Comparative transcriptome reveals the thermal stress response differences between Heilongjiang population and Xinjiang population of Lota lota

Beck, 2009, Visual proteomics of the human pathogen Leptospira interrogans, Nat. Methods, 6, 817, 10.1038/nmeth.1390 Bettge, 2009, Proliferative kidney disease (PKD) of rainbow trout, temperature- and time-related changes of tetracapsuloides bryosalmonae DNA in the kidney, Parasitol, 136, 615, 10.1017/S0031182009005800 Bolger, 2014, Trimmomatic, a flexible trimmer for illumina sequence data, Bioinformatics, 30, 2114, 10.1093/bioinformatics/btu170 Bopp, 2013, Multiple stressors of ocean ecosystems in the 21st century, projections with CMIP5 models, Biogeosciences, 10, 6225, 10.5194/bg-10-6225-2013 Cann, 2002, A human genome diversity cell line panel, Science, 296, 261, 10.1126/science.296.5566.261b Cerri, 2017, The ERN1 transcription factor gene is a target of the CCaMK/CYCLOPS complex and controls rhizobial infection in lotus japonicas, New Phytol., 215, 323, 10.1111/nph.14547 Cheng, 2009, Effects of temperature change on innate cellular and humoral immune responses of the orangespotted grouper Epinephelus coioides and its susceptibility to vibrio alginolyticus, Fish Shellfish Immunol., 26, 10.1016/j.fsi.2009.03.011 Cheviron, 2010, Transcriptomic variation and plasticity in rufous-collared sparrows (Zonotrichia capensis) along an altitudinal gradient, Mol. Ecol., 17, 4556, 10.1111/j.1365-294X.2008.03942.x Conesa, 2005, Blast2GO, a universal tool for annotation, visualization and analysis in functional genomics research, Bioinformatics, 21, 3674, 10.1093/bioinformatics/bti610 Cossins, 2005, Fish as models for environmental genomics, Nat. Rev. Genet., 6, 324, 10.1038/nrg1590 Davidson, 2014, Corset, enabling differential gene expression analysis for de novo assembled transcriptomes, Genome Biol., 15, 410 Edwards, 2011, Precision of two methods for estimating age from burbot otoliths, J. Appl. Ichthyol., 27, 43, 10.1111/j.1439-0426.2011.01842.x Eggset, 1997, Immunocompetence and duration of immunity against Vibrio salmonicida and Aeromonas salmonicida after vaccination of Atlantic salmon (Salmo Salar L.) at low and high temperatures, Fish Shellfish Immunol., 7, 247, 10.1006/fsim.1997.0080 Grabherr, 2011, Full-length transcriptome assembly from RNA-seq data without a reference genome, Nat. Biotechnol., 29, 644, 10.1038/nbt.1883 Guo, 2016, Widespread and adaptive alterations in genome-wide gene expression associated with ecological divergence of two oryza species, Mol. Biol. Evol., 33, 62, 10.1093/molbev/msv196 Han, 2013, ER-stressinduced transcriptional regulation increases protein synthesis leading to cell death, Nat. Cell Biol., 5, 481, 10.1038/ncb2738 Haslbeck, 2005, Some like it hot, the structure and function of small heat-shock proteins, Nat. Struct. Mol. Biol., 12, 842, 10.1038/nsmb993 Hölker, 2004, Colonization of the freshwater environment by a marine invader, how to cope with warm summer temperatures?, Evol. Ecol. Res., 6, 1123 Holt, 1990, The microevolutionary consequences of climate change, Trends Ecol. Evol., 5, 311, 10.1016/0169-5347(90)90088-U Hori, 2012, A moderate increase in ambient temperature modulates the Atlantic cod (Gadus morhua) spleen transcriptome response to intraperitoneal viral mimic injection, BMC Genomics, 13, 431, 10.1186/1471-2164-13-431 Hughes, 2018, Comprehensive phylogeny of ray-finned fishes (Actinopterygii) based on transcriptomic and genomic data, Proc. Natl. Acad. Sci., 115, 6249, 10.1073/pnas.1719358115 IPCC, 2001, Climate change 2001, the scientific basis Kent, 2002, BLAT-the BLAST-like alignment tool, Genome Res., 12, 656 Lahnsteiner, 1994, Fine structure of spermatozoa of the burbot, Lota Lota (Gadidae, Pisces), J. Submicrosc. Cytol. Pathol., 26, 445 Li, 2009, Fast and accurate short read alignment with burrows-wheeler transform, Bioinformatics, 25, 1754, 10.1093/bioinformatics/btp324 Li, 2006, Cd-hit, a fast program for clustering and comparing large sets of protein or nucleotide sequences, Bioinformatics, 22, 1658, 10.1093/bioinformatics/btl158 Li, 2019, Characterization and expression profiles of muscle transcriptome in schizothoracine fish, Schizothorax prenanti, Gene, 685, 156, 10.1016/j.gene.2018.10.070 Li, 2020, Expression and localization of the sorting protein SNX4 in mouse testis, Acta Univ. Med. Anhui, 55, 235 Lou, 2019, Transcriptome analyses reveal