Giải trình tự Transcriptome de Novo của Ốc Echinolittorina malaccana: Xác định các Gen Phản ứng với Căng thẳng Nhiệt và Phát triển các Tham số Di truyền cho Nghiên cứu Dân số

Amaral PP, Dinger ME, Mattick JS (2013) Non-coding RNAs in homeostasis, disease and stress responses: an evolutionary perspective. Brief Funct Genomics 12:254–278 Basirico L, Morera P, Primi V, Lacetera N, Nardone A, Bernabucci U (2011) Cellular thermotolerance is associated with heat shock protein 70.1 genetic polymorphisms in Holstein lactating cows. Cell Stress Chaperones 16:441–448 Boutet I, Tanguy A, Le Guen D, Piccino P, Hourdez S, Legendre P, Jollivet D (2009) Global depression in gene expression as a response to rapid thermal changes in vent mussels. Proc Biol Sci 276:3071–3079 Conesa A, Gotz S, Garcia-Gomez JM, Terol J, Talon M, Robles M (2005) Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21:3674–3676 Dunphy BJ, Ragg NL, Collings MG (2013) Latitudinal comparison of thermotolerance and HSP70 production in F2 larvae of the greenshell mussel (Perna canaliculus). J Exp Biol 216:1202–1209 Evans TG, Hofmann GE (2012) Defining the limits of physiological plasticity: how gene expression can assess and predict the consequences of ocean change. Phil Trans R Soc B 367:1733–1745 Feder ME, Walser JC (2005) The biological limitations of transcriptomics in elucidating stress and stress responses. J Evol Biol 18:901–910 Franks SJ, Hoffmann AA (2012) Genetics of climate change adaptation. Annu Rev Genet 46:185–208 Fu N, Wang Q, Shen HL (2013) De novo assembly, gene annotation and marker development using Illumina paired-end transcriptome sequences in celery (Apium graveolens L.). PLoS One 8:e57686 Galindo J, Moran P, Rolan-Alvarez E (2009) Comparing geographical genetic differentiation between candidate and noncandidate loci for adaptation strengthens support for parallel ecological divergence in the marine snail Littorina saxatilis. Mol Ecol 18:919–930 Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q, Chen Z, Mauceli E, Hacohen N, Gnirke A, Rhind N, Di Palma F, Birren BW, Nusbaum C, Lindblad-Toh K, Friedman N, Regev A (2011) Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol 29:644–652 Gracey AY, Chaney ML, Boomhower JP, Tyburczy WR, Connor K, Somero GN (2008) Rhythms of gene expression in a fluctuating intertidal environment. Curr Biol 18:1501–1507 Hammond LM, Hofmann GE (2010) Thermal tolerance of Strongylocentrotus purpuratus early life history stages: mortality, stress-induced gene expression and biogeographic patterns. Mar Biol 157:2677–2687 Helmuth B, Harley CD, Halpin PM, O’donnell M, Hofmann GE, Blanchette CA (2002) Climate change and latitudinal patterns of intertidal thermal stress. Science 298:1015–1017 Henderson B (2010) Integrating the cell stress response: a new view of molecular chaperones as immunological and physiological homeostatic regulators. Cell Biochem Funct 28:1–14 Hofmann GE, Todgham AE (2010) Living in the now: physiological mechanisms to tolerate a rapidly changing environment. Annu Rev Physiol 72:127–145 Hollenbeck CM, Portnoy DS, Gold JR (2012) Use of comparative genomics to develop EST-SSRs for red drum (Sciaenops ocellatus). Mar Biotechnol (NY) 14:672–680 Iseli C, Jongeneel CV, Bucher P (1999) ESTScan: a program for detecting, evaluating, and reconstructing potential coding regions in EST sequences. Proc Int Conf Intell Syst Mol Biol :138–148 Ivanina AV, Taylor C, Sokolova IM (2009) Effects of elevated temperature and cadmium exposure on stress protein response in eastern oysters Crassostrea virginica (Gmelin). Aquat Toxicol 91:245–254 Kultz D (2005) Molecular and evolutionary basis of the cellular stress response. Annu Rev Physiol 67:225–257 Langmead B, Salzberg SL (2012) Fast gapped-read alignment with Bowtie 2. Nat Methods 9:357–359 Leung AK, Sharp PA (2010) MicroRNA functions in stress responses. Mol Cell 40:205–215 Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, Genome Project Data Processing S (2009) The sequence alignment/map format and SAM tools. Bioinformatics 