Evolutionary dynamics of lincRNA transcription in nine citrus species. (18th March 2019)

• Record Type: Journal Article
• Authors: Ke, Lili; Zhou, Zhiwei; Xu, Xi‐Wen; Wang, Xia; Liu, Yuanlong; Xu, Yuantao; Huang, Yue; Wang, Shuting; Deng, Xiuxin; Chen, Ling‐Ling; Xu, Qiang
• Is Part Of: Plant journal. Volume 98:Number 5(2019)
• Page Start: 912
• Page End: 927
• Publication Date: 2019-03-18
• Subjects: long intergenic non‐coding RNAs (lincRNAs) -- evolution -- sweet orange (Citrus sinensis) -- miR166 -- fruit development; Plant molecular biology -- Periodicals; Plant cells and tissues -- Periodicals; Botany -- Periodicals; 580
• DOI: 10.1111/tpj.14279
• Languages: English
• ISSNs: 0960-7412

Abstract

Summary: Long intergenic non‐coding RNAs (lincRNAs) play important roles in various biological processes in plants. However, little information is known about the evolutionary characteristics of lincRNAs among closely related plant species. Here, we present a large‐scale comparative study of lincRNA transcription patterns in nine citrus species. By strand‐specific RNA‐sequencing, we identified 18 075 lincRNAs (14 575 lincRNA loci) from 34 tissue samples. The results indicated that the evolution of lincRNA transcription is more rapid than that of mRNAs. In total, 82.8–97.6% of sweet orange ( Citrus sinensis ) lincRNA genes were shown to have homologous sequences in other citrus genomes. However, only 15.5–28.8% of these genes had transcribed homologous lincRNAs in these citrus species, presenting a strong contrast to the high conservation of mRNA transcription (81.6–84.7%). Moreover, primitive and modern citrus lincRNAs were preferentially expressed in reproductive and vegetative organs, respectively. Evolutionarily conserved lincRNAs showed higher expression levels and lower tissue specificity than species‐specific lincRNAs. Notably, we observed a similar tissue expression pattern of homologous lincRNAs in sweet orange and pummelo ( Citrus grandis ), suggesting that these lincRNAs may be functionally conserved and selectively maintained. We also identified and validated a lincRNA with the highest expression in fruit that acts as an endogenous target mimic (eTM) of csi‐miR166c, and two lincRNAs that act as a precursor and target of csi‐miR166c, respectively. These lincRNAs together with csi‐miR166c could form an eTM166‐miR166c‐targeted lincRNA regulatory network that possibly affects citrus fruit development. Significance Statement: Here, 18 075 lincRNAs have been identified from 34 tissue samples from nine citrus species. The data uncover the rapid turnover of lincRNA transcription among different citrus species and highlights the potential contribution of the eTM166‐miR166‐targeted lincRNA regulatory network to fruit development.