{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,13]],"date-time":"2025-10-13T20:01:09Z","timestamp":1760385669183},"reference-count":37,"publisher":"Springer Science and Business Media LLC","issue":"S2","license":[{"start":{"date-parts":[[2018,3,1]],"date-time":"2018-03-01T00:00:00Z","timestamp":1519862400000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Syst Biol"],"published-print":{"date-parts":[[2018,3]]},"DOI":"10.1186\/s12918-018-0548-z","type":"journal-article","created":{"date-parts":[[2018,11,22]],"date-time":"2018-11-22T10:55:06Z","timestamp":1542884106000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":12,"title":["The mRNA and miRNA transcriptomic landscape of Panax ginseng under the high ambient temperature"],"prefix":"10.1186","volume":"12","author":[{"given":"Inuk","family":"Jung","sequence":"first","affiliation":[]},{"given":"Hyejin","family":"Kang","sequence":"additional","affiliation":[]},{"given":"Jang Uk","family":"Kim","sequence":"additional","affiliation":[]},{"given":"Hyeonsook","family":"Chang","sequence":"additional","affiliation":[]},{"given":"Sun","family":"Kim","sequence":"additional","affiliation":[]},{"given":"Woosuk","family":"Jung","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2018,3,19]]},"reference":[{"issue":"3","key":"548_CR1","doi-asserted-by":"publisher","first-page":"175","DOI":"10.1254\/jphs.CRJ05010X","volume":"100","author":"K Radad","year":"2006","unstructured":"Radad K, Gille G, Liu L, Rausch W-D. Use of ginseng in medicine with emphasis on neurodegenerative disorders. J Pharmacol Sci. 2006; 100(3):175\u201386.","journal-title":"J Pharmacol Sci"},{"key":"548_CR2","doi-asserted-by":"publisher","first-page":"97","DOI":"10.1016\/j.pbi.2015.06.016","volume":"27","author":"G Capovilla","year":"2015","unstructured":"Capovilla G, Pajoro A, Immink RG, Schmid M. Role of alternative pre-mrna splicing in temperature signaling. Curr Opin Plant Biol. 2015; 27:97\u2013103.","journal-title":"Curr Opin Plant Biol"},{"key":"548_CR3","doi-asserted-by":"publisher","first-page":"829","DOI":"10.1093\/aob\/mcs155","volume":"110.4","author":"S Souther","year":"2012","unstructured":"Souther S, Lechowicz MJ, McGraw JB. Experimental test for adaptive differentiation of ginseng populations reveals complex response to temperature. Ann Bot. 2012; 110.4:829\u201337.","journal-title":"Ann Bot"},{"issue":"20","key":"548_CR4","doi-asserted-by":"publisher","first-page":"8386","DOI":"10.1073\/pnas.0903566106","volume":"106","author":"SN Oliver","year":"2009","unstructured":"Oliver SN, Finnegan EJ, Dennis ES, Peacock WJ, Trevaskis B. Vernalization-induced flowering in cereals is associated with changes in histone methylation at the vernalization1 gene. Proc Natl Acad Sci. 2009; 106(20):8386\u201391.","journal-title":"Proc Natl Acad Sci"},{"issue":"1","key":"548_CR5","first-page":"144","volume":"26","author":"J Wen","year":"2001","unstructured":"Wen J, Plunkett GM, Mitchell AD, Wagstaff SJ. The evolution of araliaceae: a phylogenetic analysis based on its sequences of nuclear ribosomal dna. Syst Bot. 2001; 26(1):144\u201367.","journal-title":"Syst Bot"},{"issue":"6","key":"548_CR6","doi-asserted-by":"publisher","first-page":"709","DOI":"10.1007\/s00438-004-1021-9","volume":"271","author":"C Hong","year":"2004","unstructured":"Hong C, Lee S, Park J, Plaha P, Park Y, Lee Y, Choi J, Kim K, Lee J, Lee J, et al.Construction of a bac library of korean ginseng and initial analysis of bac-end sequences. Mol Gen Genomics. 