Long Non-Coding RNAs as Endogenous Target Mimics and Exploration of Their Role in Low Nutrient Stress Tolerance in Plants
Abstract
:1. Introduction
2. Role of lncRNAs as Endogenous Target Mimics for MicroRNAs
3. Long non-coding RNAs Expressed under Nitrogen and Phosphorus Deprivation
4. Putative Endogenous Target Mimics under Low Nitrogen and Phosphate Stress
5. Conclusions and Future Prospects
Funding
Conflicts of Interest
References
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Name | Features | Links | Reference |
---|---|---|---|
TAPIR | Only tool for the TM prediction in plants; applies Franco-Zorrilla rule for target mimicry; contains data for 10 plant species; RNA hybrid and miRBase are the data sources | http://bioinformatics.psb.ugent.be/webtools/tapir/ | [55] |
miRSponge | 1.6% data is from plant and others are of non-plant; experimentally validated; literature mining is the data source | http://www.bio-bigdata.net/miRSponge/ | [57] |
PeTMbase | Contains 2728 TMs for 11 species; uses Wu et al. (2013) target mimicry rule; GreeNC, PNRD, miRBase, NCBI SRA are the data sources | http://petmbase.org | [56] |
PceRBase | First database for plant TMs; 167608 TMs from 26 plant species; Phytozomev10, TAIR10, MSU RGGP & miRBase and literature are the data sources | http://bis.zju.edu.cn/pcernadb/ | [58] |
miRNA ID | eTM ID | lncRNA ID | Low N | Low P | References |
---|---|---|---|---|---|
ath-miR156a-5p | ath_eTM_miR156a-5p-2 | GRNC_ath_lcl|Athaliana_AT1G52347.1 gene = AT1G52347 | A. thaliana (P↑) | [112] | |
ath_eTM_miR156a-5p-1 | PNRD_ath_NONATHT000580 | ||||
ath-miR156b-5p | ath_eTM_miR156b-5p-2 | GRNC_ath_lcl|Athaliana_AT1G52347.1 gene = AT1G52347 | A. thaliana (N↑) | [113] | |
ath_eTM_miR156b-5p-1 | PNRD_ath_NONATHT000580 | ||||
ath-miR156c-5p | ath_eTM_miR156c-5p-2 | GRNC_ath_lcl|Athaliana_AT1G52347.1 gene = AT1G52347 | A. thaliana (N↑) | [113] | |
ath_eTM_miR156c-5p-1 | PNRD_ath_NONATHT000580 | ||||
ath-miR156d-5p | ath_eTM_miR156d-5p-2 | GRNC_ath_lcl|Athaliana_AT1G52347.1 gene = AT1G52347 | A. thaliana (N↑) | [113] | |
ath_eTM_miR156d-5p-1 | PNRD_ath_NONATHT000580 | ||||
ath-miR156e | ath_eTM_miR156e-2 | GRNC_ath_lcl|Athaliana_AT1G52347.1 gene = AT1G52347 | A. thaliana (N↑) | [113] | |
ath_eTM_miR156e-1 | PNRD_ath_NONATHT000580 | ||||
