Abstract
Main conclusion
Key miRNAs including sbi-miR169p/q, sbi-miR171g/j, sbi-miR172a/c/d, sbi-miR172e, sbi-miR319a/b, sbi-miR396a/b, miR408, sbi-miR5384, sbi-miR5565e and nov_23 were identified to function in the regulation of Cd accumulation and tolerance.
Abstract
As an energy plant, sweet sorghum shows great potential in the phytoremediation of Cd-contaminated soils. However, few studies have focused on the regulatory roles of miRNAs and their targets under Cd stress. In this study, comparative analysis of sRNAs, degradome and transcriptomics was conducted in high-Cd accumulation (H18) and low-Cd accumulation (L69) genotypes of sweet sorghum. A total of 38 conserved and 23 novel miRNAs with differential expressions were identified under Cd stress or between H18 and L69, and 114 target genes of 41 miRNAs were validated. Furthermore, 25 miRNA–mRNA pairs exhibited negatively correlated expression profiles and sbi-miR172e together with its target might participate in the distinct Cd tolerance between H18 and L69 as well as sbi-miR172a/c/d. Additionally, two groups of them: miR169p/q-nov_23 and miR408 were focused through the co-expression analysis, which might be involved in Cd uptake and tolerance by regulating their targets associated with transmembrane transportation, cytoskeleton activity, cell wall construction and ROS (reactive oxygen species) homeostasis. Further experiments exhibited that cell wall components of H18 and L69 were different when exposed to cadmium, which might be regulated by miR169p/q, miR171g/j, miR319a/b, miR396a/b, miR5384 and miR5565e through their targets. Through this study, we aim to reveal the potential miRNAs involved in sweet sorghum in response to Cd stress and provide references for developing high-Cd accumulation or high Cd-resistant germplasm of sweet sorghum that can be used in phytoremediation.
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References
Addo-Quaye C, Miller W, Axtell MJ (2009) CleaveLand: a pipeline for using degradome data to find cleaved small RNA targets. Bioinformatics 25(1):130–131. https://doi.org/10.1093/bioinformatics/btn604
Axtell MJ, Bowman JL (2008) Evolution of plant microRNAs and their targets. Trends Plant Sci 13(7):343–349. https://doi.org/10.1016/j.tplants.2008.03.009
Baxter A, Mittler R, Suzuki N (2014) ROS as key players in plant stress signaling. J Exp Bot 65(5):1229–1240. https://doi.org/10.1093/jxb/ert375
Blumenkrantz N, Asboe-Hansen G (1973) New method for quantitative determination of uronic acids. Anal Biochem 54(2):484–489. https://doi.org/10.1016/0003-2697(73)90377-1
Brunetti P, Zanella L, De Paolis A, Di Litta D, Cecchetti V, Falasca G, Barbieri M, Altamura MM, Costantino P, Cardarelli M (2015) Cadmium-inducible expression of the ABC-type transporter AtABCC3 increases phytochelatin-mediated cadmium tolerance in Arabidopsis. J Exp Bot 66(13):3815–3829. https://doi.org/10.1093/jxb/erv185
Cakir O, Candar-Cakir B, Zhang B (2015) Small RNA and degradome sequencing reveals important microRNA function in Astragalus chrysochlorus response to selenium stimuli. Plant Biotechnol J 14(2):543–556. https://doi.org/10.1111/pbi.12397
Calviño M, Messing J (2012) Sweet sorghum as a model system for bioenergy crops. Curr Opin Biotechnol 23(3):323–329. https://doi.org/10.1016/j.copbio.2011.12.002
