Systematic identification of long non‐coding RNA s during pollen development and fertilization in Brassica rapa

Summary The importance of long non‐coding RNA s (lnc RNA s) in plant development has been established, but a systematic analysis of lnc RNA s expressed during pollen development and fertilization has been elusive. We performed a time series of RNA ‐seq experiments at five developmental stages during pollen development and three different time points after pollination in Brassica rapa and identified 12 051 putative lnc RNA s. A comprehensive view of dynamic lnc RNA expression networks underpinning pollen development and fertilization was provided. B. rapa lnc RNA s share many common characteristics of lnc RNA s: relatively short length, low expression but specific in narrow time windows, and low evolutionary conservation. Gene modules and key lnc RNA s regulating reproductive development such as exine formation were uncovered. Forty‐seven cis ‐acting lnc RNA s and 451 trans ‐acting lnc RNA s were revealed to be highly coexpressed with their target protein‐coding genes. Of particular importance are the discoveries of 14 lnc RNA s that were highly coexpressed with 10 function‐known pollen‐associated coding genes. Fifteen lnc RNA s were predicted as endogenous target mimics for 13 mi RNA s, and two lnc RNA s were proved to be functional target mimics for miR160 after experimental verification and shown to function in pollen development. Our study provides the systematic identification of lnc RNA s during pollen development and fertilization in B. rapa and forms the foundation for future genetic, genomic, and evolutionary studies.