Comparative transcriptome analysis of Triticum aestivum in response to nitrogen stress

Comparative transcriptome analysis of Triticum aestivum in response to nitrogen stress Nitrogen (N) is an essential macronutrient for plant growth and development. Insufficient supply of N leads to extensive physiological and biochemical changes in plant. However, the molecular mechanisms of response to N are still unknown. In this study, global transcriptome profiles of wheat (Triticum aestivum L.) leaf and root under limited and sufficient N conditions were generated using Illumina RNA-sequencing. Then SeqPrep and Sickle were used to filter the raw reads and genes were assembled and predicted using Trinity. The Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) for wheat transcripts were obtained from GO and KEGG databases, respectively. Clusters of orthologous group terms were obtained using Blastx 2.2.24+ in STRING 9.0. Differentially expressed genes (DEGs) were then screened using edgeR software with false discovery rate <0.05 and |log2FC| ≥ 1, followed by the protein–protein interaction (PPI) network construction for DEGs using Cytoscape. As a result, 126956 transcripts were obtained. Among them, 47590 transcripts were categorized into 56 GO terms, such as metabolic process; 25607 transcripts were assigned to 42 KEGG pathways, such as metabolic pathways; and 27194 unique sequences were classified into 25 COG categories, such as transcription. Moreover, 1267 (179 up-regulated and 1088 down-regulated) and 1996 DEGs (868 up-regulated and 1128 down-regulated) were obtained in leaf and root, respectively. In the PPI networks, BRADI1G77050.1, BRADI2G40600.1 and rpl2 were found to be the hub nodes. Thus, these screened DEGs might be associated with N metabolism and stress response in wheat, especially BRADI1G77050.1, BRADI2G40600.1 and rpl2. http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Russian Journal of Plant Physiology Springer Journals

Comparative transcriptome analysis of Triticum aestivum in response to nitrogen stress

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Publisher
Springer Journals
Copyright
Copyright © 2016 by Pleiades Publishing, Ltd.
Subject
Life Sciences; Plant Physiology; Plant Sciences
ISSN
1021-4437
eISSN
1608-3407
D.O.I.
10.1134/S1021443716020175
Publisher site
See Article on Publisher Site

Abstract

Nitrogen (N) is an essential macronutrient for plant growth and development. Insufficient supply of N leads to extensive physiological and biochemical changes in plant. However, the molecular mechanisms of response to N are still unknown. In this study, global transcriptome profiles of wheat (Triticum aestivum L.) leaf and root under limited and sufficient N conditions were generated using Illumina RNA-sequencing. Then SeqPrep and Sickle were used to filter the raw reads and genes were assembled and predicted using Trinity. The Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) for wheat transcripts were obtained from GO and KEGG databases, respectively. Clusters of orthologous group terms were obtained using Blastx 2.2.24+ in STRING 9.0. Differentially expressed genes (DEGs) were then screened using edgeR software with false discovery rate <0.05 and |log2FC| ≥ 1, followed by the protein–protein interaction (PPI) network construction for DEGs using Cytoscape. As a result, 126956 transcripts were obtained. Among them, 47590 transcripts were categorized into 56 GO terms, such as metabolic process; 25607 transcripts were assigned to 42 KEGG pathways, such as metabolic pathways; and 27194 unique sequences were classified into 25 COG categories, such as transcription. Moreover, 1267 (179 up-regulated and 1088 down-regulated) and 1996 DEGs (868 up-regulated and 1128 down-regulated) were obtained in leaf and root, respectively. In the PPI networks, BRADI1G77050.1, BRADI2G40600.1 and rpl2 were found to be the hub nodes. Thus, these screened DEGs might be associated with N metabolism and stress response in wheat, especially BRADI1G77050.1, BRADI2G40600.1 and rpl2.

Journal

Russian Journal of Plant PhysiologySpringer Journals

Published: May 13, 2016

References

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