2004; 271(6):709\u201316.","journal-title":"Mol Gen Genomics"},{"issue":"6","key":"548_CR7","doi-asserted-by":"publisher","first-page":"906","DOI":"10.1111\/tpj.12441","volume":"77","author":"H-I Choi","year":"2014","unstructured":"Choi H-I, Waminal NE, Park HM, Kim N-H, Choi BS, Park M, Choi D, Lim YP, Kwon S-J, Park B-S, et al.Major repeat components covering one-third of the ginseng (panax ginseng ca meyer) genome and evidence for allotetraploidy. Plant J. 2014; 77(6):906\u201316.","journal-title":"Plant J"},{"issue":"1","key":"548_CR8","doi-asserted-by":"publisher","first-page":"138","DOI":"10.1186\/s12870-015-0527-0","volume":"15","author":"M Jayakodi","year":"2015","unstructured":"Jayakodi M, Lee S-C, Lee YS, Park H-S, Kim N-H, Jang W, Lee HO, Joh HJ, Yang T-J. Comprehensive analysis of panax ginseng root transcriptomes. BMC Plant Biol. 2015; 15(1):138.","journal-title":"BMC Plant Biol"},{"issue":"2","key":"548_CR9","doi-asserted-by":"publisher","first-page":"227","DOI":"10.5142\/jgr.2013.37.227","volume":"37","author":"R Mathiyalagan","year":"2013","unstructured":"Mathiyalagan R, Subramaniyam S, Natarajan S, Kim YJ, Sun MS, Kim SY, Kim Y-J, Yang DC. Insilico profiling of micrornas in korean ginseng (panax ginseng meyer). J Ginseng Res. 2013; 37(2):227\u201347.","journal-title":"J Ginseng Res"},{"issue":"1","key":"548_CR10","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/1471-2164-14-1","volume":"14","author":"C Li","year":"2013","unstructured":"Li C, Zhu Y, Guo X, Sun C, Luo H, Song J, Li Y, Wang L, Qian J, Chen S. Transcriptome analysis reveals ginsenosides biosynthetic genes, micrornas and simple sequence repeats in panax ginseng ca meyer. BMC Genomics. 2013; 14(1):1.","journal-title":"BMC Genomics"},{"issue":"1","key":"548_CR11","doi-asserted-by":"publisher","first-page":"1010","DOI":"10.1186\/s12864-015-2151-7","volume":"16","author":"B Wu","year":"2015","unstructured":"Wu B, Long Q, Gao Y, Wang Z, Shao T, Liu Y, Li Y, Ding W. Comprehensive characterization of a time-course transcriptional response induced by autotoxins in panax ginseng using rna-seq. BMC Genomics. 2015; 16(1):1010.","journal-title":"BMC Genomics"},{"issue":"suppl 1","key":"548_CR12","doi-asserted-by":"publisher","first-page":"140","DOI":"10.1093\/nar\/gkj112","volume":"34","author":"S Griffiths-Jones","year":"2006","unstructured":"Griffiths-Jones S, Grocock RJ, Van Dongen S, Bateman A, Enright AJ. mirbase: microrna sequences, targets and gene nomenclature. Nucleic Acids Res. 2006; 34(suppl 1):140\u20134.","journal-title":"Nucleic Acids Res"},{"issue":"3","key":"548_CR13","doi-asserted-by":"publisher","first-page":"224","DOI":"10.1007\/s00299-003-0678-6","volume":"22","author":"J Jung","year":"2003","unstructured":"Jung J, Park H-W, Hahn Y, Hur C-G, In D, Chung H-J, Liu J, Choi D-W. Discovery of genes for ginsenoside biosynthesis by analysis of ginseng expressed sequence tags. Plant Cell Rep. 2003; 22(3):224\u201330.","journal-title":"Plant Cell Rep"},{"issue":"suppl 1","key":"548_CR14","doi-asserted-by":"publisher","first-page":"61","DOI":"10.1093\/nar\/gkl842","volume":"35","author":"KD Pruitt","year":"2007","unstructured":"Pruitt KD, Tatusova T, Maglott DR. Ncbi reference sequences (refseq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res. 2007; 35(suppl 1):61\u20135.","journal-title":"Nucleic Acids Res"},{"key":"548_CR15","first-page":"926","volume":"31.6","author":"BE Suzek","year":"2014","unstructured":"Suzek BE, Wang Y, Huang H, McGarvey PB, Wu CH, Consortium U, et al.Uniref clusters: a comprehensive and scalable alternative for improving sequence similarity searches. Bioinformatics. 