Addo-Quaye C, Miller W, Axtell MJ (2009) CleaveLand: A pipeline for using degradome data to find cleaved small RNA targets. Bioinformatics 25:130–131. https://doi.org/10.1093/bioinformatics/btn604
Axtell MJ (2013) ShortStack: Comprehensive annotation and quantification of small RNA genes. RNA 19:740–751. https://doi.org/10.1261/rna.035279.112
Axtell MJ, Meyers BC (2018) Revisiting criteria for plant microRNA annotation in the era of big data. Plant Cell 30:272–284. https://doi.org/10.1105/tpc.17.00851
Bairoch A, Apweiler R (2000) The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000. Nucleic Acids Res 28:45–48
Brunetti P, Zanella L, De Paolis A, et al (2015) Cadmium-inducible expression of the ABC-type transporter AtABCC3 increases phytochelatin-mediated cadmium tolerance in Arabidopsis. J Exp Bot 66:3815–3829. https://doi.org/10.1093/jxb/erv185
Cai C, Wang X, Liu B, et al (2017) Brassica rapa genome 2.0: A reference upgrade through sequence re-assembly and gene re-annotation. Mol Plant 10:649–651. https://doi.org/10.1016/j.molp.2016.11.008
Camacho C, Coulouris G, Avagyan V, et al (2009) BLAST+: architecture and applications. BMC Bioinformatics 10:421. https://doi.org/10.1186/1471-2105-10-421
Chen C, Chen H, He Y, Xia R (2018) TBtools,a Toolkit for Biologists integrating various biological data handling tools with a user-friendly interface. bioRxiv 289660. https://doi.org/10.1101/289660
Chen Y, Zhi J, Zhang H, et al (2017) Transcriptome analysis of Phytolacca americana L. in response to cadmium stress. PLoS One 12:e0184681. https://doi.org/10.1371/journal.pone.0184681
Cheng F, Sun R, Hou X, et al (2016a) Subgenome parallel selection is associated with morphotype diversification and convergent crop domestication in Brassica rapa and Brassica oleracea. Nat Genet 48:1218–1224. https://doi.org/10.1038/ng.3634
Cheng S, Gutmann B, Zhong X, et al (2016b) Redefining the structural motifs that determine RNA binding and RNA editing by pentatricopeptide repeat proteins in land plants. Plant J 85:532–547. https://doi.org/10.1111/tpj.13121
Ding Y, Chen Z, Zhu C (2011) Microarray-based analysis of cadmium-responsive microRNAs in rice (Oryza sativa). J Exp Bot 62:3563–3573. https://doi.org/10.1093/jxb/err046
Ding Y, Gong S, Wang Y, et al (2018) MicroRNA166 modulates cadmium tolerance and accumulation in rice. Plant Physiol 177:1691–1703. https://doi.org/10.1104/pp.18.00485
Ding YF, Zhu C (2009) The role of microRNAs in copper and cadmium homeostasis. Biochem Biophys Res Commun 386:6–10. https://doi.org/10.1016/j.bbrc.2009.05.137
Dobin A, Davis CA, Schlesinger F, et al (2013) STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29:15–21. https://doi.org/10.1093/bioinformatics/bts635
Ernst J, Bar-Joseph Z (2006) STEM: A tool for the analysis of short time series gene expression data. BMC Bioinformatics 7:1–11. https://doi.org/10.1186/1471-2105-7-191
Fang X, Zhao Y, Ma Q, et al (2013) Identification and comparative analysis of cadmium tolerance-associated miRNAs and their targets in two soybean genotypes. PLoS One 8:e81471. https://doi.org/10.1371/journal.pone.0081471
Feng J, Jia W, Lv S, et al (2018) Comparative transcriptome combined with morpho-physiological analyses revealed key factors for differential cadmium accumulation in two contrasting sweet sorghum genotypes. Plant Biotechnol J 16:558–571. https://doi.org/10.1111/pbi.12795
Gao J, Sun L, Yang X, Liu JX (2013) Transcriptomic analysis of cadmium stress response in the heavy metal hyperaccumulator Sedum alfredii Hance. PLoS One 8:e64643. https://doi.org/10.1371/journal.pone.0064643
Gielen H, Remans T, Vangronsveld J, Cuypers A (2016) Toxicity responses of Cu and Cd: The involvement of miRNAs and the transcription factor SPL7. BMC Plant Biol 16:1–16. https://doi.org/10.1186/s12870-016-0830-4
