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Small RNA and degradome sequencing reveal complex miRNA regulation during cotton somatic embryogenesis.

Yang, X. and Wang, L. and Yuan, D. and Lindsey, K. and Zhang, X. (2013) 'Small RNA and degradome sequencing reveal complex miRNA regulation during cotton somatic embryogenesis.', Journal of experimental botany., 64 (6). pp. 1521-1536.


MicroRNAs (miRNAs) are endogenous non-coding ~21 nucleotide RNAs that regulate gene expression at the transcriptional and post-transcriptional levels in plants and animals. They play an important role in development, abiotic stress, and pathogen responses. miRNAs with their targets have been widely studied in model plants, but limited knowledge is available on the small RNA population of cotton (Gossypium hirsutum)—an important economic crop, and global identification of related targets through degradome sequencing has not been developed previously. In this study, small RNAs and their targets were identified during cotton somatic embryogenesis (SE) through high-throughput small RNA and degradome sequencing, comparing seedling hypocotyl and embryogenic callus (EC) of G. hirsutum YZ1. A total of 36 known miRNA families were found to be differentially expressed, of which 19 miRNA families were represented by 29 precursors. Twenty-five novel miRNAs were identified. A total of 234 transcripts in EC and 322 transcripts in control (CK) were found to be the targets of 23 and 30 known miRNA families, respectively, and 16 transcripts were targeted by eight novel miRNAs. Interestingly, four trans-acting small interfering RNAs (tas3-siRNAs) were also found in degradome libraries, three of which perfectly matched their precursors. Several targets were further validated via RNA ligase-mediated rapid amplification of 5’ cDNA ends (RLM 5’-RACE). The profiling of the miRNAs and their target genes provides new information on the miRNAs network during cotton SE.

Item Type:Article
Keywords:Degradome, Gossypium hirsutum, High throughput small RNA sequencing, miRNAs, miRNA target genes, Somatic embryogenesis, tas3-siRNA.
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Publisher statement:© The Authors [2013]. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (, which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact
Date accepted:No date available
Date deposited:29 May 2014
Date of first online publication:April 2013
Date first made open access:No date available

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