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Research article

Combined RNA-seq, small RNA and degradome sequencing approaches insights into salt-stress responses in Beta vulgaris

Junliang Li, Jie Cui, Dayou Cheng, Cuihong Dai, Tianjiao Liu, Congyu Wang, Chengfei Luo

Abstract

Background

Salinity is one of the most serious threat to agriculture worldwide. Sugar beet is an important sugar-yielding crop and has a certain tolerance to salt. While a genome-wide analysis of genes involved in salt-stress remains largely unknown in B. vulgaris.

Results

Three high-throughput sequencing approaches, namely, RNA-seq, small RNA and degradome sequencing were used to exploring the molecular basis of salt-resistance in beta vulgaris. A total of 12 230 differentially expressed genes were identified, which were mainly related to transcription factors, protein kinases, and enzymes. The small RNA sequencing resulted in the identification of 476 miRNAs included 219 known and 257 novel miRNAs, of which 130 were differentially expressed under salt-stress. A total of 2534 targets were predicted for 317 miRNAs by bioinformatics and degradome sequencing. Functional analysis of these targets suggested that miRNA-mediated post-transcriptional regulation plays a crucial role in transcriptional reprogramming under stress. The combination analysis of multi-omics revealed 209 negative correlation mRNA-miRNA pairs. All these data were used to construct a hypothetical regulatory network of beta vulgaris in response to salt stress.

Conclusion

These components and the preliminary network provides better insights into the molecular mechanism of salt-stress response, and also offers candidate genes for beet improvement.

Keywords
RNA-seq, MicroRNAs, Degradome sequencing, Salt stress, Beta vulgaris

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Introduction

Results

Discussion

Conclusions

Methods

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Tables

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Preprint: Please note that this article has not completed peer review.
Research article

Combined RNA-seq, small RNA and degradome sequencing approaches insights into salt-stress responses in Beta vulgaris

Junliang Li, Jie Cui, Dayou Cheng, Cuihong Dai, Tianjiao Liu, Congyu Wang, Chengfei Luo

STATUS: In Review

Comments: 0
PDF Downloads: 0
HTML Views: 8

Integrity Check:

  • Article

  • Peer Review Timeline

  • Related Articles

  • Comments

Abstract

Background

Salinity is one of the most serious threat to agriculture worldwide. Sugar beet is an important sugar-yielding crop and has a certain tolerance to salt. While a genome-wide analysis of genes involved in salt-stress remains largely unknown in B. vulgaris.

Results

Three high-throughput sequencing approaches, namely, RNA-seq, small RNA and degradome sequencing were used to exploring the molecular basis of salt-resistance in beta vulgaris. A total of 12 230 differentially expressed genes were identified, which were mainly related to transcription factors, protein kinases, and enzymes. The small RNA sequencing resulted in the identification of 476 miRNAs included 219 known and 257 novel miRNAs, of which 130 were differentially expressed under salt-stress. A total of 2534 targets were predicted for 317 miRNAs by bioinformatics and degradome sequencing. Functional analysis of these targets suggested that miRNA-mediated post-transcriptional regulation plays a crucial role in transcriptional reprogramming under stress. The combination analysis of multi-omics revealed 209 negative correlation mRNA-miRNA pairs. All these data were used to construct a hypothetical regulatory network of beta vulgaris in response to salt stress.

Conclusion

These components and the preliminary network provides better insights into the molecular mechanism of salt-stress response, and also offers candidate genes for beet improvement.

Figures

Introduction

Results

Discussion

Conclusions

Methods

Declarations

References

Tables

Additional Files

Learn more about our company.