AUTHOR=Zhang Fulin , Wang Juan , Li Xianguo , Zhang Jun , Liu Yuxiang , Chen Yijia , Yu Qinghui , Li Ning 

TITLE=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

JOURNAL=Frontiers in Plant Science

VOLUME=14

YEAR=2023

URL=https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2023.1204990

DOI=10.3389/fpls.2023.1204990

ISSN=1664-462X

ABSTRACT=<p>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 <italic>PAL</italic> 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 <italic>SlPAL</italic> (<italic>Solanum lycopersicum</italic>) and <italic>SpenPAL</italic> (<italic>Solanum pennellii</italic>) genes suggests that this family has a critical role in abiotic stress. Collinearity indicates that members of the tomato and Arabidopsis <italic>PAL</italic> genes family are from the same ancestor, and the <italic>SlPAL10</italic> gene is directly homologous to monocotyledonous rice and maize, suggesting that the <italic>SlPAL10</italic> gene was present before monocotyledonous differentiation. Two co-expressed gene modules containing <italic>PAL</italic> 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 <italic>PAL</italic> family gene functions in tomato, and also provides a potential application for the subsequent selection of <italic>PAL</italic> genes in tomato for root-knot nematode resistance.</p>