2014; 31.6:926\u201332.","journal-title":"Bioinformatics"},{"issue":"4","key":"548_CR16","doi-asserted-by":"publisher","first-page":"1405","DOI":"10.2134\/jeq2005.0156","volume":"35","author":"L Allen","year":"2006","unstructured":"Allen L, Albrecht SL, Boote K, Thomas JM, Newman Y, Skirvin KW. Soil organic carbon and nitrogen accumulation in plots of rhizoma perennial peanut and bahiagrass grown in elevated carbon dioxide and temperature. J Environ Qual. 2006; 35(4):1405\u201312.","journal-title":"J Environ Qual"},{"issue":"2","key":"548_CR17","doi-asserted-by":"publisher","first-page":"399","DOI":"10.2135\/cropsci2001.412399x","volume":"41","author":"Y Newman","year":"2001","unstructured":"Newman Y, Sollenberger L, Boote K, Allen L, Littell R. Carbon dioxide and temperature effects on forage dry matter production. Crop Sci. 2001; 41(2):399\u2013406.","journal-title":"Crop Sci"},{"issue":"7","key":"548_CR18","doi-asserted-by":"publisher","first-page":"644","DOI":"10.1038\/nbt.1883","volume":"29","author":"MG Grabherr","year":"2011","unstructured":"Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q, et al.Full-length transcriptome assembly from rna-seq data without a reference genome. Nat Biotechnol. 2011; 29(7):644\u201352.","journal-title":"Nat Biotechnol"},{"issue":"9","key":"548_CR19","doi-asserted-by":"publisher","first-page":"868","DOI":"10.1101\/gr.9.9.868","volume":"9","author":"X Huang","year":"1999","unstructured":"Huang X, Madan A. Cap3: A dna sequence assembly program. Genome Res. 1999; 9(9):868\u201377.","journal-title":"Genome Res"},{"issue":"4","key":"548_CR20","doi-asserted-by":"publisher","first-page":"357","DOI":"10.1038\/nmeth.1923","volume":"9","author":"B Langmead","year":"2012","unstructured":"Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012; 9(4):357\u20139.","journal-title":"Nat Methods"},{"key":"548_CR21","first-page":"D204","volume":"43.D1","author":"UniProt Consortium","year":"2014","unstructured":"UniProt Consortium. Uniprot: a hub for protein information. Nucleic Acids Res. 2014; 43.D1:D204\u201312.","journal-title":"Nucleic Acids Res"},{"issue":"1","key":"548_CR22","doi-asserted-by":"publisher","first-page":"25","DOI":"10.1038\/75556","volume":"25","author":"M Ashburner","year":"2000","unstructured":"Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, et al.Gene ontology: tool for the unification of biology. Nat Genet. 2000; 25(1):25\u20139.","journal-title":"Nat Genet"},{"issue":"1","key":"548_CR23","doi-asserted-by":"publisher","first-page":"136","DOI":"10.1093\/bioinformatics\/btp612","volume":"26","author":"L Wang","year":"2010","unstructured":"Wang L, Feng Z, Wang X, Wang X, Zhang X. Degseq: an r package for identifying differentially expressed genes from rna-seq data. Bioinformatics. 