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Genome-wide identification of GMP genes in Rosaceae and functional characterization of FaGMP4 in strawberry (Fragaria × ananassa)

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Abstract

Background

GDP-D-mannose pyrophosphorylase (GMP) is one of the key enzymes determining ascorbic acid (AsA) biosynthesis. However, little information about GMP genes is currently available for the Rosaceae species, especially in the AsA-riched cultivated octoploid strawberry (Fragaria × ananassa).

Objective

To identify the all the GMP genes in Rosaceae, as well as the predominant homologues and the role of GMP genes in strawberry AsA accumulation.

Methods

In the present study, we performed genome-wide identification and comprehensive analysis of the duplicated GMP genes in strawberry and other Rosaceae species by bioinformatics methods, the expression of the GMP genes from cultivated strawberry (Fragaria × ananassa, FaGMP) was specifically analyzed by qPCR. Finally, the FaGMP4 was transiently overexpressed in strawberry to estimate the role of GMP in regulating AsA accumulation in strawberry.

Results

As results, a total of 28 GMP genes were identified in the five Rosaceae species. The origins of duplication events analysis suggested that most GMP duplications in Rosaceae species were generated from whole genome duplication (WGD). The Ka/Ks ratio suggested that FaGMP genes underwent a stabilization selection. qPCR based expression analysis showed different patterns of FaGMP paralogs during fruit ripening, while FaGMP4 expressed higher in the variety containing higher AsA. Overexpression of FaGMP4 in strawberry significantly enhanced AsA accumulation. Furthermore, the expression of FaGMP4 under the treatment of blue and red light was largely increased in leaves while significantly inhibited in fruit. These results revealed the vital role of FaGMP4 in regulating AsA in strawberry.

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Acknowledgements

We would like to thank the Institute of Pomology and Olericulture in Sichuan Agricultural University for providing the HPLC system to determine the AsA content.

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Author notes

  1. Yuanxiu Lin and Jiahao Zhang authors contributed equally to this article.

Authors and Affiliations

  1. College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China

    Yuanxiu Lin, Jiahao Zhang, Lintai Wu, Yunting Zhang, Qing Chen, Mengyao Li, Yong Zhang, Ya Luo, Yan Wang, Xiaorong Wang & Haoru Tang

  2. Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China

    Yuanxiu Lin, Yunting Zhang, Yan Wang, Xiaorong Wang & Haoru Tang

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  1. Yuanxiu Lin
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Contributions

Conceptualization, HT; Methodology, YL, JZ, and LW; Software, YL, ML and QC; Validation, YL, JZ, and LW; Formal analysis, YL; Data curation, YL; Writing—original draft preparation, YL; Writing—review and editing, YL, YZ, YZ, YW and XW; Supervision, HT.

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Correspondence to Haoru Tang.

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Figure S2.

Multiple alignment of GMP amino acids sequences from Rosaceae and Arabidopsis. The secondary structure was constructed by the pattern of T. maritima GMP protein (accession: 2 × 5s in protein data bank). Red text represents the core for metal binding site. Black box indicates substrate binding sites (SBS); red box represents Hexapeptide repeat; blue box indicates transmembrane motif (TM).The graph above the sequences indicates the secondary structure of the proteins (pdf 560 KB)

Figure S2.

Multiple alignment of GMP amino acids sequences from Rosaceae and Arabidopsis. The secondary structure was constructed by the pattern of T. maritima GMP protein (accession: 2 × 5s in protein data bank). Red text represents the core for metal binding site. Black box indicates substrate binding sites (SBS); red box represents Hexapeptide repeat; blue box indicates transmembrane motif (TM).The graph above the sequences indicates the secondary structure of the proteins (pdf 2789 KB)

Figure S3.

The chromosome to chromosome synteny relationship between Arabidopsis and five Rosaceae species. The location of GMP gene on the chromone was represented by red triangle. The black line indicated the collinear relationship between Arabidopsis and five other Rosaceae species. The red, yellow, blue and purple lines indicated the collinear relationship between octoploid strawberry and apple, peach, European pear, woodland strawberry respectively (pdf 370 KB)

Table S1

. The correspondence of gene ID and gene name in this study (xlsx 11 KB)

Table S2.

Collinear gene pairs of GMP in Arabidopsis and Rosaceae (xlsx 2641 KB)

Table S3.

The duplication types of GMP in Rosaceae (xlsx10 KB)

Table S4

. Information of motifs in the promoter region of FaGMP genes (xlsx 16 KB)

Table S5.

Primers used in this study (xlsx 10 KB)

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Lin, Y., Zhang, J., Wu, L. et al. Genome-wide identification of GMP genes in Rosaceae and functional characterization of FaGMP4 in strawberry (Fragaria × ananassa). Genes Genom 43, 587–599 (2021). https://doi.org/10.1007/s13258-021-01062-7

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