Chen DJ, Meng YJ, Ma XX, Mao CZ, Bai YH, Cao JJ, Gu HB, Wu P, Chen M (2010) Small RNAs in angiosperms: sequence characteristics, distribution and generation. Bioinformatics 26(11):1391–1394. https://doi.org/10.1093/bioinformatics/btq150
Chen J, Xie J, Chen B, Quan M, Li Y, Li B, Zhang D (2016) Genetic variations and miRNA-target interactions contribute to natural phenotypic variations in Populus. New Phytol 212(1):150–160. https://doi.org/10.1111/nph.14040
Cheng X, Zhang S, Tao W, Zhang X, Liu J, Sun J, Zhang H, Pu L, Huang R, Chen T (2018) INDETERMINATE SPIKELET1 recruits histone deacetylase and a transcriptional repression complex to regulate rice salt tolerance. Plant Physiol 178:824–837. https://doi.org/10.1104/pp.18.00324
Cheng XL, He Q, Tang S, Wang HR, Zhang XX, Lv MJ, Liu HF, Gao Q, Zhou Y, Wang Q, Man XY, Liu J, Huang RF, Wang H, Chen T, Liu J (2021) The miR172/IDS1 signaling module confers salt tolerance through maintaining ROS homeostasis in cereal crops. New Phytol. https://doi.org/10.1111/nph.17211
Dhaka N, Sharma S, Vashisht I, Kandpal M, Sharma MK, Sharma R (2020) Small RNA profiling from meiotic and post-meiotic anthers reveals prospective miRNA-target modules for engineering male fertility in sorghum. Genomics 112:1598–1610. https://doi.org/10.1016/j.ygeno.2019.09.009
Ding Y, Chen Z, Zhu C (2011) Microarray-based analysis of cadmium-responsive microRNAs in rice (Oryza sativa). J Exp Bot 62(10):3563–3573. https://doi.org/10.1093/jxb/err046
Du Z, Zhou X, Ling Y, Zhang Z, Su Z (2010) agriGO: a GO analysis toolkit for the agricultural community. Nucleic Acids Res 38:64–70. https://doi.org/10.1093/nar/gkq310
El Sanousi RS, Hamza NB, Abdelmula AA, Mohammed IA, Gasim SM, Sanan-mishra N (2016) Differential expression of miRNAs in Sorghum bicolor under drought and salt stress. Am J Plant Sci 7:870–878. https://doi.org/10.4236/ajps.2016.76082
Fan J, Wei X, Wan L, Zhang L, Zhao X, Liu W, Hao H, Zhang H (2011) Disarrangement of actin filaments and Ca2+ gradient by CdCl2 alters cell wall construction in Arabidopsis thaliana root hairs by inhibiting vesicular trafficking. J Plant Physiol 168(11):1157–1167. https://doi.org/10.1016/j.jplph.2011.01.031
Fan P, Nie L, Jiang P, Feng J, Lv S, Chen X, Bao H, Guo J, Tai F, Wang J, Jia W, Li Y (2013) Transcriptome analysis of Salicornia europaea under saline conditions revealed the adaptive primary metabolic pathways as early events to facilitate salt adaptation. PLoS ONE 8(11):e80595–e80595. https://doi.org/10.1371/journal.pone.0080595
Feng J, Wang J, Fan P, Jia W, Nie L, Jiang P, Chen X, Lv S, Wan L, Chang S, Li S, Li Y (2015) High-throughput deep sequencing reveals that microRNAs play important roles in salt tolerance of euhalophyte Salicornia europaea. BMC Plant Biol 15:63–63. https://doi.org/10.1186/s12870-015-0451-3
Feng J, Jia W, Lv S, Bao H, Miao F, Zhang X, Wang J, Li J, Li D, Zhu C, Li S, Li Y (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(2):558–571. https://doi.org/10.1111/pbi.12795
Foster CE, Martin TM, Pauly M (2010a) Comprehensive compositional analysis of plant cell walls (Lignocellulosic biomass) part I: lignin. J vis Exp 37:1745. https://doi.org/10.3791/1745
Foster CE, Martin TM, Pauly M (2010b) Comprehensive compositional analysis of plant cell walls (lignocellulosic biomass) part II: carbohydrates. J vis Exp 37:1837. https://doi.org/10.3791/1837
