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Open Access Highly Accessed Research article

High throughput sequencing of two celery varieties small RNAs identifies microRNAs involved in temperature stress response

Meng-Yao Li, Feng Wang, Zhi-Sheng Xu, Qian Jiang, Jing Ma, Guo-Fei Tan and Ai-Sheng Xiong*

Author Affiliations

State Key Laboratory of Crop Genetics and Germplasm Enhancement, Ministry of Agriculture Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China; College of Horticulture, Nanjing Agricultural University, Nanjing, People’s Republic China

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BMC Genomics 2014, 15:242  doi:10.1186/1471-2164-15-242

Published: 27 March 2014

Abstract

Background

MicroRNAs (miRNAs) are small, non-coding RNAs of 20 to 24 nucleotides that regulate gene expression and responses to biotic and abiotic stress. Till now, no reports have previously been published concerning miRNAs in celery.

Results

Two small RNAs libraries were constructed from two celery varieties, ‘Jinnan Shiqin’ and ‘Ventura’, and characterized by deep sequencing. A total of 431 (418 known and 13 novel) and 346 (341 known and five novel) miRNAs were identified in celery varieties ‘Jinnan Shiqin’ and ‘Ventura’, respectively. Potential miRNA-target genes were predicted and annotated by screening diverse protein databases, including Gene Ontology, Cluster of Orthologous Groups and Kyoto Encyclopedia of Genes and Genomes. Significant differential expression between the two varieties was seen for 221 miRNAs. qRT-PCR was used to analyze the abundance of six miRNAs under cold and heat stress conditions. The results showed that miRNAs may have important functions in controlling temperature stress in celery.

Conclusion

A large number of miRNAs were identified in celery, and their target genes, functional annotations, and gene expression patterns have been explored.

These findings provide the first information on celery miRNAs and enhance understanding of celery miRNA regulatory mechanisms under extreme temperature stress.

Keywords:
microRNAs; Temperature stress; Deep sequencing; qRT-PCR; Celery