2010; 26(1):136\u20138.","journal-title":"Bioinformatics"},{"issue":"4","key":"548_CR24","doi-asserted-by":"publisher","first-page":"846","DOI":"10.1016\/j.bbrc.2007.06.139","volume":"360","author":"W-F Liu","year":"2007","unstructured":"Liu W-F, Zhang A, He G-J, Yan Y-B. The r3h domain stabilizes poly (a)-specific ribonuclease by stabilizing the rrm domain. Biochem Biophys Res Commun. 2007; 360(4):846\u201351.","journal-title":"Biochem Biophys Res Commun"},{"issue":"3","key":"548_CR25","doi-asserted-by":"publisher","first-page":"217","DOI":"10.1038\/nrg2049","volume":"8","author":"Y Jiao","year":"2007","unstructured":"Jiao Y, Lau OS, Deng XW. Light-regulated transcriptional networks in higher plants. Nat Rev Genet. 2007; 8(3):217\u201330.","journal-title":"Nat Rev Genet"},{"issue":"10","key":"548_CR26","doi-asserted-by":"publisher","first-page":"963","DOI":"10.1111\/j.1365-2443.2005.00892.x","volume":"10","author":"K Onai","year":"2005","unstructured":"Onai K, Ishiura M. Phytoclock 1 encoding a novel garp protein essential for the arabidopsis circadian clock. Genes Cells. 2005; 10(10):963\u201372.","journal-title":"Genes Cells"},{"issue":"9","key":"548_CR27","doi-asserted-by":"publisher","first-page":"44385","DOI":"10.1371\/journal.pone.0044385","volume":"7","author":"B Wu","year":"2012","unstructured":"Wu B, Wang M, Ma Y, Yuan L, Lu S. High-throughput sequencing and characterization of the small rna transcriptome reveal features of novel and conserved micrornas in panax ginseng. PLoS ONE. 2012; 7(9):44385.","journal-title":"PLoS ONE"},{"issue":"1","key":"548_CR28","doi-asserted-by":"publisher","first-page":"37","DOI":"10.1093\/nar\/gkr688","volume":"40","author":"MR Friedl\u00e4nder","year":"2012","unstructured":"Friedl\u00e4nder MR, Mackowiak SD, Li N, Chen W, Rajewsky N. mirdeep2 accurately identifies known and hundreds of novel microrna genes in seven animal clades. Nucleic Acids Res. 2012; 40(1):37\u201352.","journal-title":"Nucleic Acids Res"},{"issue":"suppl 2","key":"548_CR29","doi-asserted-by":"publisher","first-page":"155","DOI":"10.1093\/nar\/gkr319","volume":"39","author":"X Dai","year":"2011","unstructured":"Dai X, Zhao PX. psrnatarget: a plant small rna target analysis server. Nucleic Acids Res. 2011; 39(suppl 2):155\u20139.","journal-title":"Nucleic Acids Res"},{"issue":"7393","key":"548_CR30","doi-asserted-by":"publisher","first-page":"242","DOI":"10.1038\/nature10928","volume":"484","author":"SV Kumar","year":"2012","unstructured":"Kumar SV, Lucyshyn D, Jaeger KE, Al\u00f3s E, Alvey E, Harberd NP, Wigge PA. Transcription factor pif4 controls the thermosensory activation of flowering. Nature. 2012; 484(7393):242\u20135.","journal-title":"Nature"},{"issue":"8","key":"548_CR31","doi-asserted-by":"publisher","first-page":"802","DOI":"10.1038\/ncb2545","volume":"14","author":"E Oh","year":"2012","unstructured":"Oh E, Zhu J-Y, Wang Z-Y. Interaction between bzr1 and pif4 integrates brassinosteroid and environmental responses. Nat Cell Biol. 2012; 14(8):802\u20139.","journal-title":"Nat Cell Biol"},{"issue":"1","key":"548_CR32","doi-asserted-by":"publisher","first-page":"141","DOI":"10.1104\/pp.107.1.141","volume":"107","author":"E Mantyla","year":"1995","unstructured":"Mantyla E, Lang V, Palva ET. Role of abscisic acid in drought-induced freezing tolerance, cold acclimation, and accumulation of lt178 and rab18 proteins in arabidopsis thaliana. Plant Physiol. 