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

BMC Genomics
Sang-Yoon ShinChanseok Shin

Abstract

Nitrogen (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. Here, 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...Continue Reading

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Citations

Jan 4, 2020·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Yue LuYu Zhao
May 1, 2020·Frontiers in Plant Science·Dujun WangXingming Lian
Oct 20, 2018·BMC Plant Biology·Yafei SunShubin Sun
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Nov 18, 2020·International Journal of Molecular Sciences·Makiha FukudaSho Nishida
Apr 4, 2021·Life·Saurabh ChaudharyPrakash Chand Sharma
Jun 7, 2021·BMC Plant Biology·J Vladimir Torres-RodríguezRuairidh J H Sawers

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Datasets Mentioned

BETA
ERR037683

Methods Mentioned

BETA
transgenic
RNA-Seq
Degradome
2P-Seq
sRNA-Seq
Degradome sequencing

Software Mentioned

AgriGO
Seqdata
FASTX
CleaveLand4
PEP
Cufflinks
CleaveLand
FOLD3
TopHat

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