Gao J, Luo M, Peng H, Chen F, Li W (2019) Characterization of cadmium-responsive microRNAs and their target genes in maize (Zea mays) roots. BMC Mol Biol 20(1):14. https://doi.org/10.1186/s12867-019-0131-1
Garg V, Khan AW, Kudapa H, Kale SM, Chitikineni A, Qiwei S, Sharma M, Li C, Zhang B, Xin L, Kishor PBK, Varshney RK (2019) Integrated transcriptome, small RNA and degradome sequencing approaches provide insights into Ascochyta blight resistance in chickpea. Plant Biotechnol J 17(5):914–931. https://doi.org/10.1111/pbi.13026
German MA, Pillay M, Jeong D-H et al (2008) Global identification of microRNA–target RNA pairs by parallel analysis of RNA ends. Nat Biotechnol 26(8):941–946. https://doi.org/10.1038/nbt1417
Gnansounou E, Dauriat A, Wyman CE (2005) Refining sweet sorghum to ethanol and sugar: economic trade-offs in the context of North China. Biores Technol 96(9):985–1002. https://doi.org/10.1016/j.biortech.2004.09.015
Guerinot ML (2000) The ZIP family of metal transporters. Biochim Biophys Acta 1465(1–2):190–198. https://doi.org/10.1016/s0005-2736(00)00138-3
Gupta OP, Sharma P, Gupta RK, Sharma I (2013) MicroRNA mediated regulation of metal toxicity in plants: present status and future perspectives. Plant Mol Biol 84(1–2):1–18. https://doi.org/10.1007/s11103-013-0120-6
Gzyl J, Chmielowska-Bąk J, Przymusiński R, Gwóźdź EA (2015) Cadmium affects microtubule organization and post-translational modifications of tubulin in seedlings of soybean (Glycine max L.). Front Plant Sci 6:937–937. https://doi.org/10.3389/fpls.2015.00937
Hamza NB, Sharma N, Tripathi A, Sanan-Mishra N (2016) MicroRNA expression profiles in response to drought stress in Sorghum bicolor. Gene Expr Patterns 20:88–98. https://doi.org/10.1016/j.gep.2016.01.001
Han X, Yin H, Song X, Zhang Y, Liu M, Sang J, Jiang J, Li J, Zhuo R (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(6):1470–1483. https://doi.org/10.1111/pbi.12512
He Q, Zhu S, Zhang B (2014) MicroRNA–target gene responses to lead-induced stress in cotton (Gossypium hirsutum L.). Functi Integr Genomics 14(3):507–515. https://doi.org/10.1007/s10142-014-0378-z
Jia W, Lv S, Feng J, Li J, Li Y, Li S (2016) Morphophysiological characteristic analysis demonstrated the potential of sweet sorghum (Sorghum bicolor (L.) Moench) in the phytoremediation of cadmium-contaminated soils. Environ Sci Pollut Res 23(18):18823–18831. https://doi.org/10.1007/s11356-016-7083-5
Jia W, Miao F, Lv S, Feng J, Zhou S, Zhang X, Wang D, Li S, Li Y (2017) Identification for the capability of Cd-tolerance, accumulation and translocation of 96 sorghum genotypes. Ecotoxicol Environ Saf 145:391–397. https://doi.org/10.1016/j.ecoenv.2017.07.002
Jia H, Wang X, Wei T, Zhou R, Muhammad H, Hua L, Ren X, Guo J, Ding Y (2019) Accumulation and fixation of Cd by tomato cell wall pectin under Cd stress. Environ Exp Bot 167:103829. https://doi.org/10.1016/j.envexpbot.2019.103829
Karlova R, van Haarst JC, Maliepaard C, van de Geest H, Bovy AG, Lammers M, Angenent GC, de Maagd RA (2013) Identification of microRNA targets in tomato fruit development using high-throughput sequencing and degradome analysis. J Exp Bot 64(7):1863–1878. https://doi.org/10.1093/jxb/ert049
Katiyar A, Smita S, Chinnusamy V, Pandey DM, Bansal K (2012) Identification of miRNAs in sorghum by using bioinformatics approach. Plant Signal Behav 7:246–259. https://doi.org/10.4161/psb.18914