25:2078–2079 Liu WG, Huang XD, Lin JS, He MX (2012) Seawater acidification and elevated temperature affect gene expression patterns of the pearl oyster Pinctada fucata. PLoS One 7:e33679 Liu S, Wang X, Sun F, Zhang J, Feng J, Liu H, Rajendran KV, Sun L, Zhang Y, Jiang Y, Peatman E, Kaltenboeck L, Kucuktas H, Liu Z (2013) RNA-Seq reveals expression signatures of genes involved in oxygen transport, protein synthesis, folding, and degradation in response to heat stress in catfish. Physiol Genomics 45:462–476 Lockwood BL, Somero GN (2012) Functional determinants of temperature adaptation in enzymes of cold- versus warm-adapted mussels (Genus Mytilus). Mol Biol Evol 29:3061–3070 Lockwood BL, Sanders JG, Somero GN (2010) Transcriptomic responses to heat stress in invasive and native blue mussels (genus Mytilus): molecular correlates of invasive success. J Exp Biol 213:3548–3558 Maron BJ (2002) Hypertrophic cardiomyopathy: a systematic review. JAMA 287:1308–1320 Marshall DJ, McQuaid CD (2011) Warming reduces metabolic rate in marine snails: adaptation to fluctuating high temperatures challenges the metabolic theory of ecology. Proc Biol Sci 278:281–288 Marshall DJ, Dong YW, McQuaid CD, Williams GA (2011) Thermal adaptation in the intertidal snail Echinolittorina malaccana contradicts current theory by revealing the crucial roles of resting metabolism. J Exp Biol 214:3649–3657 Martinez-Fernandez M, Bernatchez L, Rolan-Alvarez E, Quesada H (2010) Insights into the role of differential gene expression on the ecological adaptation of the snail Littorina saxatilis. BMC Evol Biol 10:356 Micallef G, Bickerdike R, Reiff C, Fernandes JMO, Bowman AS, Martin SM (2012) Exploring the transcriptome of Atlantic salmon (Salmo salar) skin, a major defense organ. Mar Biotechnol (NY) 14:559–569 Mutz KO, Heilkenbrinker A, Lonne M, Walter JG, Stahl F (2013) Transcriptome analysis using next-generation sequencing. Curr Opin Biotechnol 24:22–30 Negri A, Oliveri C, Sforzini S, Mignione F, Viarengo A, Banni M (2013) Transcriptional response of the mussel Mytilus galloprovincialis (Lam.) following exposure to heat stress and copper. PLoS One 8:e66802 Nezis IP, Simonsen A, Sagona AP, Finley K, Gaumer S, Contamine D, Rusten TE, Stenmark H, Brech A (2008) Ref(2)P, the Drosophila melanogaster homologue of mammalian p62, is required for the formation of protein aggregates in adult brain. J Cell Biol 180:1065–1071 Parsell DA, Lindquist S (1993) The function of heat-shock proteins in stress tolerance—degradation and reactivation of damaged proteins. Annu Rev Genet 27:437–496 Pertea G, Huang X, Liang F, Antonescu V, Sultana R, Karamycheva S, Lee Y, White J, Cheung F, Parvizi B, Tsai J, Quackenbush J (2003) TIGR gene indices clustering tools (TGICL): a software system for fast clustering of large EST datasets. Bioinformatics 19:651–652 Podrabsky JE, Somero GN (2004) Changes in gene expression associated with acclimation to constant temperatures and fluctuating daily temperatures in an annual killifish Austrofundulus limnaeus. J Exp Biol 207:2237–2254 Portner HO (2010) Oxygen- and capacity-limitation of thermal tolerance: a matrix for integrating climate-related stressor effects in marine ecosystems. J Exp Biol 213:881–893 Posner M, Kiss AJ, Skiba J, Drossman A, Dolinska MB, Hejtmancik JF, Sergeev YV (2012) Functional validation of hydrophobic adaptation to physiological temperature in the small heat shock protein αA-crystallin. PLoS One 7:e34438 Rebl A, Verleih M, Kobis JM, Kuhn C, Wimmers K, Kollner B, Goldammer T (2013) Transcriptome profiling of gill tissue in regionally bred and globally farmed rainbow trout strains reveals different strategies for coping with thermal stress. Mar Biotechnol (NY) 15:445–460 Reid DG, Lal K, Mackenzie-Dodds J, Kaligis F, Littlewood DTJ, Williams ST (2006) Comparative phylogeography and species boundaries in Echinolittorina snails in the central Indo-West Pacific. J Biogeogr 33:990–1006 Richter K, Haslbeck M, Buchner J (2010) The heat shock response: life on the verge of death. Mol Cell 40:253–266 