Global micro RNA modification in cotton ( Gossypium hirsutum L.)

Summary Micro RNA s (mi RNA s) are small noncoding RNA s participating in versatile biological processes via post‐transcriptionally gene regulation. However, how mi RNA s are modified or degraded remains unknown, despite years of studies have unravelled much details of mi RNA biogenesis and function. Here, we systematically investigated mi RNA modification using six small RNA sequencing libraries generated from cotton seedling as well as cotton fibre at five developmental stages. Our results show that 1–2‐nt truncation and addition on both 5′ and 3′ ends of mi RNA s are the major modification forms. The 5′ and 3′ end mi RNA modification was almost equal in the six development stages. Truncation was more common than addition on both 5′ and 3′ end. Structure analysis of the 5′ and 3′ ends of mi RNA s and isomiRs shows that uridine is the preferential nucleotide at the first position of both 5′ and 3′ ends. According to analysis of nucleotides truncated and tailed from mi RNA s, both mi RNA s and isomiRs share a similar positional structure distribution at their 5′ and 3′ ends, respectively. Furthermore, opposite to previous reports, cytodine is more frequently truncated and tailed from the two ends of isomiRs, implying existence of a complex cytodine balance in isomiRs. Comparison of isomiR expression shows differential mi RNA modification amongst the six developmental stages in terms of selective modification form, development‐dependent modification and differential expression abundance. Our results globally uncovered mi RNA modification features in cotton, which could contribute us to understanding mi RNA 's postmature modification and its regulatory function.