Katiyar A, Smita S, Muthusamy SK, Chinnusamy V, Pandey DM, Bansal KC (2015) Identification of novel drought-responsive microRNAs and trans-acting siRNAs from Sorghum bicolor (L.) Moench by high-throughput sequencing analysis. Front Plant Sci 6:506. https://doi.org/10.3389/fpls.2015.00506
Korenkov V, Hirschi K, Crutchfield JD, Wagner GJ (2007) Enhancing tonoplast Cd/H antiport activity increases Cd, Zn, and Mn tolerance, and impacts root/shoot Cd partitioning in Nicotiana tabacum L. Planta 226(6):1379–1387. https://doi.org/10.1007/s00425-007-0577-0
Kozomara A, Griffiths-Jones S (2011) miRBase: integrating microRNA annotation and deep-sequencing data. Nucleic Acids Research 39 (Database issue):D152-D157. https://doi.org/10.1093/nar/gkq1027
Li S (2013) The roadmap of the development of biofuel industry. China Brewing 32(S1):77–81
Livak KJ, Schmittgen TD (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2−ΔΔCT method. Methods 25(4):402–408. https://doi.org/10.1006/meth.2001.1262
Lu X, Huang X (2008) Plant miRNAs and abiotic stress responses. Biochem Biophys Res Commun 368(3):458–462. https://doi.org/10.1016/j.bbrc.2008.02.007
Park J, Song W-Y, Ko D, Eom Y, Hansen TH, Schiller M, Lee TG, Martinoia E, Lee Y (2012) The phytochelatin transporters AtABCC1 and AtABCC2 mediate tolerance to cadmium and mercury. Plant J 69(2):278–288. https://doi.org/10.1111/j.1365-313X.2011.04789.x
Parrotta L, Guerriero G, Sergeant K, Cai G, Hausman J-F (2015) Target or barrier? The cell wall of early- and later-diverging plants vs cadmium toxicity: differences in the response mechanisms. Front Plant Sci 6:133–133. https://doi.org/10.3389/fpls.2015.00133
Paterson AH, Bowers JE, Bruggmann R, Dubchak I, Grimwood J, Gundlach H et al (2009) The Sorghum bicolor genome and the diversification of grasses. Nature 457:551–556. https://doi.org/10.1038/nature07723
Pizzaia D, Nogueira ML, Mondin M, Carvalho MEA, Piotto FA, Rosario MF, Azevedo RA (2019) Cadmium toxicity and its relationship with disturbances in the cytoskeleton, cell cycle and chromosome stability. Ecotoxicology 28(9):1046–1055. https://doi.org/10.1007/s10646-019-02096-0
Plaza S, Tearall KL, Zhao FJ, Buchner P, McGrath SP, Hawkesford MJ (2007) Expression and functional analysis of metal transporter genes in two contrasting ecotypes of the hyperaccumulator Thlaspi caerulescens. J Exp Bot 58(7):1717–1728. https://doi.org/10.1093/jxb/erm025
Qiao K, Tian Y, Hu Z, Chai T (2018) Wheat cell number regulator CNR10 enhances the tolerance, translocation, and accumulation of heavy metals in plants. Environ Sci Technol 53(2):860–867. https://doi.org/10.1021/acs.est.8b04021
Qiu Z, Hai B, Guo J, Li Y, Zhang L (2016) Characterization of wheat miRNAs and their target genes responsive to cadmium stress. Plant Physiol Biochem 101:60–67. https://doi.org/10.1016/j.plaphy.2016.01.020
Saito R, Smoot ME, Ono K, Ruscheinski J, Wang P-L, Lotia S, Pico AR, Bader GD, Ideker T (2012) A travel guide to Cytoscape plugins. Nat Methods 9(11):1069–1076. https://doi.org/10.1038/nmeth.2212
Scheible W, Pauly M (2004) Glycosyltransferases and cell wall biosynthesis: novel players and insights. Curr Opin Plant Biol 7(3):285–295. https://doi.org/10.1016/j.pbi.2004.03.006
Shriram V, Kumar V, Devarumath RM, Khare TS, Wani SH (2016) MicroRNAs as potential targets for abiotic stress tolerance in plants. Front Plant Sci. https://doi.org/10.3389/fpls.2016.00817
