Comparative analysis of cold-responsive genes under short-term cold stimulation and cold-adaptive genes under long-term heterogeneous environments reveals a cold adaptation mechanism in weeping forsythia

Ahrens CW, Byrne M, Rymer PD (2019) Standing genomic variation within coding and regulatory regions contributes to the adaptive capacity to climate in a foundation tree species. Mol Ecol 28:2502–2516

CAS  PubMed  Google Scholar 

Alexa A, Rahnenfuhrer J (2010) topGO: enrichment analysis for gene ontology R Package Version 2.34.0. https://rdrr.io/bioc/topGO/.

An D, Yang J, Zhang P (2012) Transcriptome profiling of low temperature-treated cassava apical shoots showed dynamic responses of tropical plant to cold stress. BMC Genomics 13:64

CAS  PubMed  PubMed Central  Google Scholar 

Arnold SJ, Pfrender ME, Jones AG (2001) The adaptive landscape as a conceptual bridge between micro- and macroevolution. Genetica 112:9–32

PubMed  Google Scholar 

Bates LS, Waldren RP, Teare ID (1973) Rapid determination of free proline for water-stress studies. Plant Soil 39:205–207

CAS  Google Scholar 

Chinnusamy V, Zhu JK, Sunkar R (2010) Gene regulation during cold stress acclimation in plants. Methods Mol Biol 639:39–55

CAS  PubMed  PubMed Central  Google Scholar 

Cushman SA, Shirk AJ, Howe GT, Murphy MA, Dyer RJ, Joost S (2018) Editorial: the least cost path from landscape genetics to landscape genomics: challenges and opportunities to explore NGS data in a spatially explicit context. Front Genet 9:215

PubMed  PubMed Central  Google Scholar 

Deng S, Ma J, Zhang L, Chen F, Sang Z, Jia Z, Ma L (2019) De novo transcriptome sequencing and gene expression profiling of Magnolia wufengensis in response to cold stress. BMC Plant Biol 19:321

PubMed  PubMed Central  Google Scholar 

Dimmer EC, Huntley RP, Alam-Faruque Y, Sawford T, O’Donovan C, Martin MJ, Bely B, Browne P, Mun Chan W, Eberhardt R, Gardner M, Laiho K, Legge D, Magrane M, Pichler K, Poggioli D, Sehra H, Auchincloss A, Axelsen K, Blatter MC, Boutet E, Braconi-Quintaje S, Breuza L, Bridge A, Coudert E, Estreicher A, Famiglietti L, Ferro-Rojas S, Feuermann M, Gos A, Gruaz-Gumowski N, Hinz U, Hulo C, James J, Jimenez S, Jungo F, Keller G, Lemercier P, Lieberherr D, Masson P, Moinat M, Pedruzzi I, Poux S, Rivoire C, Roechert B, Schneider M, Stutz A, Sundaram S, Tognolli M, Bougueleret L, Argoud-Puy G, Cusin I, Duek-Roggli P, Xenarios I, Apweiler R (2012) The UniProt-GO annotation database in 2011. Nucleic Acids Res 40:D565–D570

CAS  PubMed  Google Scholar 

Frichot E, Schoville SD, Bouchard G, Francois O (2013) Testing for associations between loci and environmental gradients using latent factor mixed models. Mol Biol Evol 30:1687–1699

CAS  PubMed  PubMed Central  Google Scholar 

Fu ZZ, Li YH, Zhang KM, Li Y (2014) Molecular data and ecological niche modeling reveal population dynamics of widespread shrub Forsythia suspensa (Oleaceae) in China’s warm-temperate zone in response to climate change during the Pleistocene. BMC Evol Biol 14:114

PubMed  PubMed Central  Google Scholar 

Gao Y, Zhang G (2019) A calcium sensor calcineurin B-like 9 negatively regulates cold tolerance via calcium signaling in Arabidopsis thaliana. Plant Signaling Behav 14:e1573099

Google Scholar 

Gill SS, Tuteja N (2010) Reactive oxygen species and antioxidant machinery in abiotic stress tolerance in crop plants. Plant Physiol Biochem 48:909–930