gma-miR156e | gma_eTM_miR156e-3 | GRNC_gma_lcl|Gmax_Glyma.18G293400.2 | Soybean (P↑) | [114] | |
gma_eTM_miR156e-2 | GRNC_gma_lcl|Gmax_Glyma.18G293400.1 | ||||
gma_eTM_miR156e-1 | GRNC_gma_lcl|Gmax_Glyma.05G242200.1 | ||||
ath-miR156f-5p | ath_eTM_miR156f-5p-2 | GRNC_ath_lcl|Athaliana_AT1G52347.1 gene = AT1G52347 | A. thaliana (N↑) | [113] | |
ath_eTM_miR156f-5p-1 | PNRD_ath_NONATHT000580 | ||||
ath-miR156g | ath_eTM_miR156g-2 | GRNC_ath_lcl|Athaliana_AT1G52347.1 gene = AT1G52347 | A. thaliana (N↑) | [113] | |
ath_eTM_miR156g-1 | PNRD_ath_NONATHT000580 | ||||
ath-miR156h | ath_eTM_miR156h-3 | GRNC_ath_lcl|Athaliana_AT3G18217.1 gene = AT3G18217 | A. thaliana (N↑) | [113] | |
ath_eTM_miR156h-2 | GRNC_ath_lcl|Athaliana_AT1G52347.1 gene = AT1G52347 | ||||
ath_eTM_miR156h-1 | PNRD_ath_NONATHT000580 | ||||
gma-miR159a-3p | gma_eTM_miR159a-3p-1 | gma_TCONS_00088249 | Soybean (P↑) | [114] | |
tae-miR159b | tae_eTM_miR159b-2 | GRNC_tae_lcl|Taestivum_Traes_2DS_9A9CAF0B0.1 | Wheat(P↑) | [115] | |
tae_eTM_miR159b-1 | GRNC_tae_lcl|Taestivum_Traes_1AL_8C8E43898.1 | ||||
zma-miR160a-3p | zma_eTM_miR160a-3p-1 | GRNC_zma_lcl|Zmays_AC211588.3_FGT002 | Maize (N↑) | [116] | |
zma-miR160a-5p | zma_eTM_miR160a-5p-5 | GRNC_zma_lcl|Zmays_GRMZM5G849473_T01 | Maize (N↑) | [116] | |
zma_eTM_miR160a-5p-4 | GRNC_zma_lcl|Zmays_GRMZM2G531719_T01 | ||||
zma_eTM_miR160a-5p-3 | GRNC_zma_lcl|Zmays_GRMZM2G149698_T05 | ||||
zma_eTM_miR160a-5p-2 | GRNC_zma_lcl|Zmays_GRMZM2G011007_T01 | ||||
zma_eTM_miR160a-5p-1 | PNRD_zma_GRMZM5G849473_T01 | ||||
zma-miR160b-5p | zma_eTM_miR160b-5p-5 | GRNC_zma_lcl|Zmays_GRMZM5G849473_T01 | Maize (N↑) | [116] | |
zma_eTM_miR160b-5p-4 | GRNC_zma_lcl|Zmays_GRMZM2G531719_T01 | ||||
zma_eTM_miR160b-5p-3 | GRNC_zma_lcl|Zmays_GRMZM2G149698_T05 | ||||
zma_eTM_miR160b-5p-2 | GRNC_zma_lcl|Zmays_GRMZM2G011007_T01 | ||||
zma_eTM_miR160b-5p-1 | PNRD_zma_GRMZM5G849473_T01 | ||||
zma-miR160c-5p | zma_eTM_miR160c-5p-5 | GRNC_zma_lcl|Zmays_GRMZM5G849473_T01 | Maize (N↑) | [116] | |
zma_eTM_miR160c-5p-4 | GRNC_zma_lcl|Zmays_GRMZM2G531719_T01 | ||||
zma_eTM_miR160c-5p-3 | GRNC_zma_lcl|Zmays_GRMZM2G149698_T05 | ||||
zma_eTM_miR160c-5p-2 | GRNC_zma_lcl|Zmays_GRMZM2G011007_T01 | ||||
zma_eTM_miR160c-5p-1 | PNRD_zma_GRMZM5G849473_T01 | ||||
zma-miR160d-3p | zma_eTM_miR160d-3p-3 | GRNC_zma_lcl|Zmays_GRMZM2G064666_T02 | Maize (N↑) | [113] | |
