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De novo transcriptome sequencing and identification of genes related to salt and PEG stress in Tetraena mongolica Maxim

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Abstract

Key message

The first transcriptome analyses of Tetraena mongolica provided 224,618 Unigenes and identified the genes that were differentially expressed under salt and drought conditions, giving some insights into the unique adaptive capacity of this relic plant.

Abstract

Tetraena mongolica Maxim, the only member of the Tetraena genus in the Zygophyllaceae, is endemic to the northwest of China. As one of the relic shrubs of the Paleo-Mediterranean flora, T. mongolica plays a key role in preserving the local ecological environment. To investigate its good adaptability in desert, we studied the transcriptome of T. mongolica under NaCl and PEG6000 stresses. Three libraries were constructed from a mixture of seedlings and mature plants of T. mongolica, and the de novo transcriptome was sequenced using an Illumina HiSeq 4000. Approximately 218.15 million clean reads were assembled de novo into 383,612 transcripts, and 116,027 All-Unigenes were identified. By aligning All-Unigene sequences against the NR database, we found that most of the All-Unigenes had very low matches with the sequences from other plants. A total of 21,112 SSRs and 6 types of SNP variants were identified. The RNA-Seq data revealed 60 transcription factor (TF) families with 3163 genes in total. Six libraries were constructed from the separate control or stressed seedlings, and the transcriptome was sequenced using a BGISEQ-500 platform. There are 1105 and 1383 differentially expressed genes (DEGs) with 42 and 54 TFs under NaCl and PEG6000 treatment, respectively. The genes that were putatively involved in salt and osmotic stresses were searched and analyzed. Quantitative reverse transcription PCR (qRT-PCR) showed that DEG expression profiles were consistent with those from RNA-seq (RNA sequencing). Overall, this study provides new insights into the molecular mechanisms that control salt and drought stress responses in T. mongolica.

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Availability of supporting data

The transcriptome sequencing raw data were deposited in the National Center for Biotechnology Information with the Accession No. PRJNA490096 and PRJNA490438.

Abbreviations

BLAST:

Basic local alignment search tool

DEGs:

Differentially expressed genes

GO:

Gene ontology

KEGG:

Kyoto encyclopedia of genes and genomes

KOG:

Eukaryotic Orthologous Groups

Nr/Nt:

Non-redundant database and nucleotide collection

PEG:

Polyethylene glycol

QC:

Quality control

qRT-PCR:

Quantitative reverse transcription PCR

RNA-seq:

RNA sequencing

TFs:

Transcription factors

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Acknowledgements

This research was supported by the National Natural Science Foundation of China (31470392, 31570407), the First Class University and Discipline Construction Project of Minzu University of China (Yldxxk201819).

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  1. College of Life and Environmental Sciences, Minzu University of China, Beijing, 100081, China

    Ningmei Chen, Jinchao Feng, Buerbatu Song, Shuai Tang, Junqing He, Yijun Zhou, Sha Shi & Xiaojing Xu

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  1. Ningmei Chen
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Contributions

XX designed the experiments. NC performed the experiments, data analysis, and drafted the manuscript. JF helped conceive the study. BS and JH helped analyze data. ST helped draft the manuscript. YZ and SS helped in design and coordination. All authors read and approved the final manuscript.

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Correspondence to Xiaojing Xu.

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T mongolica is endemic to the western part of Inner Mongolia and Ningxia, Gansu province and also subjected as nationally endangered in China. Before collecting the seeds, an oral permission was obtained from the local management of forestry after applying with introduction letters from College of Life and Environmental Sciences, Minzu University of China.

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Chen, N., Feng, J., Song, B. et al. De novo transcriptome sequencing and identification of genes related to salt and PEG stress in Tetraena mongolica Maxim. Trees 33, 1639–1656 (2019). https://doi.org/10.1007/s00468-019-01886-7

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