Genome-Wide Identification and Expression Analysis of the PLATZ Transcription Factor in Tomato

Abstract

The PLATZ (plant AT protein and zinc-binding protein) transcription factor family is involved in the regulation of plant growth and development and plant stress response. In this study, 24 SlPLATZs were identified from the cultivated tomato genome and classified into four groups based on the similarity of conserved patterns among members of the same subfamily. Fragment duplication was an important way to expand the SlPLATZ gene family in tomatoes, and the sequential order of tomato PLATZ genes in the evolution of monocotyledonous and dicotyledonous plants and the roles they played were hypothesized. Expression profiles based on quantitative real-time reverse transcription PCR showed that SlPLATZ was involved in the growth of different tissues in tomatoes. SlPLATZ21 acts mainly in the leaves. SlPLATZ9, SlPLATZ21, and SlPLATZ23 were primarily involved in the red ripening, expanding, and mature green periods of fruit, respectively. In addition, SlPLATZ1 was found to play an important role in salt stress. This study will lay the foundation for the analysis of the biological functions of SlPLATZ genes and will also provide a theoretical basis for the selection and breeding of new tomato varieties and germplasm innovation.

Keywords: PLATZ gene family; biotic/abiotic stresses; expression analysis; phylogeny analysis.

Figure 1

Location of the SlPLATZ genes on the chromosomes of Heinz tomatoes.

Figure 2

Analysis of motif structure, gene structure, and phylogenetic analysis of SlPLATZ. (A) Ten amino acid motifs in the SlPLATZ protein are indicated by a colored box. (B) The blue box indicates exons, the purple box indicates UTRs, and the gray line indicates introns.

Figure 3

Phylogenetic tree of PLATZ family members. The red rhombus indicates the cultivated tomato, whereas the green rhombus identifies the pennellii tomato. The blue line connects monocotyledons, while the purple line connects dicotyledons.

Figure 4

Gene duplication events in the genome, with the circles from outer to inner representing the chromosomes of cultivated tomatoes, the gene density, and the N ratio presented in red dots, and the ends of the red lines representing direct homologous SlPLATZ genes. The legend represents the values of the gene density, With red representing high levels and yellow representing low levels.

Figure 5

The collinearity diagram of PLATZ genes. Red lines highlight the homologous gene pairs of SlPLATZ genes, and gray lines represent genome-wide collinear gene pairs.

Figure 6

The number of cis-acting elements contained in the promoter of the SlPLATZ genes. The number of cis-acting elements involved in different regulatory pathways varies. Darker red colors indicate higher numbers of cis-acting elements. Darker blue colors indicate lower numbers of cis-acting elements.

Figure 7

An interaction network of PLATZ genes in tomato. Each node is a protein, and each edge represents the presence of interactions. The size of the node represents the number of interactions. The thickness of the edge represents the value of the combined score. Red nodes represent PLATZ proteins, blue nodes represent stress-related proteins, and gray nodes represent proteins lacking annotation.

Figure 8

Heat map of tissue-specific expression of PLATZ genes in tomato. The color bar represents the log² expression values, with red representing high expression levels and blue representing low expression levels. The gene name is shown on the right side. LA1589 20-day post-anthesis fruit (20 DPA), LA1589 10-day post-anthesis fruit (10 DPA1), LA1589 10-day post-anthesis fruit 2 (10 DPA2), LA1589 root (ROOT), LA1589 anthesis flowers (0 DPA), LA1589 vegetative meristems (MERI), LA1589 young flower buds (YFB), LA1589 young leaves (YL), LA1589 hypocotyl (HYPO), LA1589 cotyledons (COTYL), LA1589 ripening fruit (33 DPA), and LA1589 mature leaves (ML).

Figure 9

Relative expression of SlPLATZ2, SlPLATZ21, SlPLATZ23, and SlPLATZ24 in roots, stems, and leaves. p < 0.0001. The standard is the largest average marked with a, and the following unmarked averages are marked with the letter a where it is not significant until a certain average that differs significantly from it is marked with the letter b. The largest average that begins with the letter b should then be used as a benchmark for comparison with the remaining averages. Continue to append the letter b to any non-significant variances. Until they differ sufficiently, at which point they are designated with the letter c.

Figure 10

Expression analysis of the SlPLATZ genes under hormone stress during fruit development. The error bar shows the standard deviation of three biological repeats. EP—Expending period; MG—Mature green period; BP—breaker period; RRP—Red ripening period; CK—control; NAA—naphthenic acid; EBR—2,4 epibrassinolide; MT—melatonin. p < 0.0001. The standard is the largest average marked with a, and the following unmarked averages are marked with the letter a where it is not significant until a certain average that differs significantly from it is marked with the letter b. The largest average that begins with the letter b should then be used as a benchmark for comparison with the remaining averages. Continue to append the letter b to any non-significant variances. Until they differ sufficiently, at which point they are designated with the letter c. The largest average that begins with the letter c should then be used as a benchmark for comparison with the remaining averages. Continue to append the letter c to any non-significant variances. Until they differ sufficiently, at which point they are designated with the letter d.

Figure 11

Analysis of salt stress expression in SlPLATZ1 and SlPLATZ21 leaves. p < 0.0001. The standard is the largest average marked with a, and the following unmarked averages are marked with the letter a where it is not significant until a certain average that differs significantly from it is marked with the letter b. The largest average that begins with the letter b should then be used as a benchmark for comparison with the remaining averages. Continue to append the letter b to any non-significant variances. Until they differ sufficiently, at which point they are designated with the letter c.