{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,14]],"date-time":"2026-09-14T02:04:49Z","timestamp":1789351489395,"version":"build-2803163510"},"reference-count":52,"publisher":"Frontiers Media SA","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Front. Plant Sci."],"DOI":"10.3389\/fpls.2015.00202","type":"journal-article","created":{"date-parts":[[2015,4,1]],"date-time":"2015-04-01T14:10:39Z","timestamp":1427897439000},"source":"Crossref","is-referenced-by-count":57,"title":["Transcriptome-based gene profiling provides novel insights into the characteristics of radish root response to Cr stress with next-generation sequencing"],"prefix":"10.3389","volume":"6","author":[{"given":"Yang","family":"Xie","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shan","family":"Ye","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yan","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Liang","family":"Xu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xianwen","family":"Zhu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jinlan","family":"Yang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Haiyang","family":"Feng","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rugang","family":"Yu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Benard","family":"Karanja","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yiqin","family":"Gong","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Liwang","family":"Liu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2015,3,31]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"255","DOI":"10.1016\/S0981-9428(02)01366-9","article-title":"Isolation and characterisation of two divergent type 3 metallothioneins from oil palm, Elaeis guineensis","volume":"40","author":"Abdullah","year":"2002","journal-title":"Plant Physiol. Biochem"},{"key":"B2","doi-asserted-by":"publisher","first-page":"194","DOI":"10.1007\/s00128-012-0891-5","article-title":"Transcript pattern of cytochrome P450, antioxidant and ginsenoside biosynthetic pathway genes under heavy metal stress in panax ginseng meyer","volume":"90","author":"Balusamy","year":"2013","journal-title":"Bull. Environ. Contam. Toxicol"},{"key":"B3","doi-asserted-by":"publisher","first-page":"1165","DOI":"10.1214\/aos\/1013699998","article-title":"The control of the false discovery rate in multiple tesing under dependency","volume":"29","author":"Benjamini","year":"2001","journal-title":"Ann. Stat"},{"key":"B4","doi-asserted-by":"publisher","first-page":"688","DOI":"10.1016\/j.chemosphere.2008.09.082","article-title":"Comparative transcriptome analysis of arsenate and arsenite stresses in rice seedlings","volume":"74","author":"Chakrabarty","year":"2009","journal-title":"Chemosphere"},{"key":"B5","doi-asserted-by":"publisher","first-page":"313","DOI":"10.1663\/0006-8101(2004)070[0313:CAATIA]2.0.CO;2","article-title":"Chromium accumulation and toxicity in vascular plants","volume":"70","author":"Chandra","year":"2004","journal-title":"Bot. Rev"},{"key":"B6","doi-asserted-by":"publisher","first-page":"3674","DOI":"10.1093\/bioinformatics\/bti610","article-title":"Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research","volume":"21","author":"Conesa","year":"2005","journal-title":"Bioinformatics"},{"key":"B7","doi-asserted-by":"publisher","first-page":"663","DOI":"10.4161\/psb.5.6.11425","article-title":"Regulatory networks of cadmium stress in plants","volume":"5","author":"DalCorso","year":"2010","journal-title":"Plant Signal. Behav"},{"key":"B8","doi-asserted-by":"publisher","first-page":"29","DOI":"10.1186\/1471-2164-14-29","article-title":"Transcriptomic profiling of the salt-stress response in the wild recretohalophyte Reaumuria trigyna","volume":"14","author":"Dang","year":"2013","journal-title":"BMC Genomics"},{"key":"B9","doi-asserted-by":"publisher","first-page":"382","DOI":"10.1016\/j.jplph.2010.07.014","article-title":"Transcriptome analysis reveals novel genes involved in nonhost response to bacterial infection in tobacco","volume":"168","author":"Daurelio","year":"2011","journal-title":"Plant Physiol"},{"key":"B10","doi-asserted-by":"publisher","first-page":"648","DOI":"10.1186\/1471-2164-11-648","article-title":"Transcriptomic