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RNA-Seq and transcriptome analysis of nitrogen-deprivation responsive genes in Dunaliella salina TG strain

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Abstract

Nitrogen is a critical macronutrient for plant growth and development, and Dunaliella salina has various physiological responses to nitrogen deprivation, such as accumulating large amounts of carotenoids in its chloroplasts. However, little is known about the underlying global molecular response of D. salina to nitrogen deprivation. Herein, we used the Illumina platform to interrogate which genes of D. salina respond to nitrogen deprivation. The RNA-seq libraries of D. salina TG cultured under nitrogen-replete and -depleted conditions for 7 days generated 87,160,704 valid reads with an average length of 124.94 bp. De novo assembly produced 73,329 transcripts with an average length of 801 bp and 47,283 unigenes with an average length of 675 bp. 5803 unigenes were assigned to 50 gene ontology (GO) terms belonging to three main categories. A total of 6016 unigenes with 671 enzyme commission numbers were assigned to 251 predicted KEGG metabolic pathways, and 6296 unigenes were categorized into 25 KOG classifications. A total of 27,306 CDS were predicted from the 47,283 unigenes. Analysis of transcription levels revealed that 2380 genes were upregulated and 747 were downregulated during nitrogen deprivation. These nitrogen-deprivation responsive genes and differentially expressed transcriptional regulator genes were identified by GO classification. The transcriptome data may serve as a reference for further analysis of gene expression and functional genomics studies, and will facilitate the study of carotenoid biosynthesis and nitrogen metabolism in chlorophytes at the molecular level.

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Acknowledgements

This work is supported by the Open Research Fund Program of Beijing Key Lab of Plant Resource Research and Development, Beijing Technology and Business University and the National Natural Science Foundation of China (No. 31401029).

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Authors and Affiliations

  1. Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education (Tianjin University of Science & Technology), 13th Street, TEDA, Tianjin, 300457, China

    Hexin Lv, Bingbing Qi, Jiatong He & Shiru Jia

  2. Beijing Key Lab of Plant Resource Research and Development, Beijing Technology and Business University, Beijing, 100048, China

    Qiao-e Wang

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  1. Hexin Lv
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Contributions

SJ and HL conceived and designed the project. HL analyzed the data and wrote the paper. BQ performed the cultures materials preparation and qPCR analysis. QW revised the paper and JH provided bioinformatic analysis tools. All authors have read and approved the final manuscript.

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Correspondence to Hexin Lv.

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Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (XLSX 4909 kb) Supplement Table 1. Statistics of Gene Annotations by Different Databases.

Supplementary material 2 (XLSX 359 kb) Supplement Table 2. KEGG Pathway Classifications of Unigenes.

40626_2019_138_MOESM3_ESM.xlsx

Supplementary material 3 (XLSX 218 kb) Supplement Table 3. Differential Expressions of Unigenes of Cells under CM and -N.

Supplementary material 4 (XLSX 82 kb) Supplement Table 4. Clusters of DEGs by Hierarchal Analysis.

40626_2019_138_MOESM5_ESM.xlsx

Supplementary material 5 (XLSX 19 kb) Supplement Table 5. Pathway Classifications of DEGs by KEGG. S gene number: Numbers of significantly changed genes in a given KEGG pathway. B gene number: Numbers of annotated genes in a given KEGG pathway.

Supplementary material 6 (XLSX 12 kb) Supplement Table 6. Transcription regulators Classified by WEGO analysis.

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Lv, H., Wang, Qe., Qi, B. et al. RNA-Seq and transcriptome analysis of nitrogen-deprivation responsive genes in Dunaliella salina TG strain. Theor. Exp. Plant Physiol. 31, 139–155 (2019). https://doi.org/10.1007/s40626-019-00138-w

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