zma_eTM_miR160d-3p-2 | GRNC_zma_lcl|Zmays_GRMZM2G054392_T01 | ||||
zma_eTM_miR160d-3p-1 | GRNC_zma_lcl|Zmays_GRMZM2G052412_T01 | ||||
zma-miR160d-5p | zma_eTM_miR160d-5p-5 | GRNC_zma_lcl|Zmays_GRMZM5G849473_T01 | Maize (N↑) | [116] | |
zma_eTM_miR160d-5p-4 | GRNC_zma_lcl|Zmays_GRMZM2G531719_T01 | ||||
zma_eTM_miR160d-5p-3 | GRNC_zma_lcl|Zmays_GRMZM2G149698_T05 | ||||
zma_eTM_miR160d-5p-2 | GRNC_zma_lcl|Zmays_GRMZM2G011007_T01 | ||||
zma_eTM_miR160d-5p-1 | PNRD_zma_GRMZM5G849473_T01 | ||||
zma-miR160e | zma_eTM_miR160e-5 | GRNC_zma_lcl|Zmays_GRMZM5G849473_T01 | Maize (N↑) | [116] | |
zma_eTM_miR160e-4 | GRNC_zma_lcl|Zmays_GRMZM2G531719_T01 | ||||
zma_eTM_miR160e-3 | GRNC_zma_lcl|Zmays_GRMZM2G149698_T05 | ||||
zma_eTM_miR160e-2 | GRNC_zma_lcl|Zmays_GRMZM2G011007_T01 | ||||
zma_eTM_miR160e-1 | PNRD_zma_GRMZM5G849473_T01 | ||||
zma-miR160g-5p | zma_eTM_miR160g-5p-5 | GRNC_zma_lcl|Zmays_GRMZM5G849473_T01 | Maize (N↑) | [116] | |
zma_eTM_miR160g-5p-4 | GRNC_zma_lcl|Zmays_GRMZM2G531719_T01 | ||||
zma_eTM_miR160g-5p-3 | GRNC_zma_lcl|Zmays_GRMZM2G149698_T05 | ||||
zma_eTM_miR160g-5p-2 | GRNC_zma_lcl|Zmays_GRMZM2G011007_T01 | ||||
zma_eTM_miR160g-5p-1 | PNRD_zma_GRMZM5G849473_T01 | ||||
zma-miR164f-5p | zma_eTM_miR164f-5p-1 | GRNC_zma_lcl|Zmays_GRMZM2G008252_T01 | Maize (N↑) | [116] | |
zma-miR164f-3p | zma_eTM_miR164f-3p-1 | GRNC_zma_lcl|Zmays_GRMZM5G837428_T01 | Maize (N↑) | [113] | |
zma-miR166j-3p | zma_eTM_miR166j-3p-4 | GRNC_zma_lcl|Zmays_GRMZM2G134604_T01 | Maize (N↓) | [117] | |
zma_eTM_miR166j-3p-3 | zma_eTM_miR166j-3p-3 | ||||
zma_eTM_miR166j-3p-2 | zma_eTM_miR166j-3p-2 | ||||
zma_eTM_miR166j-3p-1 | zma_TCONS_00089106 | ||||
zma-miR166k-3p | zma_eTM_miR166k-3p-4 | GRNC_zma_lcl|Zmays_GRMZM2G134604_T01 | Maize (N↓) | [117] | |
zma_eTM_miR166k-3p-3 | GRNC_zma_lcl|Zmays_GRMZM2G110279_T02 | ||||
zma_eTM_miR166k-3p-2 | GRNC_zma_lcl|Zmays_GRMZM2G110279_T01 | ||||
zma_eTM_miR166k-3p-1 | zma_TCONS_00089106 | ||||
zma-miR166n-3p | zma_eTM_miR166n-3p-4 | GRNC_zma_lcl|Zmays_GRMZM2G134604_T01 | Maize (N↓) | [117] | |
zma_eTM_miR166n-3p-3 | GRNC_zma_lcl|Zmays_GRMZM2G110279_T02 | ||||
zma_eTM_miR166n-3p-2 | GRNC_zma_lcl|Zmays_GRMZM2G110279_T01 | ||||
zma_eTM_miR166n-3p-1 | zma_TCONS_00089106 | ||||
zma-miR167g-3p | zma_eTM_miR167g-3p-1 | zma_TCONS_00081049 | Maize (N↓) | [116] | |
zma-miR167g-5p | zma_eTM_miR167g-5p-2 | GRNC_zma_lcl|Zmays_GRMZM2G174168_T02 | Maize (N↓) | [116] | |
