title: Small RNA and degradome sequencing reveal complex miRNA regulation during cotton somatic embryogenesis.
abstract: 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.
authors: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China.
authors: Xiyan
authors: X
authors: Yang
authors: Lichen
authors: L
authors: Wang
authors: Daojun
authors: D
authors: Yuan
authors: Keith
authors: K
authors: Lindsey
authors: Xianlong
authors: X
authors: Zhang
mesh_terms: D001483:Base Sequence; D019295:Computational Biology; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D015723:Gene Library; D003368:Gossypium / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism; D059014:High-Throughput Nucleotide Sequencing; D035683:MicroRNAs / Q000235:genetics / Q000378:metabolism*; D008969:Molecular Sequence Data; D058439:Plant Somatic Embryogenesis Techniques; D059367:RNA Cleavage; D018749:RNA, Plant / Q000032:analysis* / Q000235:genetics; D034741:RNA, Small Interfering / Q000235:genetics / Q000378:metabolism; D012639:Seeds / Q000235:genetics / Q000254:growth & development / Q000378:metabolism; D017423:Sequence Analysis, RNA / Q000379:methods*; D014158:Transcription, Genetic
chemical_list: D035683:MicroRNAs; D018749:RNA, Plant; D034741:RNA, Small Interfering
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