Identification of tRFs and phasiRNAs in tomato (Solanum lycopersicum) and their responses to exogenous abscisic acid

Abstract Background The non-coding small RNA tRFs (tRNA-derived fragments) and phasiRNAs (plant-specific) exert important roles in plant growth, development and stress resistances. However, whether the tRFs and phasiRNAs respond to the plant important stress hormone abscisic acid (ABA) remain enigma...

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Main Authors: Wei Luan, Ya Dai, Xin-Yu Li, Yan Wang, Xiang Tao, Cai-Xia Li, Ping Mao, Xin-Rong Ma
Format: Article
Language:English
Published: BMC 2020-07-01
Series:BMC Plant Biology
Subjects:
Online Access:http://link.springer.com/article/10.1186/s12870-020-02528-8
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author Wei Luan
Ya Dai
Xin-Yu Li
Yan Wang
Xiang Tao
Cai-Xia Li
Ping Mao
Xin-Rong Ma
author_facet Wei Luan
Ya Dai
Xin-Yu Li
Yan Wang
Xiang Tao
Cai-Xia Li
Ping Mao
Xin-Rong Ma
author_sort Wei Luan
collection DOAJ
description Abstract Background The non-coding small RNA tRFs (tRNA-derived fragments) and phasiRNAs (plant-specific) exert important roles in plant growth, development and stress resistances. However, whether the tRFs and phasiRNAs respond to the plant important stress hormone abscisic acid (ABA) remain enigma. Results Here, the RNA-sequencing was implemented to decipher the landscape of tRFs and phasiRNAs in tomato (Solanum lycopersicum) leaves and their responses when foliar spraying exogenous ABA after 24 h. In total, 733 tRFs and 137 phasiRNAs were detected. The tRFs were mainly derived from the tRNAAla transporting alanine, which tended to be cleaved at the 5 ’ terminal guanine site and D loop uracil site to produce tRFAla with length of 20 nt. Most of phasiRNAs originated from NBS-LRR resistance genes. Expression analysis revealed that 156 tRFs and 68 phasiRNAs expressed differentially, respectively. Generally, exogenous ABA mainly inhibited the expression of tRFs and phasiRNAs. Furthermore, integrating analysis of target gene prediction and transcriptome data presented that ABA significantly downregulated the abundance of phsaiRNAs associated with biological and abiotic resistances. Correspondingly, their target genes such as AP2/ERF, WRKY and NBS-LRR, STK and RLK, were mainly up-regulated. Conclusions Combined with the previous analysis of ABA-response miRNAs, it was speculated that ABA can improve the plant resistances to various stresses by regulating the expression and interaction of small RNAs (such as miRNAs, tRFs, phasiRNAs) and their target genes. This study enriches the plant tRFs and phasiRNAs, providing a vital basis for further investigating ABA response-tRFs and phasiRNAs and their functions in biotic and abiotic stresses.
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spelling doaj.art-8a3512ebc86f444f85cf9799fec6b8602022-12-21T18:52:33ZengBMCBMC Plant Biology1471-22292020-07-0120111410.1186/s12870-020-02528-8Identification of tRFs and phasiRNAs in tomato (Solanum lycopersicum) and their responses to exogenous abscisic acidWei Luan0Ya Dai1Xin-Yu Li2Yan Wang3Xiang Tao4Cai-Xia Li5Ping Mao6Xin-Rong Ma7Chengdu Institute of Biology, Chinese Academy of SciencesChengdu Institute of Biology, Chinese Academy of SciencesChengdu Institute of Biology, Chinese Academy of SciencesChengdu Institute of Biology, Chinese Academy of SciencesChengdu Institute of Biology, Chinese Academy of SciencesChengdu Institute of Biology, Chinese Academy of SciencesChengdu Institute of Biology, Chinese Academy of SciencesChengdu Institute of Biology, Chinese Academy of SciencesAbstract Background The non-coding small RNA tRFs (tRNA-derived fragments) and phasiRNAs (plant-specific) exert important roles in plant growth, development and stress resistances. However, whether the tRFs and phasiRNAs respond to the plant important stress hormone abscisic acid (ABA) remain enigma. Results Here, the RNA-sequencing was implemented to decipher the landscape of tRFs and phasiRNAs in tomato (Solanum lycopersicum) leaves and their responses when foliar spraying exogenous ABA after 24 h. In total, 733 tRFs and 137 phasiRNAs were detected. The tRFs were mainly derived from the tRNAAla transporting alanine, which tended to be cleaved at the 5 ’ terminal guanine site and D loop uracil site to produce tRFAla with length of 20 nt. Most of phasiRNAs originated from NBS-LRR resistance genes. Expression analysis revealed that 156 tRFs and 68 phasiRNAs expressed differentially, respectively. Generally, exogenous ABA mainly inhibited the expression of tRFs and phasiRNAs. Furthermore, integrating analysis of target gene prediction and transcriptome data presented that ABA significantly downregulated the abundance of phsaiRNAs associated with biological and abiotic resistances. Correspondingly, their target genes such as AP2/ERF, WRKY and NBS-LRR, STK and RLK, were mainly up-regulated. Conclusions Combined with the previous analysis of ABA-response miRNAs, it was speculated that ABA can improve the plant resistances to various stresses by regulating the expression and interaction of small RNAs (such as miRNAs, tRFs, phasiRNAs) and their target genes. This study enriches the plant tRFs and phasiRNAs, providing a vital basis for further investigating ABA response-tRFs and phasiRNAs and their functions in biotic and abiotic stresses.http://link.springer.com/article/10.1186/s12870-020-02528-8tRFphasiRNAAbscisic acid (ABA)RNA-SeqTranscription factorsResistance genes
spellingShingle Wei Luan
Ya Dai
Xin-Yu Li
Yan Wang
Xiang Tao
Cai-Xia Li
Ping Mao
Xin-Rong Ma
Identification of tRFs and phasiRNAs in tomato (Solanum lycopersicum) and their responses to exogenous abscisic acid
BMC Plant Biology
tRF
phasiRNA
Abscisic acid (ABA)
RNA-Seq
Transcription factors
Resistance genes
title Identification of tRFs and phasiRNAs in tomato (Solanum lycopersicum) and their responses to exogenous abscisic acid
title_full Identification of tRFs and phasiRNAs in tomato (Solanum lycopersicum) and their responses to exogenous abscisic acid
title_fullStr Identification of tRFs and phasiRNAs in tomato (Solanum lycopersicum) and their responses to exogenous abscisic acid
title_full_unstemmed Identification of tRFs and phasiRNAs in tomato (Solanum lycopersicum) and their responses to exogenous abscisic acid
title_short Identification of tRFs and phasiRNAs in tomato (Solanum lycopersicum) and their responses to exogenous abscisic acid
title_sort identification of trfs and phasirnas in tomato solanum lycopersicum and their responses to exogenous abscisic acid
topic tRF
phasiRNA
Abscisic acid (ABA)
RNA-Seq
Transcription factors
Resistance genes
url http://link.springer.com/article/10.1186/s12870-020-02528-8
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