alterations in muscle metabolism, immune responses and reproductive behavior of japanese mantis shrimp (Oratosquilla oratoria) at different cold temperature, Comp. Biochem. Physiol. D: Genomics Proteomics, 32 Love, 2014, Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2, Genome Biol., 15, 550, 10.1186/s13059-014-0550-8 Magnadóttir, 1999, Humoral immune parameters in Atlantic cod (Gadus morhua L.): the effects of environmental temperature, Comp. Biochem. Physiol. B Biochem. Mol. Biol., 122, 181, 10.1016/S0305-0491(98)10157-8 Morris, 2014, Gene expression plasticity evolves in response to colonization of freshwater lakes in threespine stickleback, Mol. Ecol., 23, 3226, 10.1111/mec.12820 Narum, 2015, Transcriptomic response to heat stress among ecologically divergent populations of redband trout, BMC Genomics, 16, 103, 10.1186/s12864-015-1246-5 Nikcevic, 1995, The burbot (Lota Lota L.) in Yugoslavia, habitats and thermal acclimation capacity, Ichthyologia (Yugoslavia), 27, 5 Parmesan, 2006, Ecological and evolutionary responses to recent climate change, Annu. Rev. Ecol. Evol. Syst., 37, 637, 10.1146/annurev.ecolsys.37.091305.110100 Podrabsky, 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, 10.1242/jeb.01016 Pörtner, 2002, Climate variations and the physiological basis of temperature dependent biogeography, systemic to molecular hierarchy of thermal tolerance in animals, Comp. Biochem. Physiol. A Mol. Integr. Physiol., 132, 739, 10.1016/S1095-6433(02)00045-4 Pörtner, 2007, Thermal limits and adaptation in marine Antarctic ectotherms, an integrative view, Philos. Trans. R. Soc. London, Ser. A, 362, 2233, 10.1098/rstb.2006.1947 Qian, 2006, Study on hatching conditions of Lota Lota, Freshw. Fish., 36, 57 Raida, 2008, Bath vaccination of rainbow trout (Oncorhynchus mykiss) against Yersinia ruckeri, effects of temperature on protection and gene expression, Vaccine, 26, 1050, 10.1016/j.vaccine.2007.12.029 Ron, 2007, Signal integration in the endoplasmic reticulum unfolded protein response, Nat. Rev. Mol. Cell Biol., 7, 519, 10.1038/nrm2199 Shiels, 2006, Sarcolemmal ion currents and sarcoplasmic reticulum Ca2+ content in ventricular myocytes from the cold stenothermic fish, the burbot (Lota lota), J. Exp. Biol., 209, 3091, 10.1242/jeb.02321 Sonna, 2002, Molecular biology of thermoregulation invited review, effects of heat and cold stress on mammalian gene expression, J. Appl. Physiol., 92, 1725, 10.1152/japplphysiol.01143.2001 Stapanian, 2010, Worldwide status of burbot and conservation measures, Fish Fish., 11, 34, 10.1111/j.1467-2979.2009.00340.x Sunday, 2012, Thermal tolerance and the global redistribution of animals, Nat. Clim. Chang., 2, 686, 10.1038/nclimate1539 Tamura, 2011, (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods, Mol. Biol. Evol., 28, 2731, 10.1093/molbev/msr121 Tiitu, 2002, Morphology and fine structure of the heart of the burbot, a cold stenothermal fish, J. Fish Biol., 61, 106, 10.1111/j.1095-8649.2002.tb01740.x Varsamos, 2006, Husbandry stress during early life stages affects the stress response and health status of juvenile sea bass, Dicentrarchus labrax, Fish Shellfish Immunol., 20, 83, 10.1016/j.fsi.2005.04.005 Venkatash, 2003, Evolution and diversity of fish genomes, Curr. Opin. Genet. Dev., 13, 588, 10.1016/j.gde.2003.09.001 Verslycke, 2002, Effects of a changing abiotic environment on the energy metabolism in the estuarine mysid shrimp Neomysis integer (Crustacea, Mysidacea), J. Exp. Mar. Biol. Ecol., 279, 61, 10.1016/S0022-0981(02)00339-8 Vornanen, 2006, Temperature and Ca2+ dependence of H-3ryanodine binding in the burbot (Lota Lota L.) heart, Am. J. Physiol. Regul. Integr. Comp. Physiol., 290, 345, 10.1152/ajpregu.00443.2005 Wheeler, 2013, Nhmmer, DNA homology search with profile HMMs, Bioinformatics, 29, 2487, 10.1093/bioinformatics/btt403 Whitehead, 2011, Functional genomics of physiological plasticity and local adaptation in killifish, J. Hered., 102, 499, 10.1093/jhered/esq077 Yang, 2007, PAML 4: phylogenetic analysis by maximum likelihood, Mol. Biol. Evol., 24, 1586, 10.1093/molbev/msm088 Yang, 2021, Comparative transcriptomic analysis brings new insights into the response to acute temperature acclimation in burbot (Lota Lota lota), Aquac. Rep., 20 Zhang, 2008, Morphological comparison and isozyme analysis of Lota Lota populations in Duobuku’er river and Eerqisi River, J. Fish. Sci. China, 15, 386