Figures (2)  Tables (2)
    • Figure 1. 

      Statistics on the published number of lnRNA-related papers of major vegetables.

    • Figure 2. 

      The predictive model of regulatory mechanisms of lncRNAs with known functions under various developmental events or stress conditions in different vegetable crops. Full-line arrows represent positive regulatory interactions, blunt-ended bars represent negative regulation and dotted-line arrow indicates that the regulatory mechanism is unclear. White boxes with blue lines represent lncRNAs, light green boxes represent different developmental events or stresses. The letters in red denote positive regulators, while the letters in black denote negative regulators.

    • RolesSpeciesPathwaysApproachesLncRNAs
      number
      DE-LncRNAs numberRef.
      Growth and developmentSolanum lycopersicumFruit ripeningRNA-seq378[41]
      Solanum lycopersicumFruit ripeningssRNA-seq3,679677[61]
      Solanum lycopersicumFruit expansion and
      ripening
      ssRNA-seq17,674tissue- and stage-dependent[60]
      Solanum lycopersicumRIN target lncRNAs; fruit ripeningChIP-seq & RNA-seq187[38]
      Solanum lycopersicumFruit ripeningintegrate 134 data sets79,322tissue- and stage- specificity[22]
      Capsicum chinense Jacq.Fruit ripeningRNA-seq20,5631,1826[64]
      Capsicum annuumFruit ripeningRNA-seq11,999366[65]
      Capsicum annuumFruit developmentssRNA-seq2,5051,066[66]
      Brassica rapaVernalizationRNA-seq1,961254[42]
      Brassica rapa var. pekinensisVernalizationRNA-seq2,088549[68]
      Brassica
      campestris ssp. pekinensis
      VernalizationssRNA-seq1,858151[69]
      Brassica rapaPollen developmentRNA-seq12,05114[43]
      Brassica rapa ssp. pekinensisAnther developmentSMRT407[34]
      Brassica campestris ssp. pekinensisAnther developmentRNA-seq2,3841,344[72]
      Brassica rapa ssp. pekinensisCytoplasmic male sterilityRNA-seq3,312529[74]
      Brassica
      campestris
      Male sterileRNA-seq13,879361[73]
      Capsicum annuumCytoplasmic male sterilityeRNA-seq10,6551,137[75]
      Solanum lycopersicumSperm cell lineage
      development
      ssRNA-seq31,931cell/tissue-type specificity[76]
      Capsicum annuumAnthocyanin biosynthesisssRNA-seq172[44]
      Solanum tuberosumAnthocyanin BiosynthesisssRNA-seq4,3761,421[80]
      Solanum tuberosumAnthocyanin BiosynthesisRNA-seq1,0726[81]
      Daucus carotaAnthocyanin biosynthesisRNA-seq7,288639[82]
      Solanum lycopersicumTrichome formationssRNA-seq1,303196[83]
      Solanum tuberosumPotato tuber sproutingRNA-seq3,175723[87]
      Spinacia oleraceaFloweringRNA-seq1,141111[89]
      Spinacia oleraceaSex differentiationPacBio Iso-seq & RNA-seq50042[37]
      Growth and developmentBrassica napusOil
      biosynthesis
      ssRNA-seq & RNA-seq datasets8,90513[90]
      Brassica oleracea
      var. capitata
      Cuticular wax
      biosynthesis
      RNA-seq4,459148[91]
      Abiotic stressSolanum lycopersicumDrought responseRNA-seq521244[45]
      Solanum lycopersicumdrought-responseRNA-seq67,7703,053[103]
      Brassica napusDrought responseRNA-seq-477/706[104]
      Solanum tuberosumDrought responseNGS & SMRT3,445[105]
      Brassica rapaHeat responsessRNA-seq4,5941,686[46]
      Brassica junceaHeat and drought responseRNA-seq7,6131,614[107]
      Brassica rapaHeat responseRNA-seq18,2531,229[15]
      Brassica rapa ssp. pekinensisHeat responseRNA-seq27865[106]
      Brassica rapa ssp. chinensis
      (NHCC)
      Cold and heat responseRNA-seq10,0012,236[108]
      Cucumis sativus Heat responseRNA-seq2,085108[109]
      Raphanus sativusHeat responsessRNA-seq169[110]
      Solanum lycopersicumChilling injuryRNA-seq1,411239[47]
      Capsicum annuumChilling injuryRNA-seq9,848 380[111]
      Solanum lycopersicumFruit crackingRNA-seq2,508[112]
      Solanum pennellii and M82Salt responsessRNA-seq1,044154/137[48]
      Cucumis sativusWaterlogging responseRNA-seq3,738922/514/1,476/
      1,270
      [115]
      Cucumis sativusPhosphate-deficiency
      response
      ssRNA-seq14,27722[121]
      Brassica
      napus
      Cadmium toxic responsessRNA-seq5,038301[126]
      Biotic stress
      Solanum tuberosumPhytophthora infestans resistanceRNA-seq2,857133[49]
      Solanum lycopersicumPhytophthora
      infestans resistance
      RNA-seq28,256688[130]
      Solanum lycopersicum L3708Phytophthora
      infestans resistance
      RNA-seq9,011196[131]
      Solanum lycopersicumTYLCV resistancessRNA-seq1,565529[50]
      Solanum lycopersicumTYLCV resistancessRNA-seq2,056345[138]
      Biotic stress
      Solanum lycopersicumBacillus subtilis SL18r-induced tomato resistance against Botrytis cinereaRNA-seq55/34/15[51]
      Solanum lycopersicumPseudomonas putida Sneb821- induced tomato resistance against Meloidogyne incognitaRNA-seq3,37178[140]
      Solanum lycopersicumPst resistanceRNA-seq2,609Different in each comparison[52]
      Solanum lycopersicumPSTVd resistanceRNA-seq6,72644[141]
      Brassica campestris ssp.chinensis Makino Plasmodiophora brassicae resistanceRNA-seq1,492114[143]
      Brassica napusPlasmodiophora brassicae resistancessRNA-seq4,558530[144]
      Brassica rapa ssp. pekinensisDowny mildew resistanceRNA-seq3,711[145]
      Brassica napusSclerotinia sclerotiorum resistanceRNA-seq3,181931[142]
      Brassica rapaFusarium oxysporum
      resistance
      qPCR[146]
      Capsicum
      annuum
      Phytophthora
      capsica resistance
      RNA-seq2,388607[147]
      Solanum tuberosum Pectobacterium carotovorum resistancessRNA-seq1,113559[148]
      Solanum tuberosum Potato Virus Y resistance and heat stressRNA-seq4,007421[149]
      Cucumis sativusPowdery mildew resistancessRNA-seq12,903119[150]
      OthersSolanum lycopersicumEthylene signalingRNA-seq39712[151]
      Solanum
      pimpinellifolium LA1589,
      S. lycopersicum Heinz1706
      Lycopersicon specificityssRNA-seq413/70992/161[152]
      Brassica napus, B. oleracea and
      B. rapa
      Species divergenceRNA-seq1,885/1,910/
      1,299
      186 /157/161[153]
      Capsicum chinenseHeterosis effectssRNA-seq2,5251,932/ 593[154]
      Cucumis hytivusAllopolyploidizationRNA-seq2,2061,328[155]
      Brassica rapa, B. carinata, and
      B. hexaploid
      PolyploidizationRNA-seq2,725/1,672/
      2,810
      725[156]