and metabolomic shifts in rice roots in response to Cr (VI) stress","volume":"11","author":"Dubey","year":"2010","journal-title":"BMC Genomics"},{"key":"B11","doi-asserted-by":"publisher","first-page":"392","DOI":"10.1016\/j.gene.2012.09.100","article-title":"Gene expression profiling of soybean leaves and roots under salt, saline-alkali and drought stress by high-throughput Illumina sequencing","volume":"512","author":"Fan","year":"2013","journal-title":"Gene"},{"key":"B12","doi-asserted-by":"publisher","first-page":"9","DOI":"10.1007\/s10535-013-0374-5","article-title":"Brassinosteroids and their role in response of plants to abiotic stresses","volume":"58","author":"Fariduddin","year":"2014","journal-title":"Biol. Plantarum"},{"key":"B13","doi-asserted-by":"publisher","first-page":"1121","DOI":"10.1007\/s11427-011-4255-x","article-title":"Overview of available methods for diverse RNA-Seq data analyses","volume":"54","author":"Geng","year":"2011","journal-title":"Sci. China Life Sci"},{"key":"B14","doi-asserted-by":"publisher","first-page":"1446","DOI":"10.1016\/j.jplph.2009.01.015","article-title":"Expression of stress-related genes in tomato plants exposed to arsenic and chromium in nutrient solution","volume":"166","author":"Goupila","year":"2009","journal-title":"J. Plant Physiol"},{"key":"B15","doi-asserted-by":"publisher","first-page":"644","DOI":"10.1038\/nbt.1883","article-title":"Full-length transcriptome assembly from RNA-Seq data without a reference genome","volume":"29","author":"Grabherr","year":"2011","journal-title":"Nat. Biotechnol"},{"key":"B16","doi-asserted-by":"publisher","first-page":"6673","DOI":"10.1007\/s10661-011-2450-7","article-title":"Heavy metal accumulation in vegetables grown in a long-term wastewater-irrigated agricultural land of tropical India","volume":"184","author":"Gupta","year":"2012","journal-title":"Environ. Monit. Assess"},{"key":"B17","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1093\/jexbot\/53.366.1","article-title":"Cellular mechanisms for heavy metal detoxification and tolerance","volume":"53","author":"Hall","year":"2002","journal-title":"J. Exp. Bot"},{"key":"B18","doi-asserted-by":"publisher","first-page":"599","DOI":"10.1007\/s00709-011-0331-0","article-title":"Physiological changes induced by chromium stress in plants: an overview","volume":"249","author":"Hayat","year":"2011","journal-title":"Protoplasma"},{"key":"B19","doi-asserted-by":"publisher","first-page":"480","DOI":"10.1093\/nar\/gkm882","article-title":"KEGG for linking genomes to life and the environment","volume":"36","author":"Kanehisa","year":"2008","journal-title":"Nucleic Acids Res"},{"key":"B20","first-page":"337","article-title":"The biological and environmental chemistry of chromium","volume":"15","author":"Katz","year":"1994","journal-title":"J. Appl. Toxicol"},{"key":"B21","doi-asserted-by":"publisher","first-page":"83","DOI":"10.1111\/j.1469-8137.2004.01168.x","article-title":"Cloning and expression of multiple metallothioneins from hybrid poplar","volume":"164","author":"Kohler","year":"2004","journal-title":"New Phytol"},{"key":"B22","doi-asserted-by":"publisher","first-page":"1201","DOI":"10.1007\/s11033-012-2162-2","article-title":"Characterization of a vacuolar zinc transporter OZT1 in rice (Oryza sativa L.)","volume":"40","author":"Lan","year":"2013","journal-title":"Mol. Biol. Rep"},{"key":"B23","doi-asserted-by":"publisher","first-page":"182","DOI":"10.1111\/nph.12803","article-title":"Expression profiling reveals functionally redundant multiple-copy genes related to zinc, iron and cadmium responses in Brassica rapa","volume":"203","author":"Li","year":"2014","journal-title":"New Phytol"},{"key":"B24","doi-asserted-by":"publisher","first-page":"1966","DOI":"10.1093\/bioinformatics\/btp336","article-title":"SOAP2: an improved ultrafast tool for short read alignment","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"B25","doi-asserted-by":"publisher","first-page":"377","DOI":"10.1016\/j.envexpbot.2009.03.016","article-title":"Transcriptional profiling of Arabidopsis seedlings in response to heavy metal lead (Pb)","volume":"67","author":"Liu","year":"2009","journal-title":"Environ. Exp. Bot"},{"key":"B26","doi-asserted-by":"publisher","first-page":"402","DOI":"10.1006\/meth.2001.1262","article-title":"Analysis of relative gene expression data using real-time quantitative PCR and the 2-\u00ce\u201d\u00ce\u201dCT Method","volume":"25","author":"Livak","year":"2001","journal-title":"Methods"},{"key":"B27","doi-asserted-by":"publisher","first-page":"2017","DOI":"10.1093\/pcp\/pcr153","article-title":"Advances in omics and bioinformatics tools for systems analyses of plant functions","volume":"52","author":"Mochida","year":"2011","journal-title":"Plant Cell Physiol"},{"key":"B28","doi-asserted-by":"publisher","first-page":"621","DOI":"10.1038\/nmeth.1226","article-title":"Mapping and quantifying mammalian transcriptomes by RNASeq","volume":"5","author":"Mortazavi","year":"2008","journal-title":"Nat. Methods"},{"key":"B29","doi-asserted-by":"publisher","first-page":"803","DOI":"10.1007\/s00438-012-0713-9","article-title":"Transcriptome analyses of Bactericera cockerelli adults in response to \u00e2\u20ac\u0153Candidatus Liberibacter solanacearum\u00e2\u20ac\u009d infection","volume":"287","author":"Nachappa","year":"2012","journal-title":"Mol. Genet. Genomics"},{"key":"B30","doi-asserted-by":"publisher","first-page":"327","DOI":"10.1007\/s11103-004-0685-1","article-title":"Crosstalk in the responses to abiotic and biotic stresses in Arabidopsis: analysis of gene expression in cytochrome P450 gene superfamily by cDNA microarray","volume":"55","author":"Narusaka","year":"2004","journal-title":"Plant Mol. Biol"},{"key":"B31","doi-asserted-by":"publisher","first-page":"95","DOI":"10.1590\/S1677-04202005000100008","article-title":"Chromium stress in plants","volume":"17","author":"Panda","year":"2005","journal-title":"Plant Physiol"},{"key":"B32","doi-asserted-by":"publisher","first-page":"307","DOI":"10.1007\/s10661-007-0122-4","article-title":"Chromium-induced changes in ultramorphology and secondary metabolites of Phyllanthus amarus Schum & Thonn \u00e2\u20ac\u201c an hepatoprotective plant","volume":"147","author":"Rai","year":"2008","journal-title":"Environ. Monit. Assess"},{"key":"B33","doi-asserted-by":"publisher","first-page":"81","DOI":"10.1007\/s00709-013-0528-5","article-title":"Analysis of differentially expressed genes in abiotic stress response and their role in signal transduction pathways","volume":"251","author":"Sanchita, Dhawan","year":"2014","journal-title":"Protoplasma"},{"key":"B34","doi-asserted-by":"publisher","first-page":"1485","DOI":"10.1007\/s11105-013-0622-z","article-title":"Transcriptome profile analysis of maize seedlings in response to high-salinity, drought and cold stresses by deep sequencing","volume":"31","author":"Shan","year":"2013","journal-title":"Plant Mol. Biol. Rep"},{"key":"B35","doi-asserted-by":"publisher","first-page":"739","DOI":"10.1016\/j.envint.2005.02.003","article-title":"Chromium toxicity in plants","volume":"31","author":"Shanker","year":"2005","journal-title":"Enviorn. Int"},{"key":"B36","doi-asserted-by":"publisher","first-page":"375","DOI":"10.1039\/B904571F","article-title":"Chromium interactions in plants: current status and future strategies","volume":"1","author":"Shanker","year":"2009","journal-title":"Metallomics"},{"key":"B37","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1007\/978-81-322-0807-5_12","article-title":"Mechanism of plant tolerance in response to heavy metals","volume-title":"Molecular Stress Physiology of Plants","author":"Sharma","year":"2013"},{"key":"B38","doi-asserted-by":"publisher","first-page":"257","DOI":"10.3732\/ajb.1100292","article-title":"Designing a transcriptome next-generation sequencing project for a nonmodel plant species","volume":"99","author":"Strickler","year":"2012","journal-title":"Am. J. Bot"},{"key":"B39","doi-asserted-by":"publisher","first-page":"489","DOI":"10.1007\/s10534-012-9541-y","article-title":"Molecular mechanistic model of plant heavy metal tolerance","volume":"25","author":"Thapa","year":"2012","journal-title":"Biometals"},{"key":"B40","doi-asserted-by":"publisher","first-page":"34","DOI":"10.4236\/ojmetal.2013.32A1005","article-title":"Brassinosteroids and plant responses to heavy metal