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SRNAome and degradome sequencing analysis reveals specific regulation of sRNA in response to chilling injury in tomato fruit
Author(s) -
Zuo Jinhua,
Wang Qing,
Han Cong,
Ju Zheng,
Cao Dongyan,
Zhu Benzhong,
Luo Yunbo,
Gao Lipu
Publication year - 2017
Publication title -
physiologia plantarum
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.351
H-Index - 146
eISSN - 1399-3054
pISSN - 0031-9317
DOI - 10.1111/ppl.12509
Subject(s) - small interfering rna , small rna , biology , trans acting sirna , microrna , gene silencing , rna , rna silencing , gene , rna interference , deep sequencing , computational biology , genetics , microbiology and biotechnology , genome
Plant genomes encode diverse small RNA classes that function in distinct gene‐silencing pathways. To elucidate the intricate regulation of microRNAs ( miRNAs ) and endogenous small‐interfering RNAs ( siRNAs ) in response to chilling injury in tomato fruit, the deep sequencing and bioinformatic methods were combined to decipher the small RNAs landscape in the control and chilling‐injured groups. Except for the known miRNAs and ta‐ siRNAs , 85 novel miRNAs and 5 ta‐ siRNAs members belonging to 3 TAS families ( TAS5 , TAS9 and TAS10 ) were identified, 34 putative phased small RNAs and 740 cis / trans ‐natural antisense small‐interfering RNAs (nat‐ siRNAs ) were also found in our results which enriched the tomato small RNAs repository. A large number of genes targeted by those miRNAs and siRNAs were predicted to be involved in the chilling injury responsive process and five of them were verified via degradome sequencing. Based on the above results, a regulatory model that comprehensively reveals the relationships between the small RNAs and their targets was set up. This work provides a foundation for further study of the regulation of miRNAs and siRNAs in the plant in response to chilling injury.