Global identification and functional prediction of cold-related lncRNAs in eggplant


  • Yan YANG Institute of Vegetable Crops, Jiangsu Academy of Agricultural Sciences, Nanjing (CN)
  • Jingxian ZHANG Institute of Vegetable Crops, Jiangsu Academy of Agricultural Sciences, Nanjing (CN)
  • Jun LIU Institute of Vegetable Crops, Jiangsu Academy of Agricultural Sciences, Nanjing (CN)
  • Xiaohui ZHOU Institute of Vegetable Crops, Jiangsu Academy of Agricultural Sciences, Nanjing (CN)
  • Shuqing LIANG Institute of Vegetable Crops, Jiangsu Academy of Agricultural Sciences, Nanjing (CN)
  • Songyu LIU Institute of Vegetable Crops, Jiangsu Academy of Agricultural Sciences, Nanjing (CN)
  • Yong ZHUANG Institute of Vegetable Crops, Jiangsu Academy of Agricultural Sciences, Nanjing (CN)



cold stress, eggplant, functional analysis, lncRNA, target gene


Long noncoding RNAs (lncRNAs) play critical roles in plant development and stress responses. So far, identification of lncRNA in eggplant response to stresses has been limited and the role in mediating response to cold stress is yet to be characterized in eggplant. In this study, there is reported the first dataset of lncRNAs responsive to cold stress in the cold tolerant and sensitive eggplants using RNA sequencing (RNA-seq). 227 and 225 differentially expressed (DE) lncRNAs were obtained in two genotypes with differential cold-tolerance. Functional characterization through gene ontology (GO) analysis indicated that target genes were particularly related to acyl-CoA dehydrogenase activity and pseudouridine synthase activity, which could result in the tolerant phenotypes. Kyoto Encyclopaedia of Genes and Genomes (KEGG) showed that target genes in both sensitive and tolerant eggplants were mainly involved in cold responsive pathways such as oxidative phosphorylation, peroxisome, protein processing in endoplasmic reticulum, ubiquitin mediated proteolysis and so on. However, the enriched pathways obtained by enrichment analysis in cold-tolerant eggplant were different from those in cold-sensitive eggplant, which further indicated the reason for different tolerances. Our findings highlight the potential contributions of lncRNAs in regulating eggplant response to cold stress and difference in cold tolerance.


Bao Y, Howell SH (2017). The unfolded protein response supports plant development and defense as well as responses to abiotic stress. Frontiers in Plant Science 8:344.

Bar-Peled M, Raikhel NV (1997). Characterization of AtSECl2 and AtSAR1 - proteins likely involved in endoplasmic reticulum and Golgi transport. Plant Physiology 114:315-324.

Bilodeau P, Udvardi MK, Peacock WJ, Dennis ES (1999). A prolonged cold treatment‐induced cytochrome P450 gene from Arabidopsis thaliana. Plant Cell and Environment 22(7):791-800.

Boulc HP, Caullireau E, Faucher E, Gouerou M, Guérin A, Miray R, Couée I (2020). Abiotic stress signaling in extremophile land plants. Journal of Experimental Botany 71(19):5771-5785.

Cao P, Fan WJ, Li PJ, Hu YX (2021). Genome-wide profiling of long noncoding RNAs involved in wheat spike development. BMC Genomics 22:493.

Chekanova JA, Gregory BD, Reverdatto SV, Chen H, Kumar R, Hooker T, … Belostotsky DA (2007). Genome-wide high-resolution mapping of exosome substrates reveals hidden features in the Arabidopsis transcriptome. Cell 131:1340-1353.

Deng P, Wu L (2019). LncRNAs are cool regulators in cold exposure in plants. Science China Life Sciences 62(7):978-981.

Finn RD, Mistry J, Tate J, Coggill P, Heger A, Pollington JE, … Bateman A (2010). The Pfam protein families database. Nucleic Acids Research 38:211-222.

