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. 2014 Mar 27:15:242.
doi: 10.1186/1471-2164-15-242.

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, Ai-Sheng Xiong  1
Affiliations

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

Meng-Yao Li et al. BMC Genomics. .

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.

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Figures

Figure 1
Figure 1
Length distributions of small RNAs in two celery varieties.
Figure 2
Figure 2
Numbers of identical miRNA members in each family in ‘Jinnan Shiqin’ and ‘Ventura’.
Figure 3
Figure 3
First nucleotide bias of miRNAs in ‘Jinnan Shiqin’ and ‘Ventura’.
Figure 4
Figure 4
GO categories and distribution of miRNA targets in celery.
Figure 5
Figure 5
COG function classification of consensus sequences in celery.
Figure 6
Figure 6
Expression distribution of miRNAs between ‘Jinnan Shiqin’ and ‘Ventura’.
Figure 7
Figure 7
qRT-PCR analysis of miRNAs in ‘Jinnan Shiqin’ and ‘Ventura’. CK: control check. Error bars were calculated based on three replicates.
See this image and copyright information in PMC

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