Genome-wide characterization of protein phosphatase 2C genes in Populus euphratica and their expression profiling under multiple abiotic stresses

Abstract

The protein phosphatase 2Cs (PP2Cs) have been demonstrated to act as negative modulators of protein kinase and to participate in stress signal transduction, as well as plant growth and productivity processes. Populus euphratica is so extraordinarily adaptable to abiotic stresses that it is regarded as a potential model plant for exploring resistance mechanisms of woody plants. To gain insight into the functional characteristics of PP2C genes in P. euphratica, 117 non-redundant PeuPP2C-encoding genes were identified from the whole genome. These members were classified into 13 groups (A–M), each of which was relatively conserved in gene structure and protein domain. A total of 39 paralogous pairs were found to be generated by whole genome duplication events, and Ka/Ks analysis indicated that these paralogous pairs had evolved mainly from purifying selection. The cis-acting elements and expression patterns showed that all the PeuPP2Cs were involved in response to single or multiple stresses including drought, salinity, heat, cold, and ABA. Taken together, our results summarized the genome-wide characterization of PeuPP2Cs and their expression profiling across different tissues and under multiple abiotic stresses in P. euphratica. These data provide a foundation to further investigate potential function of PeuPP2Cs in conferring tolerance to various stresses in P. euphratica.

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Acknowledgments

This work was supported by National Nonprofit Institute Research Grant of the Chinese Academy of Forestry (CAFYBB2018ZY001-9), (CAFYBB2017ZY008), and the National Natural Science Foundation of China (31570669) to JH.

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Corresponding authors

Correspondence to Xuebing Xin or Jianjun Hu.

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The authors declare that they have no conflicts of interests.

Data archiving statement

All identified PP2C gene sequences of Populus euphratica were deposited into the NCBI database (https://www.ncbi.nlm.nih.gov/). The accession numbers are listed in Table S2.

Additional information

Communicated by P. Ingvarsson

Electronic supplementary material

Fig. S1
figure7

The expression levels of reporter genes for each condition tested. (PNG 56 kb)

Fig. S2
figure8

The number of each cis-acting element in the promoter region of each PeuPP2C gene. (PNG 587 kb)

High Resolution Image (TIFF 782 kb)

High Resolution Image (TIFF 5785 kb)

Table S1

Primers used in qRT-PCR analysis of the PeuPP2C genes. (XLSX 15 kb)

Table S2

The PP2C gene family identified in P. euphratica. (XLSX 18 kb)

Table S3

The complete coding sequences and the corresponding amino acid sequences of PP2C genes in P. euphratica. (XLSX 102 kb)

Table S4

The annotation of the cis-elements. (XLSX 10 kb)

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Li, J., Jia, H., Zhang, J. et al. Genome-wide characterization of protein phosphatase 2C genes in Populus euphratica and their expression profiling under multiple abiotic stresses. Tree Genetics & Genomes 14, 80 (2018). https://doi.org/10.1007/s11295-018-1291-8

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Keywords

  • Populus euphratica
  • Protein phosphatase 2C (PP2C)
  • Phylogenetic analysis
  • Expression profiling
  • Abiotic stress