Transcriptomic analyses of rice (Oryza sativa) genes and non-coding RNAs under nitrogen starvation using multiple omics technologies

Abstract

BackgroundNitrogen (N) is a key macronutrient essential for plant growth, and its availability has a strong influence on crop development. The application of synthetic N fertilizers on crops has increased substantially in recent decades; however, the applied N is not fully utilized due to the low N use efficiency of crops. To overcome this limitation, it is important to understand the genome-wide responses and functions of key genes and potential regulatory factors in N metabolism.ResultsHere, we characterized changes in the rice (Oryza sativa) transcriptome, including genes, newly identified putative long non-coding RNAs (lncRNAs), and microRNAs (miRNAs) and their target mRNAs in response to N starvation using four different transcriptome approaches. Analysis of rice genes involved in N metabolism and/or transport using strand-specific RNA-Seq identified 2588 novel putative lncRNA encoding loci. Analysis of previously published RNA-Seq datasets revealed a group of N starvation-responsive lncRNAs showing differential expression under other abiotic stress conditions. Poly A-primed sequencing (2P-Seq) revealed alternatively polyadenylated isoforms of N starvation-responsive lncRNAs and provided precise 3′ end information on the transcript models of these lncRNAs. Analysis of small RNA-Seq data identified N starvation-responsive miRNAs and down-regulation of miR169 family members, causing de-repression of NF-YA, as confirmed by strand-specific RNA-Seq and qRT-PCR. Moreover, we profiled the N starvation-responsive down-regulation of root-specific miRNA, osa-miR444a.4-3p, and Degradome sequencing confirmed MADS25 as a novel target gene.ConclusionsIn this study, we used a combination of multiple RNA-Seq analyses to extensively profile the expression of genes, newly identified lncRNAs, and microRNAs in N-starved rice roots and shoots. Data generated in this study provide an in-depth understanding of the regulatory pathways modulated by N starvation-responsive miRNAs. The results of comprehensive, large-scale data analysis provide valuable information on multiple aspects of the rice transcriptome, which may be useful in understanding the responses of rice plants to changes in the N supply status of soil.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-4897-1) contains supplementary material, which is available to authorized users.

Reprogramming of 24nt siRNAs in rice gametes

“…For each cell or tissue type, we prepared at least three biological replicates ( Supplemental Table S1). We also included several published small RNA libraries from vegetative tissues: wild-type root (Shin et al 2018), and ddm1a ddm1b double mutant leaf (which we refer to simply as ddm1) and its wild-type control (Tan et al 2016;Tan et al 2018).…”

Overexpression of OsMYB305 in Rice Enhances the Nitrogen Uptake Under Low-Nitrogen Condition

“…Up-regulated expression of AtNRT2.1 stimulated by glucose depends on hexokinase (HXK) activity and pentose phosphate pathway (PPP) metabolism (Lejay et al, 2008;Bussell et al, 2013;de Jong et al, 2014). Overexpression of the hexose transporter STP13 increased the endogenous sucrose content, up-regulated NRT2.2 expression, and enhanced nitrate uptake in Arabidopsis under low-N condition (Schofield et al, 2009). In rice, exogenous sucrose supplementation increased the accumulation of OsNRT2.1, OsNRT2.2, OsNRT2.3, and OsNAR2.1 transcripts (Feng et al, 2011).…”

“…Extensive transcriptome analyses have been conducted on rice to identify genome-wide changes in gene expression in response to nitrogen starvation (Lian et al, 2006;Cai et al, 2012;Yang et al, 2015;Hsieh et al, 2018;Shin et al, 2018). These studies revealed that in order to contend with nitrogen deficiency, rice must modulate the expression levels of extensive genes involved in N assimilation, C metabolism, root architecture formation, chlorophyll biosynthesis and stress response.…”

The Emerging Role of Long Non-Coding RNAs in Plant Defense Against Fungal Stress

“…A total of 2542 lincRNA candidates in Populus trichocarpa (P. trichocarpa) [26], nearly 10,000 lncRNAs in maize (Zea mays L.) [27][28][29][30], as well as 682 high-confidence lncRNAs in cassava [31] were identified. In rice, by performing whole-transcriptome strand-specific RNA sequencing (ssRNA-seq), 2224 lncRNAs involved in the reproductive process [32] and 2588 novel putative lncRNA encoding loci under nitrogen starvation were verified [33]. In Brassica, 1885, 1910, and 1299 lncRNAs at the whole genome level were identified for B. napus, B. oleracea, and B. rapa, respectively [34].…”