Soudek P, Petrová Š, Vaňková R, Song J, Vaněk T (2014) Accumulation of heavy metals using Sorghum sp. Chemosphere 104:15–24. https://doi.org/10.1016/j.chemosphere.2013.09.079
Spielmann J, Ahmadi H, Scheepers M, Weber M, Nitsche S, Carnol M, Bosman B, Kroymann J, Motte P, Clemens S, Hanikenne M (2020) The two copies of the zinc and cadmium ZIP6 transporter of Arabidopsis halleri have distinct effects on cadmium tolerance. Plant Cell Environ 43(9):2143–2157. https://doi.org/10.1111/pce.13806
Srivastava S, Srivastava AK, Suprasanna P, D’Souza SF (2012) Identification and profiling of arsenic stress-induced microRNAs in Brassica juncea. J Exp Bot 64(1):303–315. https://doi.org/10.1093/jxb/ers333
Srivastava S, Zheng Y, Kudapa H, Jagadeeswaran G, Hivrale V, Varshney RK, Sunkar R (2015) High throughput sequencing of small RNA component of leaves and inflorescence revealed conserved and novel miRNAs as well as phasiRNA loci in chickpea. Plant Sci 235:46–57. https://doi.org/10.1016/j.plantsci.2015.03.002
Sunkar R, Jagadeeswaran G (2008) In silico identification of conserved microRNAs in large number of diverse plant species. BMC Plant Biol 8:37–37. https://doi.org/10.1186/1471-2229-8-37
Tian T, You Q, Zhang L, Yi X, Yan H, Xu W, Su Z (2016) SorghumFDB: sorghum functional genomics database with multidimensional network analysis. Database. https://doi.org/10.1093/database/baw099
Wan L, Zhang H (2012) Cadmium toxicity: effects on cytoskeleton, vesicular trafficking and cell wall construction. Plant Signal Behav 7(3):345–348. https://doi.org/10.4161/psb.18992
Wan LC, Zhang H, Lu S, Zhang L, Qiu Z, Zhao Y, Zeng QY, Lin J (2012) Transcriptome-wide identification and characterization of miRNAs from Pinus densata. BMC Genomics 13:132–132. https://doi.org/10.1186/1471-2164-13-132
Wang LK, Feng ZX, Wang X, Wang XW, Zhang XG (2010) DEGseq: an R package for identifying differentially expressed genes from RNA-seq data. Bioinformatics 26:136–138. https://doi.org/10.1093/bioinformatics/btp612
Wang X, Chen C, Wang J (2017) Cadmium phytoextraction from loam soil in tropical southern China by Sorghum bicolor. Int J Phytorem 19(6):572–578. https://doi.org/10.1080/15226514.2016.1267704
Wojas S, Hennig J, Plaza S, Geisler M, Siemianowski O, Skłodowska A, Ruszczyńska A, Bulska E, Antosiewicz DM (2009) Ectopic expression of Arabidopsis ABC transporter MRP7 modifies cadmium root-to-shoot transport and accumulation. Environ Pollut 157(10):2781–2789. https://doi.org/10.1016/j.envpol.2009.04.024
Woods J (2001) The potential for energy production using sweet sorghum in southern Africa. Energy Sustain Dev 5(1):31–38. https://doi.org/10.1016/s0973-0826(09)60018-1
Wu Q, Shigaki T, Williams KA, Han J-S, Kim CK, Hirschi KD, Park S (2011) Expression of an Arabidopsis Ca2+/H+ antiporter CAX1 variant in petunia enhances cadmium tolerance and accumulation. J Plant Physiol 168(2):167–173. https://doi.org/10.1016/j.jplph.2010.06.005
Xie F, Jones DC, Wang Q, Sun R, Zhang B (2015) Small RNA sequencing identifies miRNA roles in ovule and fibre development. Plant Biotechnol J 13(3):355–369. https://doi.org/10.1111/pbi.12296
Xu L, Wang Y, Zhai L, Xu Y, Wang L, Zhu X, Gong Y, Yu R, Limera C, Liu L (2013) Genome-wide identification and characterization of cadmium-responsive microRNAs and their target genes in radish (Raphanus sativus L.) roots. J Exp Bot 64(14):4271–4287. https://doi.org/10.1093/jxb/ert240