CAS  PubMed  Google Scholar 

Heath RL, Packer L (1968) Photoperoxidation in isolated chloroplast: I. Kinetics and stoichiometry of fatty acids peroxidation. Arch Biochem Biophys 125:189–198

CAS  PubMed  Google Scholar 

Imadi SR, Kazi AG, Ahanger MA, Gucel S, Ahmad P (2015) Plant transcriptomics and responses to environmental stress: an overview. J Genet 94:525–537

CAS  PubMed  Google Scholar 

Jin JJ, Zhang H, Zhang JF, Liu P, Chen X (2017) Integrated transcriptomics and metabolomics analysis to characterize cold stress responses in Nicotiana tabacum. BMC Genomics 18:496

PubMed  PubMed Central  Google Scholar 

Jing T, Zhang N, Gao T, Zhao M, Jin J, Chen Y, Xu M, Wan X, Schwab W, Song C (2019) Glucosylation of (Z)-3-hexenol informs intraspecies interactions in plants: a case study in Camellia sinensis. Plant Cell Environ 42:1352–1367

CAS  PubMed  Google Scholar 

Kanehisaa M, Goto S (2000) KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res 28:27–30

Google Scholar 

Kim D, Langmead B, Salzberg SL (2015) HISAT: a fast spliced aligner with low memory requirements. Nat Methods 12:357–360

CAS  PubMed  PubMed Central  Google Scholar 

Li B, Ning LY, Zhang JW, Bao MZ, Zhang W (2015) Transcriptional profiling of Petunia seedlings reveals candidate regulators of the cold stress response. Front Plant Sci 6:1–16

Google Scholar 

Li Y, Zhang XX, Mao RL, Yang J, Miao CY, Li Z, Qiu XY (2017) Ten years of landscape genomics: challenges and opportunities. Front Plant Sci 8:2136

PubMed  PubMed Central  Google Scholar 

Li LF, Cushman SA, He YX, Li Y (2020a) Genome sequencing and population genomics modeling provide insights into local adaptation of weeping forsythia. Hortic Res 7:130

PubMed  PubMed Central  Google Scholar 

Li W, Chen Y, Ye M, Lu H, Wang D, Chen Q (2020b) Evolutionary history of the C-repeat binding factor/dehydration-responsive element-binding 1 (CBF/DREB1) protein family in 43 plant species and characterization of CBF/DREB1 proteins in Solanum tuberosum. BMC Evol Biol 20:142

PubMed  PubMed Central  Google Scholar 

Lichtenthaler HK, Wellburn AR (1983) Determination of total carotenoids and chlorophylls a and b of leaf extracts in different solvents. Biochem Soc Trans 11:591–592

CAS  Google Scholar 

Livak KJ, Schmittgen TD (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2−△△CT method. Methods 25:402–408

CAS  PubMed  Google Scholar 

Long L, Yang WW, Liao P, Guo YW, Kumar A, Gao W (2019) Transcriptome analysis reveals differentially expressed ERF transcription factors associated with salt response in cotton. Plant Sci 281:72–81

CAS  PubMed  Google Scholar 

Love MI, Huber W, Anders S (2014) Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol 15:550

PubMed  PubMed Central  Google Scholar 

Lytvyn DI, Raynaud C, Yemets AI, Bergounioux C, Blume YB (2016) Involvement of inositol biosynthesis and nitric oxide in the mediation of UV-B induced oxidative stress. Front Plant Sci 7:430

PubMed  PubMed Central  Google Scholar 

Mao X, Cai T, Olyarchuk JG, Wei L (2005) Automated genome annotation and pathway identification using the KEGG Orthology (KO) as a controlled vocabulary. Bioinformatics 21:3787–3793

CAS  PubMed  Google Scholar 

Nejadsadeghi L, Maali-Amiri R, Zeinali H, Ramezanpour S, Sadeghzade B (2015) Membrane fatty acid compositions and cold-induced responses in tetraploid and hexaploid wheats. Mol Biol Rep 42:363–372

