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

Abstract

The importance of long non-coding RNAs (lncRNAs) in plant development has been established, but a systematic analysis of lncRNAs 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 lncRNAs. A comprehensive view of dynamic lncRNA expression networks underpinning pollen development and fertilization was provided. B. rapa lncRNAs share many common characteristics of lncRNAs: relatively short length, low expression but specific in narrow time windows, and low evolutionary conservation. Gene modules and key lncRNAs regulating reproductive development such as exine formation were uncovered. Forty-seven cis-acting lncRNAs and 451 trans-acting lncRNAs were revealed to be highly coexpressed with their target protein-coding genes. Of particular importance are the discoveries of 14 lncRNAs that were highly coexpressed with 10 function-known pollen-associated coding genes. Fifteen lncRNAs were predicted as endogenous target mimics for 13 miRNAs, and two lncRNAs 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 lncRNAs during pollen development and fertilization in B. rapa and forms the foundation for future genetic, genomic, and evolutionary studies.

Transcriptome analysis implicates involvement of long noncoding RNAs in cytoplasmic male sterility and fertility restoration in cotton

“…4b). The miRNA binding sequences were well conserved and the bulge region frequently varied among different species, consistent with previous studies of Arabidopsis and rice [18] and Brassica [19]. Further analysis is necessary to understand the role of the two lncRNAs predicted to be eTMs.…”

“…In the present study, 80,695 lncRNAs were identified by analyzing almost 910 million clean reads, of which 18,755, 20,837, and 21,346 unique lncRNAs were specifically expressed in the A, B, and R lines, respectively. As previously reported [14], we observed that the number of identified lncRNAs during anther development is larger than the numbers identified in Arabidopsis, maize, and Gossypium arboreum [7,8,20] but similar to the numbers identified in wheat [15], Brassica rapa [19], analysis indicated that genes that show transcription regulator activity (GO: 0030528) and involved in morphogenesis (GO: 0010927) might perform critical roles in pollen exine formation [19]. In the current study, 43,347 and 44,739 lncRNAs were differentially expressed in the A-B and A-R comparisons, respectively.…”

“…For example, the lncRNA IPS1 in Arabidopsis acts as an eTM of ath-miR399 to regulate PHOS2 and a 3 nt bulge is present in the 10th and 11th nt positions of the miRNA [16]. In Brassica, two lncRNAs are eTMs of miR160 and function in pollen formation and male fertility [19]. In tomato, a lncRNA acts as an eTM of miR166 and may regulate Tomato yellow leaf curl virus resistance [45].…”

Systematic identification of long noncoding RNAs expressed during light‐induced anthocyanin accumulation in apple fruit

“…Previous studies functionally characterized eTMs of miR160 in A. thaliana and rice (Wu et al ., ), and similar eTMs for miR160 have been reported for Populus trichocarpa (Zhou et al ., ), Brassica rapa (Huang et al ., ), banana ( Musa spp.) (Muthusamy et al ., ) and others.…”

“…A rapidly increasing number of lncRNAs have been identified in plants and associated with various biological processes, including fruit ripening (Tang et al ., ; Li et al ., ), reproduction (Zhang et al ., ,b; Huang et al ., ), disease resistance (Zhang et al ., ), stress responses (Qin et al ., ), photomorphogenesis (Wang et al ., ) and phosphate homeostasis (Franco‐Zorrilla et al ., ).…”