Genome-wide identification and characterization of novel microRNAs in seed development of soybean

MicroRNAs (miRNAs) are important and ubiquitous regulators of gene expression in eukaryotes. However, the information about miRNAs population and their regulatory functions involving in soybean seed development remains incomplete. Base on the Dicer-like1-mediated cleavage signals during miRNA processing could be employed for novel miRNA discovery, a genome-wide search for miRNA candidates involved in seed development was carried out. As a result, 17 novel miRNAs, 14 isoforms of miRNA (isomiRs) and 31 previously validated miRNAs were discovered. These novel miRNAs and isomiRs represented tissue-specific expression and the isomiRs showed significantly higher abundance than that of their miRNA counterparts in different tissues. After target prediction and degradome sequencing data-based validation, 13 novel miRNA–target pairs were further identified. Besides, five targets of 22-nt iso-gma-miR393h were found to be triggered to produce secondary trans-acting siRNA (ta-siRNAs). Summarily, our results could expand the repertoire of miRNAs with potentially important functions in soybean.
Identification of novel microRNAs and their targets in soybean.

微小RNA（MicroRNAs, miRNAs）是真核生物中一类重要且广泛存在的基因表达调控因子。然而，目前关于大豆种子发育过程中相关miRNA的群体特征及其调控功能的信息仍不完整。基于miRNA加工过程中类Dicer酶1（Dicer-like1）介导的切割信号可用于新型miRNA发现这一策略，本研究针对参与大豆种子发育的miRNA候选物开展了全基因组筛选。最终共鉴定出17种新型miRNA、14种miRNA变体（isomiRs）以及31种已验证的已知miRNA。这些新型miRNA及其变体均呈现组织特异性表达模式，且在不同组织中，miRNA变体的表达丰度显著高于其对应的miRNA。经靶基因预测及降解组测序数据验证后，本研究进一步鉴定得到13组新型miRNA-靶基因互作对。此外，研究发现22 nt长度的iso-gma-miR393h的5个靶基因可被其切割并产生次级反式作用小干扰RNA（ta-siRNAs）。综上，本研究结果拓展了大豆中具备潜在重要调控功能的miRNA资源库。
大豆中新型微小RNA及其靶基因的鉴定