Genome-Wide Identification of PLATZ Transcription Factors in Ginkgo biloba L. and Their Expression Characteristics During Seed Development

Abstract

Plant AT-rich protein and zinc-binding protein (PLATZ) is a class of plant-specific zinc-dependent DNA-binding protein that binds to A/T-rich DNA sequences. PLATZ plays an important role in seed development, water tolerance, and cell proliferation in early plant growth. In this study, 11 GbPLATZs were identified from the ginkgo genome with complete PLATZ-conserved domains, which represents a smaller number compared with angiosperms. Multi-species phylogenetic analysis showed that PLATZ genes were conserved in seed plants, and the 11 members were represented by four groups, among which groups I and II were closely related. Analysis of gene structures, sequence module characteristics, and expression patterns showed that GbPLATZs were similar within and differed between groups. RNA-seq and qRT-PCR results showed that GbPLATZs had distinct expression patterns. Most genes were associated with seed development, among which six genes were highly related. Subcellular localization experiments showed that six GbPLATZ proteins related to seed development were localized in the nucleus, suggesting that they might function as traditional transcription factors. This study provides a basis for understanding the structural differentiation, evolutionary characteristics, expression profile, and potential functions of PLATZ transcription factors in Ginkgo biloba.

Keywords: Ginkgo biloba L.; PLATZ; expression pattern; seed development; subcellular localization.

Figure 1

SeqLogo of two conserved regions of the PLATZ transcription factor in ginkgo.

Figure 2

Phylogenetic analysis of the GbPLATZs. (A) Maximum likelihood trees of 11 PLATZ transcription factors in Ginkgo biloba. I–IV represents four categories based on phylogenetic topology. (B) Maximum likelihood tree for ginkgo (Gb), Norway spruce (MA), maize (Zm), and Arabidopsis (AT) PLATZ TFs, where GbPLATZs and their branches are represented in red. The gymnosperms branches are highlighted in brown. The branch length is proportional to the rate of amino acid change. The size of a point on a branch represents the bootstrap value of the branch.

Figure 3

Mapping of GbPLATZs gene in ginkgo chromosomes. The dark gray number represents the corresponding chromosome, the length of the green bar represents the length range of the chromosome, the scale on the left represents the distance on the chromosome position, and the 11 GbPLATZ genes are represented in red. The Roman letters under the gene name represent the group.

Figure 4

Motif structure, gene structure, and family conservation analysis of GbPLATZs. (A) The 12 MEME motifs are similar within groups and different between groups. (B) According to genome annotation data, GbPLATZ gene structure, and batch-SMART analysis, the type and location of the conservative domain are presented here, with rectangles for exons, horizontal lines for introns, green for CDS regions, and other colors for corresponding conservative domains.

Figure 5

Protein secondary and tertiary structure prediction of GbPLATZs. (A) Prediction of protein secondary structure based on SOPMA. (B) Protein tertiary structure prediction based on AlphaFold2, protein coloring represents the pLDDT confidence measure, and green and white arrows represent the approximate location of domain 1 and domain 2, respectively.

Figure 6

Cis-acting elements related to seeds from PLACE prediction results upstream of GbPLATZs. SUM represents the total number of cis-acting elements upstream of the 11 GbPLATZs. COUNT represents the number of GbPLATZs whose upstream regions contain the respective elements.

Figure 7

Expression pattern analysis of GbPLATZs. (A) Expression of GbPLATZs in different tissues based on NCBI data. TPM values calculated by READ_NUM were homogenized. The darker the red, the higher the expression level; the darker the blue, the lower the expression level. The evolution tree on the left of the heat map was drawn based on GbPLATZ gene sequence data and is consistent with Figure 2A. (B) The expression level of GbPLATZs during PEG 6000 treatment based on NCBI data. The x-axis represents the time of PEG 6000 treatment, the y-axis represents the TPM value, and the dotted lines separate genes with distinct expression patterns. (C) Real-time quantitative data of each gene based on plant materials used in this study, the x-axis represents the different tissues. R, root; S, stem; L, leaf; M, micro-strobilus; O, ovulate-strobilus; Jun-K, kernel in June; Oct-K, kernel in October; and T, testa. F-test: ** < 0.01, * < 0.05.

Figure 8

The subcellular localization of GbPLATZ proteins in ginkgo. The fusion location of the GFP gene sequence is shown on the left. Scale bars = 10 μm.