasan et al. 2013 Panagrellus redivivus 1 lab RNAseq StCyr et al. 2008 Coregonus spp. 1, 3 both Microarray Stillman et al. 2009 Petrolisthes cinctipes 2 lab Microarray Stoll et al. 2009 Blochmannia floridanus 1 lab Microarray Su et al. 2013 Phalaenopsis aphrodite 3 lab Microarray Sun et al. 2012 Pomacea canaliculata 1 lab RNAseq Sussarellu et al. 2010 Crassostrea gigas 2 lab Microarray Sutherland et al. 2012 Lepeophtheirus salmonis 2 lab Microarray Szoevenyi et al. 2011 Funaria hygrometrica 1 lab RNAseq Szoevenyi et al. 2013 Funaria hygrometrica 1 lab RNAseq Tatematsu et al. 2005 Arabidopsis thaliana 1 lab Microarray Taylor et al. 2005 Populus x euramericana 2 lab Microarray Teo et al. 2009 Gracilaria changii 2 lab Microarray Teulier et al. 2012 Aptenodytes patagonicus 1, 3 field Microarray Thompson et al. 2011 Prochlorococcus spp. 2 lab Microarray Timmerhaus et al. 2012 Salmo salar 2 lab Microarray Timmermans et al. 2009 Timmins-Schiffman et al. 2013 Folsomia candida 2 lab Microarray 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