Complex Phylogeny and Expression Patterns of the NITRATE TRANSPORTER 1/PEPTIDE TRANSPORTER Family Genes in Tomato

The NITRATE TRANSPORTER 1/PEPTIDE TRANSPORTER family (NPF) proteins play important roles in transporting substrates, such as nitrate, peptides, amino acids, dicarboxylates, malate, glucosinolates, indole acetic acid, abscisic acid, and jasmonic acid. However, there is limited information on the NPF genes in tomato (Solanum lycopersicum L.), in contrast to Arabidopsis. Our study aimed to reveal general information about tomato NPFs and to analyze the transcriptional responses of some members using plant nitrogen status. We identified 85 SlNPF genes, and a phylogenetic analysis organized them into nine major clades. Thirty motifs were found based on NPF amino acid sequence alignments. Chromosomal locations and gene duplication events of SlNPF family genes were also analyzed. An uneven distribution of SlNPF genes was discovered among tomato chromosomes. Twenty-five SlNPF genes resulted from whole-genome triplication (WGT)/segmental duplication in Solanaceae. Our results showed that ancient whole-genome triplication and tandem duplication mainly contributed to the expansion of the SlNPF genes. In the NPF family, 19 orthologous genes were identified between tomato and Arabidopsis, suggesting that at least 19 NPF genes were present in a common ancestor before Arabidopsis and tomato differentiated. In addition, we analyzed the expression patterns of the SlNPF family genes in various tomato tissues. We monitored 49 root-specific SlNPF genes that showed varied expression patterns under different N status. Among them, SINPF9, -34, -58 and -60 were significantly induced by both low and high levels of nitrate. Our findings provide a foundation for future research on this gene family.

Automated summary

The NPF gene family in tomato exhibits diversity and shows different transcriptional responses under plant nitrogen status. Whole-genome triplication and tandem duplication are major contributions to the expansion of SlNPF genes. The identification of 19 orthologous genes suggests the presence of at least 19 NPF genes in a common ancestor before Arabidopsis and tomato diverged.