Gao Z, Li J, Luo M, Li H, Chen Q, Wang L, … Ma C (2019). Characterization and cloning of grape circular RNAs identified the cold resistance-related Vv-circATS1. Plant Physiology 180(2):966-985.

Guttman M, Garber M, Levin JZ, Donaghey J, Robinson J, Adiconis X, … Regev A (2010). Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs. Nature Biotechnology 28(5):503-510.

Heo JB, Sung S (2011). Vernalization-mediated epigenetic silencing by a long intronic noncoding RNA. Science 331(6013):76-79.

Kanehisa M, Araki M, Goto S, Hattori M, Hirakawa M, Itoh M, … Yamanishi Y (2007). KEGG for linking genomes to life and the environment. Nucleic Acids Research 36:480-484.

Kim D, Langmead B, Salzberg SL (2015). HISAT: a fast spliced aligner with low memory requirements. Nature Methods 12 (4):357-360.

Kindgren P, Ard R, Ivanov M, Marquardt S (2018). Transcriptional read-through of the long non-coding RNA SVALKA governs plant cold acclimation. Nature Communication 9(1):4561.

Kong L, Zhang Y, Ye ZQ, Liu XQ, Zhao SQ, Wei LP, Gao G (2007). CPC: assess the protein-coding potential of transcripts using sequence features and support vector machine. Nucleic Acids Research 35:345-349.

Kwon C, Lee JH, Yun HS (2020). SNAREs in plant biotic and abiotic stress responses. Molecules and Cells 43(6):501-508.

Li SX, Cheng ZH, Dong SM, Li ZB, Zou LP, Zhao PJ, … Peng M (2022). Global identification of full-length cassava lncRNAs unveils the role of cold-responsive intergenic lncRNA1 in cold stress response. Plant Cell and Environment 45(2):412-426.

Li SX, Yu X, Lei N, Cheng ZB, Zhao PJ, He YK, … Peng M (2017). Genome-wide identification and functional prediction of cold and/or drought-responsive lncRNAs in cassava. Scientific Reports 7(1):45981.

Li XH, Xing XX, Xu SX, Zhang MZ, Wang Y, Wu HY, … Yang TZ (2018). Genome-wide identification and functional prediction of tobacco lncRNAs responsive to root-knot nematode stress. PLoS One 13(11):e0204506.

Lin DZ, Kong RR, Chen L, Wang YL, Wu LL, Xu JL, … Dong YJ (2020). Chloroplast development at low temperature requires the pseudouridine synthase gene TCD3 in rice. Scientific Reports 10(1):8518.

Liu WH, Cheng CZ, Lin YL, XuHan X, Lai ZX (2018). Genome-wide identification and characterization of mRNAs and lncRNAs involved in cold stress in the wild banana (Musa itinerans). PLoS One 13(7):e0200002.

Lucero L, Ferrero L, Fonouni Farde C, Ariel F (2021). Functional classification of plant long noncoding RNAs: a transcript is known by the company it keeps. New Phytologist 229:1251-1260.

Mao XZ, Cai T, Olyarchuk JG, Wei LP (2005). Automated genome annotation and pathway identification using the KEGG Orthology (KO) as a controlled vocabulary. Bioinformatics 21(19):3787-3793.

Park C, Seo Y (2015). Heat shock proteins: a review of the molecular chaperones for plant immunity. The Plant Pathology Journal 31(4):323-333.

Ponting CP, Oliver PL, Reik W (2009). Evolution and functions of long noncoding RNAs. Cell 136:629-641.

Qing J, Zhong J, Du QX, Du LY, Du HY, Liu PF, … Wang L (2022). Genome-wide analysis of the long noncoding RNAs and mRNAs involved in flower bud development of Eucommia ulmoides Oliver. Scientia Horticulturae 300:111038.

