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Transcriptome-wide identification and expression profile analysis of the bHLH family genes in Camellia sinensis

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Abstract

The tea plant is an important commercial horticulture crop cultivated worldwide. Yield and quality of this plant are influenced by abiotic stress. The bHLH family transcription factors play a pivotal role in the growth and development, including abiotic stress response, of plants. A growing number of bHLH proteins have been functionally characterized in plants. However, few studies have focused on the bHLH proteins in tea plants. In this study, 120 CsbHLH TFs were identified from tea plants using computational prediction method. Structural analysis detected 23 conservative residues, with over 50% identities in the bHLH domain. Moreover, 103 CsbHLH proteins were assumed to bind DNA and encompassed 98 E-Box binders and 85 G-Box binders. The CsbHLH proteins were grouped into 20 subfamilies based on phylogenetic analysis and a previous classification system. A survey of transcriptome profiling screened 22 and 39 CsbHLH genes that were upregulated under heat and drought stress. Nine CsbHLH genes were validated using qRT-PCR. Results were approximately in accordance with transcriptome data. These genes could be induced by one or more abiotic stresses.

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Abbreviations

ABA:

Abscisic acid

AIB:

ABA-inducible bHLH-type transcription factor

bHLH:

Basic helix-loop-helix

BLAST:

Basic Local Alignment Search Tool

BRs:

Brassinosteroids

CBF:

C-repeat binding factor

COE:

Collier/Olf-1/EBF

FPKM:

Fragments per kilobase of transcript per million mapped reads

GO:

Gene ontology

HMM:

Hidden Markov model

JA:

Jasmonic acid

MEGA:

Molecular evolutionary genetics analysis

MEME:

Multiple Em for motif elicitation

NCBI:

National Center for Biotechnology Information

NJ:

Neighbor-joining

PAS:

Per-Arnt-Sim

PEG:

Polyethylene glycol

qRT-PCR:

Quantitative real-time polymerase chain reaction

RNA-Seq:

RNA sequencing

TF:

Transcription factor

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Acknowledgements

The research was supported by the National Natural Science Foundation of China (31570691).

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Authors and Affiliations

  1. Tea Science Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China

    Xin Cui, Yong-Xin Wang, Zhi-Wei Liu, Wen-Li Wang, Hui Li & Jing Zhuang

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  1. Xin Cui
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  2. Yong-Xin Wang
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  3. Zhi-Wei Liu
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  4. Wen-Li Wang
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  5. Hui Li
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  6. Jing Zhuang
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Contributions

Conceived and designed the experiments: JZ, XC. Performed the experiments: XC, YXW, ZWL, WLW, HL. Analyzed the data: XC, YXW, JZ. Contributed reagents/materials/analysis tools: JZ. Wrote the paper: XC. Revised the paper: JZ, XC, YXW. All authors read and approved the final manuscript.

Corresponding author

Correspondence to Jing Zhuang.

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Figure S1

Multiple alignments of CsbHLH proteins (GIF 368 kb)

High resolution image (TIFF 10597 kb)

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Cui, X., Wang, YX., Liu, ZW. et al. Transcriptome-wide identification and expression profile analysis of the bHLH family genes in Camellia sinensis. Funct Integr Genomics 18, 489–503 (2018). https://doi.org/10.1007/s10142-018-0608-x

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