Robinson MD, Mccarthy DJ, Smyth GK (2010) edgeR: a bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26:139–140 Robinson N, Sahoo PK, Baranski M, Das Mahapatra K, Saha JN, Das S, Mishra Y, Das P, Barman HK, Eknath AE (2012) Expressed sequences and polymorphisms in rohu carp (Labeo rohita, Hamilton) revealed by mRNA-seq. Mar Biotechnol (NY) 14:620–633 Ronges D, Walsh JP, Sinclair BJ, Stillman JH (2012) Changes in extreme cold tolerance, membrane composition and cardiac transcriptome during the first day of thermal acclimation in the porcelain crab Petrolisthes cinctipes. J Exp Biol 215:1824–1836 Runcie DE, Garfield DA, Babbitt CC, Wygoda JA, Mukherjee S, Wray GA (2012) Genetics of gene expression responses to temperature stress in a sea urchin gene network. Mol Ecol 21:4547–4562 Sanford E, Kelly MW (2011) Local adaptation in marine invertebrates. Annu Rev Mar Sci 3:509–535 Schoville SD, Barreto FS, Moy GW, Wolff A, Burton RS (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 Evol Biol 12:170 Smith S, Bernatchez L, Beheregaray LB (2013) RNA-seq analysis reveals extensive transcriptional plasticity to temperature stress in a freshwater fish species. BMC Genomics 14:375 Somero GN (2010) The physiology of climate change: how potentials for acclimatization and genetic adaptation will determine ‘winners’ and ‘losers’. J Exp Biol 213:912–920 Sorensen JG, Nielsen MM, Kruhoffer M, Justesen J, Loeschcke V (2005) Full genome gene expression analysis of the heat stress response, in Drosophila melanogaster. Cell Stress Chaperones 10:312–328 Stenseng E, Braby CE, Somero GN (2005) Evolutionary and acclimation-induced variation in the thermal limits of heart function in congeneric marine snails (genus Tegula): implications for vertical zonation. Biol Bull 208:138–144 Stillman JH, Tagmount A (2009) Seasonal and latitudinal acclimatization of cardiac transcriptome responses to thermal stress in porcelain crabs, Petrolisthes cinctipes. Mol Ecol 18:4206–4226 Thiel T, Michalek W, Varshney RK, Graner A (2003) Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L). Theor Appl Genet 106:411–422 Thomas JO, Travers AA (2001) HMG1 and 2, and related ‘architectural’ DNA-binding proteins. Trends Biochem Sci 26:167–174 Tomanek L (2010) Variation in the heat shock response and its implication for predicting the effect of global climate change on species’ biogeographical distribution ranges and metabolic costs. J Exp Biol 213:971–979 Truebano M, Burns G, Thorne MS, Hillyard G, Peck LS, Skibinski DOF, Clark MS (2010) Transcriptional response to heat stress in the Antarctic bivalve Laternula elliptica. J Exp Mar Biol Ecol 391:65–72 Vandenkoornhuyse P, Dufresne A, Quaiser A, Gouesbet G, Binet F, Francez AJ, Mahe S, Bormans M, Lagadeuc Y, Couee I (2010) Integration of molecular functions at the ecosystemic level: breakthroughs and future goals of environmental genomics and post-genomics. Ecol Lett 13:776–791 Verghese J, Abrams J, Wang Y, Morano KA (2012) Biology of the heat shock response and protein chaperones: budding yeast (Saccharomyces cerevisiae) as a model system. Microbiol Mol Biol Rev 76:115–158 Walters RJ, Blanckenhorn WU, Berger D, Woods A (2012) Forecasting extinction risk of ectotherms under climate warming: an evolutionary perspective. Funct Ecol 26:1324–1338 Wei Z, Wang W, Hu P, Lyon GJ, Hakonarson H (2011) SNVer: a statistical tool for variant calling in analysis of pooled or individual next-generation sequencing data. Nucleic Acids Res 39:e132 Werner GD, Gemmell P, Grosser S, Hamer R, Shimeld SM (2013) Analysis of a deep transcriptome from the mantle tissue of Patella vulgata Linnaeus (Mollusca: Gastropoda: Patellidae) reveals candidate biomineralising genes. Mar Biotechnol (NY) 15:230–243 Whitehead A (2012) Comparative genomics in ecological physiology: toward a more nuanced understanding of acclimation and adaptation. J Exp Biol 215:884–891 Zuo W, Moses ME, West GB, Hou C, Brown JH (2012) A general model for effects of temperature on ectotherm ontogenetic growth and development. Proc Biol Sci 279:1840–1846