In-silico identification and analysis of miRNAs from germinating seeds in Paris polyphylla var. yunnanensis by deep sequencing

Abstract

Paris polyphylla var. yunnanensis is a traditional Chinese medicine and the morphophysiological dormancy in seeds severally limits the materials supply in pharmacy. MicroRNAs (miRNAs) comprise key regulatory modules in the process of seed dormancy and germination. However, little is known about the role of miRNAs during seed germination in this species. Here, P. polyphylla var. yunnanensis seeds were primed with 200 mg/L GA and incubated at constant 20 °C. This protocol caused to the initiation of seed germination in the 20th day and the achievement of 80% germination rate in the 80th day. High-throughput sequencing was employed to identify and characterize miRNAs in six libraries (20d, 40d and 60d of germinating seeds) combined with their corresponding transcriptome data. A total of 293 known miRNAs and 692 putative novel miRNAs were identified based on the assembled 122,933 unigenes with the mean length of 1040 bp. The predicted targets of these miRNAs were enriched in the cell, metabolism and genetic information processing during seed germination, in which transport, primary metabolic process and translation were the most abundant, respectively. Our results will provide a new molecular basis about seed germination in P. polyphylla var. yunnanensis.