1995; 107(1):141\u20138.","journal-title":"Plant Physiol"},{"issue":"6","key":"548_CR33","doi-asserted-by":"publisher","first-page":"1108","DOI":"10.1111\/tpj.12712","volume":"80","author":"L-G Cui","year":"2014","unstructured":"Cui L-G, Shan J-X, Shi M, Gao J-P, Lin H-X. The mir156-spl9-dfr pathway coordinates the relationship between development and abiotic stress tolerance in plants. Plant J. 2014; 80(6):1108\u201317.","journal-title":"Plant J"},{"key":"548_CR34","doi-asserted-by":"publisher","first-page":"2145","DOI":"10.1038\/ncomms3145","volume":"4","author":"P May","year":"2013","unstructured":"May P, Liao W, Wu Y, Shuai B, McCombie WR, Zhang MQ, Liu QA. The effects of carbon dioxide and temperature on microrna expression in arabidopsis development. Nat Commun. 2013; 4:2145.","journal-title":"Nat Commun"},{"issue":"5","key":"548_CR35","doi-asserted-by":"publisher","first-page":"892","DOI":"10.1111\/j.1438-8677.2012.00696.x","volume":"15","author":"M Baucher","year":"2013","unstructured":"Baucher M, Moussawi J, Vandeputte OM, Monteyne D, Mol A, P\u00e9rez-Morga D, El Jaziri M. A role for the mir396\/grf network in specification of organ type during flower development, as supported by ectopic expression of populus trichocarpa mir396c in transgenic tobacco. Plant Biol. 2013; 15(5):892\u20138.","journal-title":"Plant Biol"},{"issue":"3","key":"548_CR36","doi-asserted-by":"publisher","first-page":"633","DOI":"10.1093\/emboj\/cdg74","volume":"22","author":"G Szittya","year":"2003","unstructured":"Szittya G, Silhavy D, Moln\u00e1r A, Havelda Z, Lovas \u00c1, Lakatos L, B\u00e1nfalvi Z, Burgy\u00e1n J. Low temperature inhibits rna silencing-mediated defence by the control of sirna generation. EMBO J. 2003; 22(3):633\u201340.","journal-title":"EMBO J"},{"issue":"4","key":"548_CR37","doi-asserted-by":"publisher","first-page":"196","DOI":"10.1016\/j.tplants.2012.01.010","volume":"17","author":"R Sunkar","year":"2012","unstructured":"Sunkar R, Li Y-F, Jagadeeswaran G. Functions of micrornas in plant stress responses. Trends Plant Sci. 2012; 17(4):196\u2013203.","journal-title":"Trends Plant Sci"}],"container-title":["BMC Systems Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12918-018-0548-z.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/s12918-018-0548-z\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12918-018-0548-z.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,3,18]],"date-time":"2019-03-18T20:10:47Z","timestamp":1552939847000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcsystbiol.biomedcentral.com\/articles\/10.1186\/s12918-018-0548-z"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2018,3]]},"references-count":37,"journal-issue":{"issue":"S2","published-print":{"date-parts":[[2018,3]]}},"alternative-id":["548"],"URL":"https:\/\/doi.org\/10.1186\/s12918-018-0548-z","relation":{},"ISSN":["1752-0509"],"issn-type":[{"type":"electronic","value":"1752-0509"}],"subject":[],"published":{"date-parts":[[2018,3]]},"assertion":[{"value":"19 March 2018","order":1,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"Not applicable.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"Not applicable.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"The authors declare that they have no competing interests.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}},{"value":"Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Publisher\u2019s Note"}}],"article-number":"27"}}