CAS  PubMed  Google Scholar 

Niu Y, Zhang HB, Yang QX, Chen LY, Yan KL (2003) Studies on culturing technology of Forsythia suspensa in Hexi district. J Gansu Agr Univ 38:234–237

Google Scholar 

Niu RX, Zhao XM, Wang CB, Wang FL (2020) Transcriptome profiling of Prunus persica branches reveals candidate genes potentially involved in freezing tolerance. Sci Hort 259:108775

CAS  Google Scholar 

Ouyang W, Cao Z, Xiong D, Li G, Li X (2020) Decoding the plant genome: from epigenome to 3D organization. J Genet Genomics 47:425–435

PubMed  Google Scholar 

Peng J, Peng K, Li J (2018) Climate-growth response of Chinese white pine (Pinus armandii) at different age groups in the Baiyunshan National Nature Reserve, central China. Dendrochronologia 49:102–109

Google Scholar 

Pertea M, Pertea GM, Antonescu CM, Chang TC, Mendell JT, Salzberg SL (2015) StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nat Biotechnol 33:290–295

CAS  PubMed  PubMed Central  Google Scholar 

Rellstab C, Gugerli F, Eckert AJ, Hancock AM, Holderegger R (2015) A practical guide to environmental association analysis in landscape genomics. Mol Ecol 24:4348–4370

PubMed  Google Scholar 

Rosati C, Cadic A, Duron M, Ingouff M, Simoneau P (1999) Molecular characterization of the anthocyanidin synthase gene in Forsythia×intermedia reveals organ-specific expression during flower development. Plant Sci 149:73–79

CAS  Google Scholar 

Sharma A, Shahzad B, Rehman A, Bhardwaj R, Landi M, Zheng B (2019) Response of phenylpropanoid pathway and the role of polyphenols in plants under abiotic stress. Molecules 24:2452

CAS  PubMed  PubMed Central  Google Scholar 

Simpson GG (1944) Tempo and mode in evolution. Columbia University Press, New York

Google Scholar 

Tan YF, Millar AH, Taylor AL (2012) Components of mitochondrial oxidative phosphorylation vary in abundance following exposure to cold and chemical stresses. J Proteome Res 11:3860–3879

CAS  PubMed  Google Scholar 

Walker DJ, Romero P, Correal E (2010) Cold tolerance, water relations and accumulation of osmolytes in Bituminaria bituminosa. Biol Plantarum 54:293–298

Google Scholar 

Wang ZJ, Xie SH, Ma YP, Hu Y, Zhu XL, Liu JH (2005) Technology of seedling and afforestation of F. suspensa. Pract Forest Technol 8:14

CAS  Google Scholar 

Wang XC, Zhao QY, Ma CL, Zhang ZH, Cao HL, Kong YM, Yue C, Hao XY, Chen L, Ma JQ, Jin JQ, Li X, Yang YJ (2013a) Global transcriptome profiles of Camellia sinensis during cold acclimation. BMC Genomics 14:415

PubMed  PubMed Central  Google Scholar 

Wang YJ, Yang JS, Yuan CP, Liu JG, Li DH, Dong ST (2013b) Characteristics of senescence and antioxidant enzyme activities in leaves at different plant parts of summer maize with the super-high yielding potential after anthesis. Acta Agron Sin 39:2183–2191

CAS  Google Scholar 

Wang P, Yang C, Chen H, Song C, Zhang X, Wang D (2017) Transcriptomic basis for drought-resistance in Brassica napus L. Sci Rep 7:40532

CAS  PubMed  PubMed Central  Google Scholar 

Wang TQ, Cheng T, Yan HF, Wang Y (2018) TCM treatment of anemopyretic cold rule analysis. J Tianjin Univ Tradit Chin Med 37:113–117

Google Scholar 

Wu DX, Kukkonen S, Luoranen J, Pulkkinen P, Heinonen J, Pappinen A, Repo T (2019) Influence of late autumn preconditioning temperature on frost hardiness of apple, blueberry and blackcurrant saplings. Sci Hort 258:108755

CAS  Google Scholar 

Comments (0)

No login
gif