Gielen H, Vangronsveld J, Cuypers A (2017) Cd-induced Cu deficiency responses in Arabidopsis thaliana: are phytochelatins involved? Plant Cell Environ 40:390–400. https://doi.org/10.1111/pce.12876
Han X, Yin H, Song X, et al (2016) Integration of small RNAs, degradome and transcriptome sequencing in hyperaccumulator Sedum alfredii uncovers a complex regulatory network and provides insights into cadmium phytoremediation. Plant Biotechnol J 14:1470–1483. https://doi.org/10.1111/pbi.12512
Hashimoto M, Endo T, Peltier G, et al (2003) A nucleus-encoded factor, CRR2, is essential for the expression of chloroplast ndhB in Arabidopsis. Plant J 36:541–549. https://doi.org/10.1046/j.1365-313X.2003.01900.x
Hildebrand M, Hallick RB, Passavant CW, Bourque DP (1988) Trans-splicing in chloroplasts: the rps12 loci of Nicotiana tabacum. Proc Natl Acad Sci 85:372–376. https://doi.org/10.1073/pnas.85.2.372
Huang Y, He C, Shen C, et al (2017) Toxicity of cadmium and its health risks from leafy vegetable consumption. Food Funct 8:1373–1401. https://doi.org/10.1039/c6fo01580h
Jia T, Zhang B, You C, et al (2017) The Arabidopsis MOS4-associated complex promotes microRNA biogenesis and precursor messenger RNA splicing. Plant Cell 29:2626–2643. https://doi.org/10.1105/tpc.17.00370
Jian H, Yang B, Zhang A, et al (2018) Genome-wide identification of microRNAs in response to cadmium stress in oilseed rape (Brassica napus L.) Using High-Throughput Sequencing. Int J Mol Sci 19:1431. https://doi.org/10.3390/ijms19051431
Kang XP, Gao JP, Zhao JJ, et al (2017) Identification of cadmium-responsive microRNAs in Solanum torvum by high-throughput sequencing. Russ J Plant Physiol 64:283–300. https://doi.org/10.1134/S1021443717020066
Khan KY, Ali B, Cui X, et al (2017) Effect of humic acid amendment on cadmium bioavailability and accumulation by pak choi (Brassica rapa ssp. chinensis L.) to alleviate dietary toxicity risk. Arch Agron Soil Sci 63:1431–1442. https://doi.org/10.1080/03650340.2017.1283018
Kim B, Yu H-J, Park S-G, et al (2012) Identification and profiling of novel microRNAs in the Brassica rapa genome based on small RNA deep sequencing. BMC Plant Biol 12:218. https://doi.org/10.1186/1471-2229-12-218
Li S, Le B, Ma X, et al (2016) Biogenesis of phased siRNAs on membrane-bound polysomes in Arabidopsis. Elife 5:1–24. https://doi.org/10.7554/eLife.22750
Lin YF, Aarts MGM (2012) The molecular mechanism of zinc and cadmium stress response in plants. Cell Mol Life Sci 69:3187–3206. https://doi.org/10.1007/s00018-012-1089-z
Liu H, Zhao H, Wu L, et al (2017) Heavy metal ATPase 3 (HMA3) confers cadmium hypertolerance on the cadmium/zinc hyperaccumulator Sedum plumbizincicola. New Phytol 215:687–698. https://doi.org/10.1111/nph.14622
Love MI, Huber W, Anders S (2014) Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol 15:550. https://doi.org/10.1186/s13059-014-0550-8
Manna S (2015) An overview of pentatricopeptide repeat proteins and their applications. Biochimie 113:93–99. https://doi.org/10.1016/j.biochi.2015.04.004
Martin M (2011) Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet.journal 17:10. https://doi.org/10.14806/ej.17.1.200
McCarthy FM, Gresham CR, Buza TJ, et al (2011) AgBase: supporting functional modeling in agricultural organisms. Nucleic Acids Res 39:D497–D506. https://doi.org/10.1093/nar/gkq1115
Nakamura SI, Akiyama C, Sasaki T, et al (2008) Effect of cadmium on the chemical composition of xylem exudate from oilseed rape plants (Brassica napus L.). Soil Sci Plant Nutr 54:118–127. https://doi.org/10.1111/j.1747-0765.2007.00214.x
