Genome-wide screening and functional analysis identify a large number of long noncoding RNAs involved in the sexual reproduction of rice

摘要

Background: Long noncoding RNAs (lnc RNAs) play important roles in a wide range of biological processes in mammals and plants. However, the systematic examination of lnc RNAs in plants lags behind that in mammals. Recently, lnc RNAs have been identified in Arabidopsis and wheat; however, no systematic screening of potential lnc RNAs has been reported for the rice genome. Results: In this study, we perform whole transcriptome strand-specific RNA sequencing (ss RNA-seq) of samples from rice anthers, pistils, and seeds 5 days after pollination and from shoots 14 days after germination. Using these data, together with 40 available rice RNA-seq datasets, we systematically analyze rice lnc RNAs and definitively identify lnc RNAs that are involved in the reproductive process. The results show that rice lnc RNAs have some different characteristics compared to those of Arabidopsis and mammals and are expressed in a highly tissue-specific or stage-specific manner. We further verify the functions of a set of lnc RNAs that are preferentially expressed in reproductive stages and identify several lnc RNAs as competing endogenous RNAs (ce RNAs), which sequester mi R160 or mi R164 in a type of target mimicry. More importantly, one lnc RNA, XLOC_057324, is demonstrated to play a role in panicle development and fertility. We also develop a source of rice lnc RNA-associated insertional mutants. Conclusions: Genome-wide screening and functional analysis enabled the identification of a set of lnc RNAs that are involved in the sexual reproduction of rice. The results also provide a source of lnc RNAs and associated insertional mutants in rice.