stress","volume":"3","author":"V\u00c3\u00a1zquez","year":"2013","journal-title":"Open J. Metal"},{"key":"B41","doi-asserted-by":"publisher","first-page":"136","DOI":"10.1093\/bioinformatics\/btp612","article-title":"DEGseq: an R package for identifying differentially expressed genes from RNA-seq data","volume":"26","author":"Wang","year":"2010","journal-title":"Bioinformatics"},{"key":"B42","doi-asserted-by":"publisher","first-page":"e66539","DOI":"10.1371\/journal.pone.0066539","article-title":"Transcriptome profiling of radish (Raphanus sativus L.) root and identification of genes involved in response to lead (Pb) stress with next generation sequencing","volume":"8","author":"Wang","year":"2013","journal-title":"PLoS ONE"},{"key":"B43","doi-asserted-by":"publisher","first-page":"398","DOI":"10.1016\/j.bbrc.2012.06.119","article-title":"Evaluation of reference genes for gene expression studies in radish (Raphanus sativus L.) using quantitative real-time PCR","volume":"424","author":"Xu","year":"2012","journal-title":"Biochem. Biophys. Res. Co"},{"key":"B44","doi-asserted-by":"publisher","first-page":"167","DOI":"10.1016\/j.sajb.2009.10.007","article-title":"Heavy metals toxicity in plants: an overview on the role of glutathione and phytochelatins in heavy metal stress tolerance of plants","volume":"76","author":"Yadav","year":"2010","journal-title":"South Afr. J. Bot"},{"key":"B45","doi-asserted-by":"publisher","first-page":"423","DOI":"10.1093\/jxb\/erp313","article-title":"Gene expression analysis in cadmium-stressed roots of a low cadmium-accumulating solanaceous plant, Solanum torvum.","volume":"61","author":"Yamaguchi","year":"2010","journal-title":"J. Exp. Bot"},{"key":"B46","doi-asserted-by":"publisher","first-page":"293","DOI":"10.1093\/nar\/gkl031","article-title":"WEGO: a web tool for plotting GO annotations","volume":"34","author":"Ye","year":"2006","journal-title":"Nucleic Acids Res"},{"key":"B47","doi-asserted-by":"publisher","first-page":"97","DOI":"10.1111\/j.1469-8137.2012.04154.x","article-title":"Comparative transcriptome analysis of transporters, phytohormone and lipid metabolism pathways in response to arsenic stress in rice (Oryza sativa)","volume":"195","author":"Yu","year":"2012","journal-title":"New Phytol"},{"key":"B48","doi-asserted-by":"publisher","first-page":"293","DOI":"10.1007\/s004250050403","article-title":"Chromium accumulation, translocation and chemical speciation in vegetable crops","volume":"206","author":"Zayed","year":"1998","journal-title":"Planta"},{"key":"B49","doi-asserted-by":"publisher","first-page":"255","DOI":"10.1007\/s12011-012-9362-4","article-title":"Glutathione-Mediated alleviation of chromium toxicity in rice plants","volume":"148","author":"Zeng","year":"2012","journal-title":"Biol. Trace Elem. Res"},{"key":"B50","doi-asserted-by":"publisher","first-page":"21","DOI":"10.1007\/s00438-012-0727-3","article-title":"Digital gene expression analysis of early root infection resistance to Sporisorium reilianumf. sp.zeae in maize","volume":"288","author":"Zhang","year":"2013","journal-title":"Mol. Genet. Genomics"},{"key":"B51","doi-asserted-by":"publisher","first-page":"e42082","DOI":"10.1371\/journal.pone.0042082","article-title":"De novo sequencing and characterization of the floral transcriptome of Dendrocalamus latiflorus (Poaceae: Bambusoideae)","volume":"7","author":"Zhang","year":"2012","journal-title":"PLoS ONE"},{"key":"B52","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1007\/978-3-642-38469-1_2","article-title":"Metal transporters in plants","volume-title":"Heavy Metal Stress in Plants","author":"Zitka","year":"2013"}],"container-title":["Frontiers in Plant Science"],"original-title":[],"deposited":{"date-parts":[[2017,6,23]],"date-time":"2017-06-23T08:21:48Z","timestamp":1498206108000},"score":1,"resource":{"primary":{"URL":"http:\/\/www.frontiersin.org\/Plant_Biotechnology\/10.3389\/fpls.2015.00202\/abstract"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2015,3,31]]},"references-count":52,"URL":"https:\/\/doi.org\/10.3389\/fpls.2015.00202","relation":{},"ISSN":["1664-462X"],"issn-type":[{"value":"1664-462X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2015,3,31]]}}}