Uncover small RNAs in citrus somatic embryogenesis. Citrus sinensis

To uncover the involvement of miRNAs and siRNAs in somatic embryogenesis of the perennial woody crop citrus, we carried out high-throughput (Illumina) sequencing (HTS) of sRNAs and RNA degradome tags in non-embryogenic and embryogenic tissue of Valencia sweet orange. A total of 191 stem-loop structures were identified, emanating 50 known and 45 novel miRNAs, 130 miniature inverted-repeat transposable elements (MITEs) derived small interfering RNAs (siRNAs) and 94 other siRNAs. Combining with the result of degradome sequencing, a total of 235 phased siRNAs (phasiRNAs), and 195 cleaved target genes were identified for miRNAs/siRNAs. Overall design: Small RNA and degradome libraries of nonembryogenic callus (NEC), embryogenic callus (EC) and embryogenic callus exposed to somatic embryo induction for 1, 2, 3, 4 weeks (E1-4) of Valencia sweet orange (Citrus sinensis) were sequenced by Illumina platform, one biological replicates