Small RNA and degradome deep sequencing reveal respective roles of cold-related microRNAs across Chinese wild grapevine and cultivated grapevine

Pengfei Wang,Fengshan Ren,Yongmei Wang,Hongmei Shi,Yang Yang

doi:10.1186/s12864-019-6111-5

Pengfei Wang, Fengshan Ren + Show 3 more

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https://doi.org/10.1186/s12864-019-6111-5

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Abstract

BackgroundChinese wild grapevine (Vitis amurensis) has remarkable cold stress tolerance, exceeding that of the common cultivated grapevine (Vitis vinifera L.).ResultHere, we surveyed the expression dynamics of microRNAs (miRNAs) across Chinese wild grapevine (cv. Beibinghong) and cultivated grapevine (cv. Cabernet Sauvignon) under cold stress using high-throughput sequencing. We identified 186 known miRNAs in cultivated grape and 427 known miRNAs in Beibinghong. Of the identified miRNAs, 59 are conserved miRNAs orthologous in Cabernet Sauvignon and Beibinghong. In addition, 105 and 129 novel miRNAs were identified in Cabernet Sauvignon and Beibinghong, respectively. The expression of some miRNAs was related to cold stress both in Cabernet Sauvignon and Beibinghong. Many cold-related miRNAs in Cabernet Sauvignon and Beibinghong were predicted to target stress response-related genes such as MYB, WRKY, bHLH transcription factor genes, and heat shock protein genes. However, the expression tendency under cold treatment of many of these miRNAs was different between Cabernet Sauvignon and Beibinghong. Different modes of expression of cultivated and Chinese wild grape miRNAs were indicated in key pathways under cold stress by degradome, target prediction, GO, and KEGG analyses.ConclusionOur study indicated three likely reasons that led to the different cold stress tolerance levels of Cabernet Sauvignon and Beibinghong. Specifically, there may be (1) differential expression of orthologous miRNAs between cultivated grapevine and Chinese wild grape; (2) species-specific miRNAs or target genes; or (3) different regulatory models of miRNAs in cultivated and Chinese wild grape in some key pathways.

Highlights

Chinese wild grapevine (Vitis amurensis) has remarkable cold stress tolerance, exceeding that of the common cultivated grapevine (Vitis vinifera L.)
MicroRNA is an 18–24 nucleotide-long noncoding small RNA that can regulate gene expression by blocking protein translation through binding with the 3′ untranslated region (3’UTR) of the target gene mRNA in animals [1]
Cold stress could activate the Inducer of C-REPEAT BINDING FACTOR (CBF) Expression (ICE) gene, which is a type of basic helix-loop-helix gene, via the ABAindependent pathway [1, 11,12,13,14], and ICE may activate the downstream transcription factor C-repeat (CRT)-binding factors (CBF) or dehydration-responsive element binding (DREB) that binds to C-repeat elements (CRT)/lowtemperature-response elements (LTRE) [1, 11]

Summary

Introduction

Chinese wild grapevine (Vitis amurensis) has remarkable cold stress tolerance, exceeding that of the common cultivated grapevine (Vitis vinifera L.). MicroRNA (miRNA) is an 18–24 nucleotide-long noncoding small RNA (sRNA) that can regulate gene expression by blocking protein translation through binding with the 3′ untranslated region (3’UTR) of the target gene mRNA in animals [1]. MiRNAs can negatively regulate target gene mRNA by two major mechanisms: transcript cleavage and translational inhibition [2, 3]. Cold stress could activate the Inducer of CBF Expression (ICE) gene, which is a type of basic helix-loop-helix (bHLH) gene, via the ABAindependent pathway [1, 11,12,13,14], and ICE may activate the downstream transcription factor C-repeat (CRT)-binding factors (CBF) or dehydration-responsive element binding (DREB) that binds to C-repeat elements (CRT)/lowtemperature-response elements (LTRE) [1, 11].

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