Pall GS, Hamilton AJ (2008) Improved northern blot method for enhanced detection of small RNA. Nat Protoc 3:1077–1084. https://doi.org/10.1038/nprot.2008.67
Qiu Q, Wang Y, Yang Z, et al (2011a) Responses of different Chinese flowering cabbage (Brassica parachinensis L.) cultivars to cadmium and lead exposure: screening for Cd + Pb pollution-safe cultivars. CLEAN - Soil, Air, Water 39:925–932. https://doi.org/10.1002/clen.201000275
Qiu Q, Wang Y, Yang Z, Yuan J (2011b) Effects of phosphorus supplied in soil on subcellular distribution and chemical forms of cadmium in two Chinese flowering cabbage (Brassica parachinensis L.) cultivars differing in cadmium accumulation. Food Chem Toxicol 49:2260–2267. https://doi.org/10.1016/j.fct.2011.06.024
Rizwan M, Ali S, Zia ur Rehman M, et al (2018) Cadmium phytoremediation potential of Brassica crop species: A review. Sci Total Environ 631–632:1175–1191. https://doi.org/10.1016/j.scitotenv.2018.03.104
Ruwe H, Schmitz-Linneweber C (2012) Short non-coding RNA fragments accumulating in chloroplasts: Footprints of RNA binding proteins? Nucleic Acids Res 40:3106–3116. https://doi.org/10.1093/nar/gkr1138
Ruwe H, Wang G, Gusewski S, Schmitz-Linneweber C (2016) Systematic analysis of plant mitochondrial and chloroplast small RNAs suggests organelle-specific mRNA stabilization mechanisms. Nucleic Acids Res 44:7406–7417. https://doi.org/10.1093/nar/gkw466
Sanità Di Toppi L, Gabbrielli R (1999) Response to cadmium in higher plants. Environ Exp Bot 41:105–130. https://doi.org/10.1016/S0098-8472(98)00058-6
Sarwar N, Saifullah, Malhi SS, et al (2010) Role of mineral nutrition in minimizing cadmium accumulation by plants. J Sci Food Agric 90:925–937. https://doi.org/10.1002/jsfa.3916
Sasaki A, Yamaji N, Ma JF (2014) Overexpression of OsHMA3 enhances Cd tolerance and expression of Zn transporter genes in rice. J Exp Bot 65:6013–6021. https://doi.org/10.1093/jxb/eru340
Sasaki A, Yamaji N, Yokosho K, Ma JF (2012) Nramp5 is a major transporter responsible for manganese and cadmium uptake in rice. Plant Cell 24:2155–2167. https://doi.org/10.1105/tpc.112.096925
Schaaf G, Ludewig U, Erenoglu BE, et al (2004) ZmYS1 functions as a proton-coupled symporter for phytosiderophore- and nicotianamine-chelated metals. J Biol Chem 279:9091–9096. https://doi.org/10.1074/jbc.M311799200
Shikanai T, Fujii S (2013) Function of PPR proteins in plastid gene expression. RNA Biol 10:1446–1456. https://doi.org/10.4161/rna.25207
Shriram V, Kumar V, Devarumath RM, et al (2016) MicroRNAs as potential targets for abiotic stress tolerance in plants. Front Plant Sci 7:1–18. https://doi.org/10.3389/fpls.2016.00817
Sun C, Wu J, Liang J, et al (2015) Impacts of whole-genome triplication on MIRNA evolution in Brassica rapa. Genome Biol Evol 7:3085–3096. https://doi.org/10.1093/gbe/evv206
Supek F, Bošnjak M, Škunca N, Šmuc T (2011) REVIGO summarizes and visualizes long lists of gene ontology terms. PLoS One 6:e21800. https://doi.org/10.1371/journal.pone.0021800
Tang Z, Cai H, Li J, et al (2017) Allelic variation of NtNramp5 associated with cultivar variation in cadmium accumulation in tobacco. Plant Cell Physiol 58:1583–1593. https://doi.org/10.1093/pcp/pcx087
Ueno D, Yamaji N, Kono I, et al (2010) Gene limiting cadmium accumulation in rice. Proc Natl Acad Sci 107:16500–16505. https://doi.org/10.1073/pnas.1005396107
Verret F, Gravot A, Auroy P, et al (2004) Overexpression of AtHMA4 enhances root-to-shoot translocation of zinc and cadmium and plant metal tolerance. FEBS Lett 576:306–312. https://doi.org/10.1016/j.febslet.2004.09.023
Wang C, Cui H-M, Huang T-H, et al (2016) Identification and validation of reference genes for RT-qPCR analysis in non-heading chinese cabbage flowers. Front Plant Sci 7:1–12. https://doi.org/10.3389/fpls.2016.00811