Rurek M, Czołpińska M, Pawłowski T, Krzesiński W, Spiżewski T (2018). Cold and heat stress diversely alter both cauliflower respiration and distinct mitochondrial proteins including OXPHOS components and matrix enzymes. International Journal of Molecular Sciences 19(3):877.

Shen EH, Zhu XT, Hua SJ, Chen HY, Ye CY, Zhou LH, … Chen X (2018). Genome-wide identification of oil biosynthesis-related long non-coding RNAs in allopolyploid Brassica napus. BMC Genomics 19(1):475.

Sun L, Luo HT, Bu DC, Zhao GG, Yu KT, Zhang CH, … Zhao Y (2013). Utilizing sequence intrinsic composition to classify protein-coding and long non-coding transcripts. Nucleic Acids Research 41(17):e166.

Sun XL, Ji W, Ding XD, Bai X, Cai H, Yang SS, … Zhu YM (2013). GsVAMP72, a novel Glycine soja R-SNARE protein, is involved in regulating plant salt tolerance and ABA sensitivity. Plant Cell, Tissue and Organ Culture 113(2):199-215.

Sun ZF, Huang K, Han ZJ, Wang P, Fang YD (2020). Genome-wide identification of Arabidopsis long noncoding RNAs in response to the blue light. Scientific Reports 10(1):6629.

Swiezewski S, Liu F, Magusin A, Dean C (2009). Cold-induced silencing by long antisense transcripts of an Arabidopsis polycomb target. Nature 462(7274):799-802.

Tak H, Negi S, Rajpurohit YS, Misra HS, Ganapathi TR (2020). MusaMPK5, a mitogen activated protein kinase is involved in regulation of cold tolerance in banana. Plant Physiology and Biochemistry 146:112-123.

Tang W, Thompson WA (2019). OsmiR528 enhances cold stress tolerance by repressing expression of stress response-related transcription factor genes in plant cells. Current Genomics 20(2):100-114.

Tao X, Wang MX, Dai Y, Wang Y, Fan YF, Mao P, Ma XR (2017). Identification and expression profile of CYPome in perennial ryegrass and tall fescue in response to temperature stress. Frontiers in Plant Science 8:1519.

Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, Van Baren MJ, … Pachter L (2010). Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nature Biotechnology 28(5):511-515.

Wang GN, Wang XF, Zhang Y, Yang J, Li ZK, Wu LZ, … Ma ZY (2021). Dynamic characteristics and functional analysis provide new insights into long non-coding RNA responsive to Verticillium dahliae infection in Gossypium hirsutum. BMC Plant Biology 21(1):68.

Wang KC, Chang HY (2011). Molecular mechanisms of long noncoding RNAs. Molecular Cell 43(6):904-914.

Wang ML, Zhang XY, Li QH, Chen X, Li XH (2019). Comparative transcriptome analysis to elucidate the enhanced thermos tolerance of tea plants (Camellia sinensis) treated with exogenous calcium. Planta 249(3):775-786.

Wang PF, Dai LM, Ai J, Wang YM, Ren FS (2019). Identification and functional prediction of cold-related long non-coding RNA (lncRNA) in grapevine. Scientific Reports 9(1):6638.

Wu L, Liu S, Qi HR, Cai H, Xu M (2020). Research progress on plant long non-coding RNA. Plants 9(4):408.

Yan J, Zhao CZ, Zhou JP, Yang Y, Wang PC, Zhu XH, … Zhu JK (2016). The miR165/166 mediated regulatory module plays critical roles in ABA homeostasis and response in Arabidopsis thaliana. PLoS Genetics 12(11):e1006416.

Yang X, Liu F, Zhang Y, Wang L, Cheng YF (2017). Cold-responsive miRNAs and their target genes in the wild eggplant species Solanum aculeatissimum. BMC Genomics 18:1000.

