Identification of PLATZ genes in Malus and expression characteristics of MdPLATZs in response to drought and ABA stresses

Abstract

Plant AT-rich sequences and zinc-binding proteins (PLATZ) play crucial roles in response to environmental stresses. Nevertheless, PLATZ gene family has not been systemically studied in Rosaceae species, such as in apple, pear, peach, or strawberry. In this study, a total of 134 PLATZ proteins were identified from nine Rosaceae genomes and were classified into seven phylogenetic groups. Subsequently, the chromosomal localization, duplication, and collinearity relationship for apple PLATZ genes were investigated, and segmental duplication is a major driving-force in the expansion of PLATZ in Malus. Expression profiles analysis showed that PLATZs had distinct expression patterns in different tissues, and multiple genes were significantly changed after drought and ABA treatments. Furthermore, the co-expression network combined with RNA-seq data showed that PLATZ might be involved in drought stress by regulating ABA signaling pathway. In summary, this study is the first in-depth and systematic identification of PLATZ gene family in Rosaceae species, especially for apple, and provided specific PLATZ gene resource for further functional research in response to abiotic stress.

Keywords: Malus; PLATZ; Rosaceae species; co-expression network; drought stress.

Figure 1

The maximum-likelihood phylogenetic tree of the PLATZ genes. I-VII represent seven groups marked in different colors. The blue, orange, and green pentacles represent the PLATZ genes from Malus, other Rosaceae species (Fragaria vesca v4.0, Prunus persica, and Pyrus communis L.), and model plants (A. thaliana and O. sativa), respectively.

Figure 2

Distribution of conserved motifs and exon–intron structures of the PLATZ family genes in Malus species. The phylogenetic tree was constructed by MEGA-6, using full-length amino acid sequences (1000 Bootstrap replicates and LG substitution model). Different colors in the branches indicate different groups. Green and yellow boxes indicate the coding sequences and the untranslated regions, black lines represent the introns. A total of 8 motifs (motif 1-8) were predicted by MEME tool, and the boxes with different colors indicate different motifs.

Figure 3

Synteny relationships of the PLATZ genes in Malus species. (A–E) The chromosomal distribution and intra-genomic collinearity of the Mdg, Md, Mdhf, Msi, and Msy genomes. Different homologous gene pairs are connected by different colored lines in five Malus species. The light red ribbons represent syntenic blocks in the Malus genome, and the segmental duplication events are marked in different colors. (F) Boxplot showing the statistics of Ka/Ks values of the gene pairs in five apple species.

Figure 4

Collinear analysis between Md and other four Malus species (Mdhf, Mdg, Msi, and Msy). The position distribution of the PLATZ gene was marked with boxes on 17 chromosomes. Collinear gene pairs in apple genomes were linked by gray lines, the black lines inter-connectted the collinear gene pairs of the PLATZ gene family.

Figure 5

Expression of MdPLATZ genes in different tissues including root, stem, leaf, tree shoot apex, dormant buds, flower, stigma, style, ovary, filament, anther, pollen, petals, sepal, receptacle, and fruit.

Figure 6

Expression analysis of MdPLATZs under drought and ABA treatments. (A) The expression levels of MdPLATZs in apple roots under drought stress. (B) Pearson’s correlation of the expression patterns of 17 MdPLATZ genes under drought stress. (C) The expression levels of MdPLATZs in apple roots under ABA treatment. (D) Pearson’s correlation of expression patterns in 17 MdPLATZ genes under ABA treatment. **indicates a significance correlation at the levels of p < 0.01.

Figure 7

Subcellular localization of three MdPLATZ proteins. 35S::MdPLATZ2, 35S::MdPLATZ 10, 35S::MdPLATZ11::GFP, pHBT-NLS-mCherry, and 35S::GFP control were transiently expressed in N. benthamiana leaves and were detected under a confocal microscope. Scale bars represent 10 μm.

Figure 8

The co-expression network of MdPLATZ genes in Malus. (A) Co-expression network between 17 MdPLATZ and their co-expressed genes. The light green nodes indicate co-expressed genes, and the dark green nodes represent MdPLATZs. (B) Expressions of 412 PLATZ co-expressed genes in apple leaves from RNA-seq data under drought stress. (C, D) GO and KEGG enrichment analysis of the 412 co-expressed genes.