Wang J, Yuan J, Yang Z, et al (2009) Variation in cadmium accumulation among 30 cultivars and cadmium subcellular distribution in 2 selected cultivars of water spinach (Ipomoea aquatica Forsk.). J Agric Food Chem 57:8942–8949. https://doi.org/10.1021/jf900812s
Wickham H (2016) ggplot2. Springer International Publishing, Cham
Wójcik M, Tukiendorf A (2011) Glutathione in adaptation of Arabidopsis thaliana to cadmium stress. Biol Plant 55:125–132. https://doi.org/10.1007/s10535-011-0017-7
Wu J, Liu B, Cheng F, et al (2012) Sequencing of Chloroplast Genome Using Whole Cellular DNA and Solexa Sequencing Technology. Front Plant Sci 3:1–7. https://doi.org/10.3389/fpls.2012.00243
Wu Z, Zhao X, Sun X, et al (2015) Xylem transport and gene expression play decisive roles in cadmium accumulation in shoots of two oilseed rape cultivars (Brassica napus). Chemosphere 119:1217–1223. https://doi.org/10.1016/j.chemosphere.2014.09.099
Xu H, Yu C, Xia X, et al (2018) Comparative transcriptome analysis of duckweed ( Landoltia punctata ) in response to cadmium provides insights into molecular mechanisms underlying hyperaccumulation. Chemosphere 190:154–165. https://doi.org/10.1016/j.chemosphere.2017.09.146
Yamasaki H, Hayashi M, Fukazawa M, et al (2009) SQUAMOSA promoter binding protein-like7 is a central regulator for copper homeostasis in Arabidopsis. PLANT CELL ONLINE 21:347–361. https://doi.org/10.1105/tpc.108.060137
Yao X, Cai Y, Yu D, Liang G (2018) bHLH104 confers tolerance to cadmium stress in Arabidopsis thaliana. J Integr Plant Biol 60:691–702. https://doi.org/10.1111/jipb.12658
Yu R, Tang Y, Liu C, et al (2017a) Comparative transcriptomic analysis reveals the roles of ROS scavenging genes in response to cadmium in two pak choi cultivars. Sci Rep 7:9217. https://doi.org/10.1038/s41598-017-09838-2
Yu Y, Jia T, Chen X (2017b) The ‘how’ and ‘where’ of plant microRNAs. New Phytol 216:1002–1017. https://doi.org/10.1111/nph.14834
Zhai J, Arikit S, Simon SA, et al (2014) Rapid construction of parallel analysis of RNA end (PARE) libraries for Illumina sequencing. Methods 67:84–90. https://doi.org/10.1016/j.ymeth.2013.06.025
Zhang J, Martinoia E, Lee Y (2018a) Vacuolar transporters for cadmium and arsenic in plants and their applications in phytoremediation and crop development. Plant Cell Physiol 59:1317–1325. https://doi.org/10.1093/pcp/pcy006
Zhang J, Zhang M, Shohag MJI, et al (2016) Enhanced expression of SaHMA3 plays critical roles in Cd hyperaccumulation and hypertolerance in Cd hyperaccumulator Sedum alfredii Hance. Planta 243:577–589. https://doi.org/10.1007/s00425-015-2429-7
Zhang LW, Song JB, Shu XX, et al (2013) MiR395 is involved in detoxification of cadmium in Brassica napus. J Hazard Mater 250–251:204–211. https://doi.org/10.1016/j.jhazmat.2013.01.053
Zhang XD, Meng JG, Zhao KX, et al (2018b) Annotation and characterization of Cd-responsive metal transporter genes in rapeseed (Brassica napus). BioMetals 31:107–121. https://doi.org/10.1007/s10534-017-0072-4
Zhou Q, Yang Y-C, Shen C, et al (2017) Comparative analysis between low- and high-cadmium-accumulating cultivars of Brassica parachinensis to identify difference of cadmium-induced microRNA and their targets. Plant Soil 420:223–237. https://doi.org/10.1007/s11104-017-3380-0
Zhou ZS, Song JB, Yang ZM (2012a) Genome-wide identification of Brassica napus microRNAs and their targets in response to cadmium. J Exp Bot 63:4597–4613. https://doi.org/10.1093/jxb/ers136
Zhou ZS, Zeng HQ, Liu ZP, Yang ZM (2012b) Genome-wide identification of Medicago truncatula microRNAs and their targets reveals their differential regulation by heavy metal. Plant, Cell Environ 35:86–99. https://doi.org/10.1111/j.1365-3040.2011.02418.x