zma_eTM_miR167g-5p-1 | GRNC_zma_lcl|Zmays_GRMZM2G174168_T01 | ||||
zma-miR167h-3p | zma_eTM_miR167h-3p-7 | GRNC_zma_lcl|Zmays_GRMZM2G326635_T01 | Maize (N↓) | [116] | |
zma_eTM_miR167h-3p-6 | GRNC_zma_lcl|Zmays_GRMZM2G175272_T03 | ||||
zma_eTM_miR167h-3p-5 | GRNC_zma_lcl|Zmays_GRMZM2G159741_T04 | ||||
zma_eTM_miR167h-3p-4 | GRNC_zma_lcl|Zmays_GRMZM2G158766_T04 | ||||
zma_eTM_miR167h-3p-3 | GRNC_zma_lcl|Zmays_GRMZM2G125239_T04 | ||||
zma_eTM_miR167h-3p-2 | PNRD_zma_TCONS_00034773 | ||||
zma_eTM_miR167h-3p-1 | zma_TCONS_00012947 | ||||
zma-miR167h-5p | zma_eTM_miR167h-5p-2 | GRNC_zma_lcl|Zmays_GRMZM2G174168_T02 | Maize (N↓) | [116] | |
zma_eTM_miR167h-5p-1 | GRNC_zma_lcl|Zmays_GRMZM2G174168_T01 | ||||
gma-miR169f | gma_eTM_miR169f-3 | GRNC_gma_lcl|Gmax_Glyma.19G136600.8 | Soybean (N↑) | [118] | |
gma_eTM_miR169f-2 | GRNC_gma_lcl|Gmax_Glyma.19G136600.3 | ||||
gma_eTM_miR169f-1 | GRNC_gma_lcl|Gmax_Glyma.19G136600.2 | ||||
gma-miR169g | gma_eTM_miR169g-3 | GRNC_gma_lcl|Gmax_Glyma.19G136600.8 | Soybean (N↑) | [118] | |
gma_eTM_miR169g-2 | GRNC_gma_lcl|Gmax_Glyma.19G136600.3 | ||||
gma_eTM_miR169g-1 | GRNC_gma_lcl|Gmax_Glyma.19G136600.2 | ||||
ath-miR169a-3p | ath_eTM_miR169a-3p-2 | GRNC_ath_lcl|Athaliana_AT1G44940.2 | A. thaliana(P↓) | [113] | |
ath_eTM_miR169a-3p-1 | GRNC_ath_lcl|Athaliana_AT1G44940.1 | ||||
zma-miR319a-5p | zma_eTM_miR319a-5p-4 | GRNC_zma_lcl|Zmays_GRMZM2G438722_T03 | Maize (N↑) | [116] | |
zma_eTM_miR319a-5p-3 | zma_TCONS_00089764 | ||||
zma_eTM_miR319a-5p-2 | zma_TCONS_00089763 | ||||
zma_eTM_miR319a-5p-1 | zma_TCONS_00024738 | ||||
zma-miR395d-5p | zma_eTM_miR395d-5p-1 | zma_TCONS_00091080 | Maize (N↓) | [116] | |
zma-miR395g-5p | zma_eTM_miR395g-5p-1 | zma_TCONS_00091080 | |||
gma-miR398b | gma_eTM_miR398b-1 | GRNC_gma_lcl|Gmax_Glyma.12G204100.1 | Soybean (P↓) | [114] | |
ath-miR399f | ath_eTM_miR399f-5 | GRNC_ath_lcl|Athaliana_AT5G03545.1 | A. thaliana (N↑↓) | A. thaliana (P↑) | [113] |
ath_eTM_miR399f-4 | GRNC_ath_lcl|Athaliana_AT3G09922.1 | ||||
ath_eTM_miR399f-3 | PNRD_ath_At4-2 | ||||
ath-miR399e | ath_eTM_miR399f-2 | PNRD_ath_At4 | |||
ath_eTM_miR399f-1 | PNRD_ath_AtIPS1 | ||||
ath_eTM_miR399e-1 | GRNC_ath_lcl|Athaliana_AT1G53708.1 | A. thaliana (N↑↓) | A. thaliana (P↑) | [113] | |
