Planta

, Volume 247, Issue 3, pp 715–732 | Cite as

Transcriptomic and proteomic feature of salt stress-regulated network in Jerusalem artichoke (Helianthus tuberosus L.) root based on de novo assembly sequencing analysis

  • Aiqin Zhang
  • Dongming Han
  • Yu Wang
  • Huifang Mu
  • Tong Zhang
  • Xiufeng Yan
  • Qiuying Pang
Original Article

Abstract

Main Conclusion

Ribosome activation and sugar metabolic process mainly act on the regulation of salt tolerance in the bioenergy crop Helianthus tuberosus L. as dissected by integrated transcriptomic and proteomic analyses.

Helianthus tuberosus L. is an important halophyte plant that can survive in saline–alkali soil. It is vitally necessary to build an available genomic resource to investigate the molecular mechanisms underlying salt tolerance in H. tuberosus. De novo assembly and annotation of transcriptomes were built for H. tuberosus using a HiSeq 4000 platform. 293,823 transcripts were identified and annotated into 190,567 unigenes. In addition, iTRAQ-labeled quantitative proteomics was carried out to detect global protein profiling as a response to salt stress. Comparative omics analysis showed that 5432 genes and 43 proteins were differentially expressed in H. tuberosus under salt stress, which were enriched in the following processes: carbohydrate metabolism, ribosome activation and translation, oxidation–reduction and ion binding. The reprogramming of transcript and protein works suggested that the induced activity of ribosome and sugar signaling may endue H. tuberosus with salt tolerance. With high-quality sequencing and annotation, the obtained transcriptomics and proteomics provide a robust genomic resource for dissecting the regulatory molecular mechanism of H. tuberosus in response to salt stress.

Keywords

Energy crop iTRAQ labeling RNA-Seq transcriptome Salt tolerance 

Abbreviations

DEPC

Diethy pyrocarbonate

DEGs

Differentially expressed genes

FPKM

Fragments per kilobase per transcript per million mapped reads

MDHAR

Monodehydroascorbate reductase

LEA

Late embryogenesis abundant

RSEM

RNA-seq by expectation maximization

Notes

Acknowledgements

This work was supported by the National Natural Science Foundation of China (No. 31470467) and the Fundamental Research Funds for the Central Universities (2572016DA05 and 2572016AA15).

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflicts of interest.

Supplementary material

425_2017_2818_MOESM1_ESM.pptx (685 kb)
Supplementary Fig. S1 Assembled transcripts of H. tuberosus search against Blast Nr. Plant species classification of the unigenes based on the best species similarity, distribution of e-value showed in blast analysis of de novo assembled transcriptomes, sequence similarity distribution of unigenes with the top Nr hits (PPTX 685 kb)
425_2017_2818_MOESM2_ESM.pptx (106 kb)
Supplementary Fig. S2 Annotation of all the unigenes from H. tuberosus transcriptome. Number of genes annotated by five representatively databases (Blast Nr, Swiss Prot, GO, Pfam, KO) was showed in Venn diagram (PPTX 105 kb)
425_2017_2818_MOESM3_ESM.pptx (141 kb)
Supplementary Fig. S3 Correlation of iTRAQ quantification among control and salt-treated samples (PPTX 141 kb)
425_2017_2818_MOESM4_ESM.pptx (74 kb)
Supplementary Fig. S4 Volcano plot of differentially expressed proteins in H. tuberosus root under salt stress. The differentially expressed proteins were set with 0.85≥fold change≥1.2 and P-value≤0.05 calculated by Student’s t-test (PPTX 73 kb)
425_2017_2818_MOESM5_ESM.xlsx (10 kb)
Supplementary Table S1 Transcriptome annotation statistics of integrated database (XLSX 9 kb)
425_2017_2818_MOESM6_ESM.xlsx (71.3 mb)
Supplementary Table S2 Assembled transcripts were BLAST searched against the NCBI nonredundant database (XLSX 73053 kb)
425_2017_2818_MOESM7_ESM.xlsx (2.7 mb)
Supplementary Table S3 Assembled transcripts were annotated by Gene Ontology (XLSX 2715 kb)
425_2017_2818_MOESM8_ESM.xlsx (1.7 mb)
Supplementary Table S4 GO classification of all annotated unigenes (XLSX 1722 kb)
425_2017_2818_MOESM9_ESM.xlsx (100 kb)
Supplementary Table S5 KEGG classification of all annotated unigenes (XLSX 99 kb)
425_2017_2818_MOESM10_ESM.xlsx (11 kb)
Supplementary Table S6 Fragments per kilobase per transcript per million mapped reads (FPKM) interval in three independent biological replicates of control (JA-RC/JA-TC) and salt treated samples (JA-RT/JA-TT) of H. tuberosus (XLSX 11 kb)
425_2017_2818_MOESM11_ESM.xlsx (151 kb)
Supplementary Table S7 Expression of the up-regulated transcripts in H. tuberosus root under salt stress (XLSX 151 kb)
425_2017_2818_MOESM12_ESM.xlsx (244 kb)
Supplementary Table S8 Expression of the down-regulated transcripts in H. tuberosus root under salt stress (XLSX 243 kb)
425_2017_2818_MOESM13_ESM.xlsx (784 kb)
Supplementary Table S9 Comprehensive annotation of up-regulated genes by integrated databases (XLSX 783 kb)
425_2017_2818_MOESM14_ESM.xlsx (1 mb)
Supplementary Table S10 Comprehensive annotation of down-regulated genes by integrated databases (XLSX 1066 kb)
425_2017_2818_MOESM15_ESM.xlsx (324 kb)
Supplementary Table S11 GO terms enrichment of all the up-regulated genes (XLSX 323 kb)
425_2017_2818_MOESM16_ESM.xlsx (366 kb)
Supplementary Table S12 GO terms enrichment of all the down-regulated genes (XLSX 366 kb)
425_2017_2818_MOESM17_ESM.xlsx (10 kb)
Supplementary Table S13 Primer sequences used in RT-PCR analysis (XLSX 9 kb)
425_2017_2818_MOESM18_ESM.xlsx (500 kb)
Supplementary Table S14 All the identified protein groups from iTRAQ quantitative proteomic analysis (XLSX 499 kb)

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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2017

Authors and Affiliations

  • Aiqin Zhang
    • 1
  • Dongming Han
    • 1
  • Yu Wang
    • 2
  • Huifang Mu
    • 1
  • Tong Zhang
    • 3
  • Xiufeng Yan
    • 1
  • Qiuying Pang
    • 1
  1. 1.Alkali Soil Natural Environmental Science CenterNortheast Forestry University/Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of EducationHarbinChina
  2. 2.School of Life Science and TechnologyHarbin Institute of TechnologyHarbinChina
  3. 3.Department of BiologyUniversity of FloridaGainesvilleUSA

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