Xu L, Wang Y, Liu W, Wang J, Zhu X, Zhang K, Yu R, Wang R, Xie Y, Zhang W, Gong Y, Liu L (2015) De novo sequencing of root transcriptome reveals complex cadmium-responsive regulatory networks in radish (Raphanus sativus L.). Plant Sci 236:313–323. https://doi.org/10.1016/j.plantsci.2015.04.015
Yan HL, Xu WX, Xie JY, Gao YW, Wu LL, Sun L, Feng L, Chen X, Zhang T, Dai CH, Li T, Lin XN, Zhang ZY, Wang XQ, Li FM, Zhu XY, Li JJ, Li ZC, Chen CY, Ma M, Zhang HL, He ZY (2019) Variation of a major facilitator superfamily gene contributes to differential cadmium accumulation between rice subspecies. Nat Commun 10(1):3301–3301. https://doi.org/10.1038/s41467-019-10977-5
Yang JL, Zhu XF, Peng YX, Zheng C, Li GX, Liu Y, Shi YZ, Zheng SJ (2011) Cell wall hemicellulose contributes significantly to aluminum adsorption and root growth in Arabidopsis. Plant Physiol 155(4):1885–1892. https://doi.org/10.1104/pp.111.172221
Yu J, Zhang T, Zhong J, Zhang X, Tan T (2012) Biorefinery of sweet sorghum stem. Biotechnol Adv 30(4):811–816. https://doi.org/10.1016/j.biotechadv.2012.01.014
Yu HL, Cong L, Zhu ZX, Wang CY, Zou JQ, Tao CJ, Shi ZS, Lu XC (2015) Identification of differentially expressed microRNA in the stems and leaves during sugar accumulation in sweet sorghum. Gene 571:221–230. https://doi.org/10.1016/j.gene.2015.06.056
Zhang L, Zheng Y, Jagadeeswaran G, Li YF, Gowdu K, Sunkar R (2011) Identification and temporal expression analysis of conserved and novel microRNAs in Sorghum. Genomics 98:460–468. https://doi.org/10.1016/j.ygeno.2011.08.005
Zhang LW, Song JB, Shu XX, Zhang Y, Yang ZM (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 HY, Zhao X, Li JG, Cai HQ, Deng XW, Li L (2014) MicroRNA408 is critical for the HY5-SPL7 gene network that mediates the coordinated response to light and copper. Plant Cell 26(12):4933–4953. https://doi.org/10.1105/tpc.114.127340
Zhou ZS, Zeng HQ, Liu ZP, Yang ZM (2011) Genome-wide identification of Medicago truncatula microRNAs and their targets reveals their differential regulation by heavy metal. Plant Cell Environ 35(1):86–99. https://doi.org/10.1111/j.1365-3040.2011.02418.x
Zhou ZS, Song JB, Yang ZM (2012) Genome-wide identification of Brassica napus microRNAs and their targets in response to cadmium. J Exp Bot 63(12):4597–4613. https://doi.org/10.1093/jxb/ers136
Zhou LL, Tian SP, Qin GZ (2019) RNA methylomes reveal the m6A-mediated regulation of DNA demethylase gene SlDML2 in tomato fruit ripening. Genome Biol 20:156. https://doi.org/10.1186/s13059-019-1771-7
Zhuang P, Shu W, Li Z, Liao B, Li J, Shao J (2009) Removal of metals by sorghum plants from contaminated land. J Environ Sci 21(10):1432–1437. https://doi.org/10.1016/s1001-0742(08)62436-5
Acknowledgements
We thank Dr. Guozheng Qin and Dr. Yinzheng Wang, Institute of Botany, Chinese Academy of Sciences, for generously providing us with pGreenII-0800 vector, and kind assistance on dual-luciferase reporter assay respectively. This study was supported by the National Key Research and Development Program of China (Grant No. 2018YFD0800700), the Strategic Priority Research Program of Chinese Academy of Sciences (Grant No. XDA24010306), and the National Natural Science Foundation of China (Grant No. 31971837).
