High-throughput analysis of small RNAs and characterization of novel microRNAs affected by abiotic stress in a local celery cultivar

• Deep sequencing was performed to identify small RNAs in a local celery cultivar.
• The rRNA, tRNA, snRNA, snoRNA and repeat sequences were annotated to the sRNAs.
• Thirty-five known families and 11 novel miRNAs were identified.
• Five novel miRNAs were up-regulated by abiotic stress; five were down-regulated.
• First miRNAs characterization by high-throughput deep sequencing in celery.

‘Liuhe Huangxinqin’, a Chinese celery cultivar, has yellow or pale green leaves, which distinguishes it from other celery cultivars. This study characterized the various sRNAs identified by deep sequencing and clarified how the novel microRNAs (miRNAs) responded to abiotic stresses (heat, cold, salinity and drought). A total of 3,243,608 clean reads and 1,028,137 unique reads ranging from 16 to 30 nucleotides were obtained. By aligning them to multiple databases, the rRNA, tRNA, snRNA, snoRNA and repeat sequences were annotated to the small RNAs (sRNAs). Four hundred fifty-seven unique reads, belonging to 35 known miRNA families, and 12 novel miRNAs were identified. The average minimum free energy index value of the novel miRNAs was 0.89, with a range of 0.50–1.39. Five novel miRNAs were showed to be up-regulated by abiotic stress; six novel miRNAs were down-regulated by abiotic stress. A total of 8 potential target genes were predicted for 3 out of 12 novel miRNAs by Targetfinder. The analysis of putative targets and miRNAs indicated that the novel miRNAs played multiple roles in abiotic related gene regulation process in celery.