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Expression and evolutionary analysis of soluble inorganic pyrophosphatase gene family in pear and four other Rosaceae species

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Abstract

In plants, soluble inorganic pyrophosphatase (PPA) play an indispensable role in inorganic pyrophosphate hydrolysis. However, the expression and the evolutionary history of PPA gene family remain unclear in pear and Rosaceae species. In this study, thirty-nine PPA genes were identified from five Rosaceae species including pear (Pyrus bretschneideri), apple (Malus domestica), peach (Prunus persica), strawberry (Fragaria vesca) and Japanese apricot/mei (Prunus mume). Based on the structural characteristics of the genes and phylogenetic analysis, members of PPA gene family were classified into two main subfamilies (A and B). Whole-genome duplication (WGD) and dispersed gene duplication were the main force, which drove the expansion of PPA gene family in pear and other Rosaceae species. Purifying selection played a dominant role in the evolution of PPA genes. Subcellular localization analysis demonstrated that pear PPA genes located in the cytosol, chloroplasts or near the nuclear envelope. PPA genes showed multiple expression patterns in different pear tissues. Several members of PPA gene family presented particularly higher expression level in only one of the six tissues, such as PbrPPA2, PbrPPA5 and PbrPPA8. Expression analysis showed that five PPA genes were involved in the growth of pear pollen tube, meanwhile four PPA genes could respond to excess of PPi in pear pollen tube. Overall, we established a comprehensive landscape in the functional characterization and evolution of PPA gene family in pear and Rosaceae species, and provided gene expression data for exploring the functional roles of PPA genes in the growth of pear pollen tube.

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Acknowledgements

This work was funded by the National Key Research and Development Program of China (2018YFD1000107), National Natural Science Foundation of China (31830081, 31772256, 31772276), “Taishan Scholar” project from Shandong Province of China, the Earmarked Fund for China Agriculture Research System (CARS-28), Jiangsu Province Science and Technology Support Program (BE2018389) and the Fundamental Research Funds for the Central Universities (JCQY201903).

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CT and XZ: Experiments performance and the manuscript writing. XQ, WK and CT: Manuscript revision and confirmation. CT, JW and SZ: Conceived and designed the experiments. All the participators have read and confirmed the paper.

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Correspondence to Juyou Wu or Shaoling Zhang.

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The authors declared no conflict of competing interest.

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Handling Editor: Ales Kovarik.

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Online Resource 1. Logo of motifs in PbrPPA protein sequences using MEME.

Online Resource 2. Number of exons between subfamily A and subfamily B. Numbers of exons in PPA genes were collected from pear, apple, peach, strawberry and Japanese apricot.

Online Resource 3. List of PPA genes identified in five Rosaceae species and Arabidopsis with their sequence properties.

Online Resource 4. Predicted properties of the putative PPA protein sequences encoded by genes from Pyrus bretschneideri.

Online Resource 5. List of primers used in the paper.

Online Resource 6. Melting curves of eleven putative PPA genes showing single peaks.

Online Resource 7. Alignments of PPA proteins used for the phylogenetic analysis.

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Tang, C., Qiao, X., Zhu, X. et al. Expression and evolutionary analysis of soluble inorganic pyrophosphatase gene family in pear and four other Rosaceae species. Plant Syst Evol 306, 46 (2020). https://doi.org/10.1007/s00606-020-01628-0

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  • DOI: https://doi.org/10.1007/s00606-020-01628-0

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