ath-miR399d | ath_eTM_miR399d-5 | GRNC_ath_lcl|Athaliana_AT5G03545.1 | A. thaliana (N↑↓) | A. thaliana (P↑) | [113] |
ath_eTM_miR399d-4 | GRNC_ath_lcl|Athaliana_AT3G09922.1 | ||||
ath_eTM_miR399d-3 | PNRD_ath_At4-2 | ||||
ath-miR399b | ath_eTM_miR399d-2 | PNRD_ath_At4 | |||
ath_eTM_miR399d-1 | PNRD_ath_AtIPS1 | ||||
ath_eTM_miR399b-6 | GRNC_ath_lcl|Athaliana_AT5G03545.1 | A. thaliana (N↑↓) | A. thaliana (P↑) | [113] | |
ath_eTM_miR399b-5 | GRNC_ath_lcl|Athaliana_AT3G09922.1 | ||||
ath_eTM_miR399b-4 | GRNC_ath_lcl|Athaliana_AT1G53708.1 | ||||
ath-miR399a | ath_eTM_miR399b-3 | PNRD_ath_At4-2 | |||
ath_eTM_miR399b-2 | PNRD_ath_At4 | ||||
ath_eTM_miR399b-1 | PNRD_ath_AtIPS1 | ||||
ath_eTM_miR399a-6 | GRNC_ath_lcl|Athaliana_AT5G03545.1 | A. thaliana (N↑↓) | A. thaliana (P↑) | [113] | |
ath_eTM_miR399a-5 | GRNC_ath_lcl|Athaliana_AT3G09922.1 | ||||
ath_eTM_miR399a-4 | GRNC_ath_lcl|Athaliana_AT1G53708.1 | ||||
ath_eTM_miR399a-3 | PNRD_ath_At4-2 | ||||
ath_eTM_miR399a-2 | PNRD_ath_At4 | ||||
ath_eTM_miR399a-1 | PNRD_ath_AtIPS1 | ||||
tae-miR408 | tae_eTM_miR408-2 | GRNC_tae_lcl|Taestivum_Traes_5BL_EED36D3B9.35 | Wheat (P↓) | [115] | |
tae_eTM_miR408-1 | tae_TCONS_00103503 | ||||
osa-miR444a-3p.2 | osa_eTM_miR444a-3p.2-1 | GRNC_osa_lcl|Osativa_LOC_Os12g19080.1 | Rice((N↑) | [119] | |
ath-miR827 | ath_eTM_miR827-2 | GRNC_ath_lcl|Athaliana_AT3G02832.1 gene = AT3G02832 | A. thaliana (P↑) | [112] | |
ath_eTM_miR827-1 | PNRD_ath_NONATHT001723 | ||||
ath-miR828 | ath_eTM_miR828-1 | PNRD_ath_NONATHT000094 | A. thaliana (P↑) | [112] |
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Borah, P.; Das, A.; Milner, M.J.; Ali, A.; Bentley, A.R.; Pandey, R. Long Non-Coding RNAs as Endogenous Target Mimics and Exploration of Their Role in Low Nutrient Stress Tolerance in Plants. Genes 2018, 9, 459. https://doi.org/10.3390/genes9090459
Borah P, Das A, Milner MJ, Ali A, Bentley AR, Pandey R. Long Non-Coding RNAs as Endogenous Target Mimics and Exploration of Their Role in Low Nutrient Stress Tolerance in Plants. Genes. 2018; 9(9):459. https://doi.org/10.3390/genes9090459
Chicago/Turabian StyleBorah, Priyanka, Antara Das, Matthew J. Milner, Arif Ali, Alison R. Bentley, and Renu Pandey. 2018. "Long Non-Coding RNAs as Endogenous Target Mimics and Exploration of Their Role in Low Nutrient Stress Tolerance in Plants" Genes 9, no. 9: 459. https://doi.org/10.3390/genes9090459