Abstract
The conserved BURP-containing proteins are specific to plants and play a crucial role in plant growth, development, and response to abiotic stresses. However, less is known about the systematic characterization of BURP-containing proteins in apple. This study aimed to identify and analyze all BURP-containing genes in the apple genome, as well as to examine their expression patterns through various bioinformatics methods. Eighteen members of BURP-containing genes were identified in apple, six members lacked signal peptides, and the secondary structure was mainly a Random coil of BURP-containing genes. Gene structure and Motif analysis showed that proteins have similar structures and are conserved at the C-terminal. Cis-acting element analysis revealed that the proteins contain phytohormone and stress response elements, and chromosomal localization revealed that the family is unevenly distributed across eight chromosomes, with duplication of fragments leading to the expansion of family proteins. Tissue expression showed that MdPG3 and MdPG4 were expressed in different tissues and different varieties, MdRD2 and MdRD7 were highly expressed in ‘M74’ fruits and MdRD7 in ‘M49’ leaves, while MdUSP1 was highly expressed in ‘GD’ roots. The quantitative real-time PCR analysis showed that the expressions of six and seven genes were significantly up-regulated under NaCl and PEG treatments, respectively, whereas MdRD7 was significantly up-regulated under NaCl and PEG treatment over time. This study offers a comprehensive identification and expression analysis of BURP-containing proteins in apple. The findings provide a theoretical foundation for further exploration of the functions of this protein family.
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Data availability
The datasets generated and analyzed during the current study are available in the Phytozome 13 repository (https://phytozome-next.jgi.doe.gov/) and the apple repository (https://iris.angers.inra.fr/gddh13/).
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Acknowledgements
We express our gratitude to Shanghai Tengyun Biotechnology Co., Ltd. for their development of the Hiplot Pro platform (https://hiplot.com.cn/) and their provision of technical assistance and valuable data analysis and visualization tools.
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This work was supported by the National Key Research and Development Program of China (2022YFD1602106) and Science and Technology Major Project of Gansu Province (22ZD6NA045). The funding bodies had no roles in the experimental design or collection, analysis and interpretation of data in writing the manuscript.
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JM conceived and designed the research. JR performed the experiments, and drafted the manuscript. LF, LG, HG and SL analyzed data and helped in the preparation of the manuscript. All authors discussed the results and commented on the manuscript.
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Ren, J., Feng, L., Guo, L. et al. Genome-wide identification and expression analysis of the BURP domain-containing genes in Malus domestica. Physiol Mol Biol Plants 29, 1717–1731 (2023). https://doi.org/10.1007/s12298-023-01393-7
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DOI: https://doi.org/10.1007/s12298-023-01393-7