      Table 1. 

      List of long non-coding RNAs (lncRNAs) identified in major vegetable crops.

    • SpeciesLncRNA nameBiological functionsInteraction targetsReferences
      Solanum lycopersicumlncRNA000170Trichome formationSolyc10g006360[83]
      lncRNA1459, lncRNA1840Fruit ripening[61, 62]
      lncRNA2155Fruit ripeningRIN[38]
      ACoS-AS1Trans-splicing; carotenoids biosynthesisSlPSY1[63]
      lncRNA33732Resistance to Phytophthora infestansRBOH[132]
      lncRNA16397Resistance to Phytophthora infestansSlGRX21, SlGRX22[130]
      lncRNA15492Resistance to Phytophthora infestansSl-miR482a[133]
      lncRNA08489Resistance to Phytophthora infestansmiR482e-3p[134]
      lncRNA23468Resistance to Phytophthora infestansmiR-482b[135]
      lncRNA39026Resistance to Phytophthora infestansmiR-168a[136]
      lncRNA40787Resistance to Phytophthora infestansmiR394[137]
      lncRNA42705, lncRNA08711Resistance to Phytophthora infestansmiR159[131]
      slylnc0049, slylnc0761Resistance to TYLCV[50]
      S-slylnc0957Resistance to TYLCV[138]
      SlLNR1Resistance to TYLCV[139]
      MSTRG18363Bacillus subtilis SL18r-induced tomato resistance against Botrytis cinereamiR1918[51]
      lncRNA44664,Pseudomonas putida Sneb821- induced tomato resistance against Meloidogyne incognitamiR396[140]
      lncRNA48734Pseudomonas putida Sneb821- induced tomato resistance against Meloidogyne incognitamiR156[140]
      Brassica oleraceaBoNR8Seed germination; root and silique growth[21]
      Brassica rapabra-eTM160-1, bra-eTM160-2Pollen developmentmiR160-5p[43]
      Brassica rapa ssp. pekinensisMSTRG.19915Resistance to downy mildewBrMAPK15[145]
      Brassica campestrisbra-miR5718HGPollen tube growthmiR5718[73]
      BcMF11Pollen development; male fertility[39, 40]
      Solanum tuberosumStFLORETuber development; drought responseStCDF1[88]
      StLNC0004Resistance to Phytophthora infestansNbEXT[49]

      Table 2. 

      Summary of functionally validated lncRNAs in major vegetables.