Genome-wide identification and expression analyses of phenylalanine ammonia-lyase gene family members from tomato (Solanum lycopersicum) reveal their role in root-knot nematode infection

Fulin Zhang; Juan Wang; Xianguo Li; Jun Zhang; Yuxiang Liu; Yijia Chen; Qinghui Yu; Ning Li

doi:10.3389/fpls.2023.1204990

Genome-wide identification and expression analyses of phenylalanine ammonia-lyase gene family members from tomato (Solanum lycopersicum) reveal their role in root-knot nematode infection

Front Plant Sci. 2023 Jun 6:14:1204990. doi: 10.3389/fpls.2023.1204990. eCollection 2023.

Authors

Fulin Zhang^{1

2

3}, Juan Wang^{1

2}, Xianguo Li^{1

2

3}, Jun Zhang⁴, Yuxiang Liu^{1

2

3}, Yijia Chen^{1

2

3}, Qinghui Yu^{1

2}, Ning Li^{1

2}

Affiliations

¹ Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China.
² The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China.
³ College of Horticulture, Xinjiang Agricultural University, Urumqi, China.
⁴ Comprehensive Proving Ground, Xinjiang Academy of Agricultural Sciences, Urumqi, China.

Abstract

Phenylalanine ammonia-lyase (PAL) is a key enzyme and rate-limiting enzyme of phenylpropanoid metabolism, which is a very important pathway in plants, and the secondary products it produces play an important role in plant growth and development, disease resistance, and stress resistance responses. However, PALs still lack systematic characterization in tomato. Based on a bioinformatics methods, PAL family genes were identified and characterized from tomato. qRT-PCR was used to study the expression of PAL genes in cultivated tomato after root-knot nematode infection. In this study, 14 and 11 PAL genes were identified in cultivated and wild tomatoes, and phylogenetic analysis classified them into three subfamilies, with different subfamilies of PAL proteins evolving in different directions in monocotyledonous and dicotyledonous plants. The extensive presence of stress, growth, hormone, and light response elements in the promoter sequences of SlPAL (Solanum lycopersicum) and SpenPAL (Solanum pennellii) genes suggests that this family has a critical role in abiotic stress. Collinearity indicates that members of the tomato and Arabidopsis PAL genes family are from the same ancestor, and the SlPAL10 gene is directly homologous to monocotyledonous rice and maize, suggesting that the SlPAL10 gene was present before monocotyledonous differentiation. Two co-expressed gene modules containing PAL genes were screened by WGCNA, and the core genes in the network were mined and functionally annotated by calculating the connectivity of genes within the modules. In addition, the expression of some genes changed significantly after root-knot nematode infection, with up-regulation of 4 genes and down-regulation of 3 genes. This result provides a data reference for the study of PAL family gene functions in tomato, and also provides a potential application for the subsequent selection of PAL genes in tomato for root-knot nematode resistance.

Keywords: PAL gene family; bioinformatics; phylogenetic; root-knot nematode; tomato.

Grants and funding

This work was supported by Opening Foundation of Xinjiang Key Laboratory (XJTSGS-2023001), the National Natural Science Foundation of China (32260763) and the Science and Technology Innovation Special Incubation Project of Xinjiang Academy of Agricultural Sciences (xjkcpy-2021001). The funders had no role in the study design, data analysis and manuscript writing, but only provided financial support.