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Figure S2
. Statistics of sRNAs in the four libraries. (a) and (b), Length distribution of total (a) and unique (b) small RNAs. (c) and (d), length distribution of conserved miRNAs (c) and novel miRNAs (d). nt, nucleotides. (JPG 52 KB)
Figure S2
. Statistics of sRNAs in the four libraries. (a) and (b), Length distribution of total (a) and unique (b) small RNAs. (c) and (d), length distribution of conserved miRNAs (c) and novel miRNAs (d). nt, nucleotides. (JPG 52 KB)
Figure S3
. Number of conserved miRNAs in each family in S. bicolor. (JPG 670 KB)
Figure S4
. Validation of expression profiles of miRNAs. Two-week-old H18 and L69 seedlings were treated with 0 and 10 µM CdCl2 for 24 h, and then root tissues were collected for validating the deep sequencing results through qRT-PCR. Seven miRNAs of miR397a-3p (a), miR397a-5p (b), miR169p/q (c), miR408 (d), miR319a/b (e), miR172a/c/d (f) and miR529 (g) were selected to check their expression level and the correlation analysis between the results of deep sequencing and qRT-PCR (h) was conducted (P < 0.05). (JPG 470 KB)
Figure S5
. Target plots (T-plots) for targets of three conserved and one novel miRNAs in categories 0 and 1 confirmed by degradome sequencing. (a) sbi-miR408 and its target Sobic.008G093600 (unknown protein); (b) sbi-miR164c and its target Sobic.004G191700 (ANAC100, Arabidopsis NAC domain-containing protein 100; transcription factor); (c) sbi-miR156h and its target Sobic.010G254200 (similar to squamosa promoter-binding-like protein 12); (d) nov_23 and its target Sobic.003G364700 (unknown protein). (JPG 446 KB)
Figure S6. The co-expression subnetwork of miR169p/q-nov_23 and miR408 modules
. Interaction network of miR169p/q-nov_23 (a) and miR408 (b) modules were performed using Cytoscape network platform. Hexagonal nodes represent miRNAs and circular nodes represent mRNAs. Blue lines represent positive interaction and red lines represent negative interaction. Yellow nodes represent transporters. (JPG 401 KB)
425_2021_3669_MOESM17_ESM.xlsx
Table S10. Targets of conserved miRNAs identified by degradome sequencing with categories 0 and 1 in H18-CK, L69-CK, H18-Cd and L69-Cd. (XLSX 19 KB)
425_2021_3669_MOESM18_ESM.xlsx
Table S11. Targets of novel miRNAs identified by degradome sequencing with categories 0 and 1 in H18-CK, L69-CK, H18-Cd and L69-Cd. (XLSX 11 KB)
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Jia, W., Lin, K., Lou, T. et al. Comparative analysis of sRNAs, degradome and transcriptomics in sweet sorghum reveals the regulatory roles of miRNAs in Cd accumulation and tolerance. Planta 254, 16 (2021). https://doi.org/10.1007/s00425-021-03669-2
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DOI: https://doi.org/10.1007/s00425-021-03669-2