Table 1. The model or non-model species investigated (Class), organised by phylum, their habitat, the NGS platform and methodology, applications (research question) and tissues studied using NGS techniques in thermal adaptation references.

Species	Habitat	Platform	Methodology	Research question						Tissue	Type of study	References
				Transcriptome characterisation	SNPs finding	Microsat finding	Population genetic	DGE profiling	GO terms and candidate gene finding
Model
Arthropoda
Drosophila melanogaster (Insecta)	Terrestrial	Illumina	DNA-seq		x		x		x	Whole body (adults)	Observational	Kolaczkowski et al., 2011
		Illumina	DNA-seq		x		x		x	Whole body (adults)	Observational	Fabian et al., 2012
		Illumina	DNA-seq		x		x		x	Whole body (adults)	Experimental evolution	Tobler et al., 2014
		Illumina	DNA-seq		x		x		x	Whole body (adults)	Observational	Reinhardt et al., 2014
Echinodermata
Strongylocentrotus purpuratus (Echinoidea)	Marine	SOLiD, Illumina	RNA-seq					x	x	Embryo	Heat stress	Runcie et al., 2012
			RNA-seq					x	x	Tube foot	Common garden	Pespeni et al., 2013
Non-model
Annelida
Alvinella pompejana (Polychaeta)	Marine	454, Illumina	RNA-seq	x						Whole body	Genetic reference	Holder et al., 2013
Arthropoda
Erynnis propertius (Insecta)	Terrestrial	454	RNA-seq	x	x					Whole body (larvae)	Genetic reference	O'Neil et al., 2010
Euphausia superb (Malacostraca)	Marine	454	RNA-seq	x	x	x				Whole body	Genetic reference	Clark et al., 2011
Liposcelis entomophila (Insecta)	Terrestrial	Illumina	RNA-seq	x	x	x				Whole body	Genetic reference	Wei et al., 2013
Papilio zelicaon (Insecta)	Terrestrial	454	RNA-seq	x	x					Whole body (larvae)	Genetic reference	O'Neil et al., 2010
Tigriopus californicus (Maxillopoda)	Marine	Illumina	RNA-seq	x				x	x	Whole body	Heat stress	Schoville et al., 2012
Chordata
Ictalurus furcatus/Ictalurus punctatus (Actinopterygii)	Freshwater	Illumina	RNA-seq	x				x	x	Gill, liver	Heat stress; common garden	Liu et al., 2013
Lates calcarifer (Actinopterygii)	Marine	Illumina	RNA-seq	x				x	x	Muscle	Heat stress; common garden	Newton et al., 2013
Melanotaenia duboulayi (Actinopterygii)	Freshwater	Illumina	RNA-seq	x				x	x	Liver	Heat stress	Smith et al., 2013
Ochotona princeps (Mammalia)	Terrestrial	454	RNA-seq	x	x		x		x	Brain, gonad, heart, liver, lung	Observational	Lemay et al., 2013
Oncorhynchus mykiss (Actinopterygii)	Freshwater	Illumina	RNA-seq	x				x	x	Gill	Common garden	Tan et al., 2012
		Illumina	DNA(RAD)-seq		x		x		x	Liver	Observational	Narum et al., 2013
Pagothenia borchgrevinki (Actinopterygii)	Marine	454, Illumina	RNA-seq	x						Gill, liver	Genetic reference	Bilyk and Cheng, 2013
Paradoxornis webbianus (Aves)	Terrestrial	Illumina	RNA-seq	x	x	x				Brain, liver	Genetic reference	Chu et al., 2012
Poecile atricapillus (Aves)	Terrestrial	Illumina	RNA-seq	x				x	x	Hippocampi	Common garden	Pravosudov et al., 2013
Salmo salar (Actinopterygii)	Marine	454	RNA-seq	x				x	x	Liver	Heat stress	Olsvik, et al., 2013
Trematomus bernacchii (Actinopterygii)	Marine	454	RNA-seq	x				x	x	Brain, gill, Liver	Heat stress	Huth and Place, 2013
Cnidaria
Acropora millepora (Cnidaria)	Marine	454	RNA-seq	x	x					Whole body (larvae)	Genetic reference	Meyer et al., 2009
		SOLiD	RNA-seq					x	x	Whole body (larvae)	Heat stress	Meyer et al. 2011
Acropora palmate (Cnidaria)	Marine	454	RNA-seq	x	x	x	x		x	Whole body (larvae)	Observational	Polato et al., 2011
Porites astreoides (Anthozoa)	Marine	454	RNA-seq	x				x	x	Skeleton	Heat stress	Kenkel et al., 2013
Mollusca
Crassostrea gigas (Bivalvia)	Marine	SOLiD	RNA-seq					x	x	Mantle	Heat stress	Clark et al., 2013
Haliotis rufescens (Gastropoda)	Marine	Illumina	RNA-seq	x	x		x		x	Mantle	Observational	De Wit and Palumbi, 2013
Macoma balthica (Bivalvia)	Marine	454	RNA-seq	x	x		x		x	Whole body	Observational	Pante et al., 2012
Nucella lapillus (Gastropoda)	Marine	Illumina	DNA(RAD)-seq; RNA-seq	x	x		x		x	Whole body	Observational	Chu et al., 2014
Villosa lienosa (Bivalvia)	Freshwater	Illumina	RNA-seq	x				x	x	Mantle, muscle, gill	Heat stress	Wang et al., 2012

Abbreviations: DGE, differential gene expression; GO, gene ontology; NGS, next-generation sequencing; SNP, single-nucleotide polymorphism.