Yang Y, Liu J, Zhou XH, Liu SF, Zhuang Y (2020). Transcriptomics analysis unravels the response to low temperature in sensitive and tolerant eggplants. Scientia Horticulturae 271:109468.

Ye XX, Wang S, Zhao XJ, Gao N, Wang Y, Yang YM, … Liu SK (2022). Role of lncRNAs in cis- and trans-regulatory responses to salt in Populus trichocarpa. The Plant Journal 110:978-993

Young MD, Wakefield MJ, Smyth GK, Oshlack A (2010). Gene ontology analysis for RNA-seq: accounting for selection bias. Genome biology 11(2):14.

Yu L, Yan J, Yang YJ, He LZ, Zhu WM (2016). Enhanced tolerance to chilling stress in tomato by overexpression of a mitogen-activated protein kinase, SlMPK7. Plant Molecular Biology Reporter 34(1):76-88.

Yu W, Gius D, Onyango P, Muldoon-Jacobs K, Karp J, Feinberg AP, Cui H (2008). Epigenetic silencing of tumour suppressor gene p15 by its antisense RNA. Nature 451(7175):202-206.

Zhang HL, Hou J, Liu J, Zhang JP, Song BT, Xie CH (2017). The roles of starch metabolic pathways in the cold-induced sweetening process in potatoes. Starch - Stärke 69:1600194.

Zhang QL, Guo J, Deng XY, Wang F, Chen JY, Lin LB (2019). Comparative transcriptomic analysis provides insights into the response to the benzo(a)pyrene stress in aquatic firefly (Luciola leii). Science of the Total Environment 661:226-234.

Zhang XP, Shen J, Xu QJ, Dong J, Song LR, Wang W, Shen FF (2021). Long noncoding RNA lncRNA354 functions as a competing endogenous RNA of miR160b to regulate ARF genes in response to salt stress in upland cotton. Plant Cell and Environment 44(10):3302-3321.

Zhang ZF, Xu Y, Yang F, Xiao BZ, Li GL (2021). Rice LncPedia: a comprehensive database of rice long non-coding RNAs. Plant Biotechnology Journal 19(8):1492-1494.

Zhao MG, Wang TZ, Sun TY, Yu XX, Tian R, Zhang WH (2020). Identification of tissue-specific and cold-responsive lncRNAs in Medicago truncatula by high-throughput RNA sequencing. BMC Plant Biology 20(1):99.

Zhao RR, Xie HD, Lv SN, Zheng Y, Yu MM, Shen L, Sheng JP (2013). LeMAPK4 participated in cold-induced ethylene production in tomato fruit. Journal of the Science of Food and Agriculture 93(5):1003-1009.

Zhao XY, Li JR, Lian B, Gu HQ, Li Y, Qi YJ (2018). Global identification of Arabidopsis lncRNAs reveals the regulation of MAF4 by a natural antisense RNA. Nature Communication 9(1):5056.

Zhu QH, Wang MB (2012). Molecular functions of long non-coding RNAs in plants. Genes 3(1):176-190.

Zhu XF, Liu Y, Gai XT, Zhou Y, Xia ZY, Chen LJ, … Xuan YH (2019). SNARE proteins SYP22 and VAMP727 negatively regulate plant defense. Plant Signal Behaviour 14(7):e1610300.

Zhuo CL, Liang L, Zhao YQ, Guo ZF, Lu SY (2018). A cold responsive ethylene responsive factor from Medicago falcata confers cold tolerance by up-regulation of polyamine turnover, antioxidant protection, and proline accumulation. Plant Cell and Environment 41:2021-2032.



How to Cite

YANG, Y., ZHANG, J., LIU, J., ZHOU, X., LIANG, S., LIU, S., & ZHUANG, Y. (2022). Global identification and functional prediction of cold-related lncRNAs in eggplant. Notulae Botanicae Horti Agrobotanici Cluj-Napoca, 50(4), 12931.



Research Articles
DOI: 10.15835/nbha50312931