Genome-wide Identification and Analysis of PLATZ Transcription Factor Gene Family in Foxtail Millet

doi:10.11983/CBB22147

Abstract

Abstract: The PLATZ transcription factor family is a class of plant-specific zinc-dependent DNA-binding proteins that play an indispensable role in plant growth and development and stress resistance. However, the PLATZ family genes have not been systematically analyzed in foxtail millet (Setaria italica). In this study, 17 PLATZ genes in the foxtail millet genome were identified and systematically named. The SiPLATZ genes were divided into five subfamilies by phylogenetic analysis, and members of the same subfamily have similar gene structures and motifs. Cis-acting element analysis demonstrated that the SiPLATZ genes may play a role in endosperm development and various stress-resistant responses. The K_a/K_s ratio analysis indicates that duplicated genes are subject to purifying selection. There were significant differences in the expression of SiPLATZ genes in different tissues and developmental stages, which were mainly divided into two categories: high expression in roots, leaves, and stems, and in spikes and seeds. This reflects the complexity of the physiological functions of SiPLATZ genes and their possible involvement in regulating seed growth and multiple stress responses. In addition, the co-expression network constructed in combination with WGCNA analysis revealed that SiPLATZ6, SiPLATZ8, SiPLATZ9 and SiPLATZ11 may be the candidates for genetic improvement of foxtail millet yield and functional gene research. These results lay the foundation for further studies on the biological functions of PLATZ transcription factors in foxtail millet growth and development.

Key words: PLATZ, foxtail millet, genome-wide identification, tissue specific expression, WGCNA

Rong Sun, Yulu Yang, Yajun Li, Hui Zhang, Xukai Li. Genome-wide Identification and Analysis of PLATZ Transcription Factor Gene Family in Foxtail Millet[J]. Chinese Bulletin of Botany, 2023, 58(4): 548-559.

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URL: https://www.chinbullbotany.com/EN/10.11983/CBB22147

https://www.chinbullbotany.com/EN/Y2023/V58/I4/548

Figures/Tables 8

Table 1 Physicochemical properties of the proteins encoded by SiPLATZ gene family in foxtail millet

Gene name	Locus ID	Protein length (aa)	Molecular weight (kDa)	Isoelectric point	Instability index	Predicted sub-cellular localization
SiPLATZ1	Si1g06060	210	22.98	6.65	45.46	Nucleus
SiPLATZ2	Si1g06070	182	19.81	9.32	43.97	Nucleus
SiPLATZ3	Si1g06080	248	26.72	5.45	45.38	Nucleus, mitochondrion
SiPLATZ4	Si1g06100	143	15.56	9.05	42.96	Nucleus, chloroplast
SiPLATZ5	Si1g06720	237	27.18	8.75	54.77	Nucleus
SiPLATZ6	Si1g07690	257	27.79	8.63	45.93	Chloroplast
SiPLATZ7	Si1g26800	198	21.94	9.05	69.15	Nucleus
SiPLATZ8	Si1g28470	247	27.37	9.07	56.56	Nucleus
SiPLATZ9	Si4g17460	242	26.07	8.65	47.57	Nucleus, cell membrane, chloroplast
SiPLATZ10	Si4g20160	243	26.84	9.47	60.37	Nucleus
SiPLATZ11	Si5g17000	214	24.38	7.90	63.39	Nucleus
SiPLATZ12	Si5g19690	209	23.92	6.50	66.21	Nucleus
SiPLATZ13	Si6g24710	207	22.35	9.15	47.83	Nucleus, chloroplast
SiPLATZ14	Si7g22910	251	27.42	9.23	51.67	Nucleus
SiPLATZ15	Si9g30780	246	26.90	9.16	56.51	Nucleus
SiPLATZ16	Si9g36990	256	29.23	6.02	70.27	Nucleus
SiPLATZ17	Si9g47270	239	26.34	9.37	52.33	Nucleus

Figure 1 Phylogenetic relationships of PLATZ family proteins in foxtail millet, rice, maize and Arabidopsis The branch color and filled base color on the phylogenetic tree distinguish subgroups of the PLATZ gene family, and the branch length indicates the genetic distance of the gene. Genes in round nodes are consistent with the grouping of Wang et al. (2018), genes in square nodes (4 genes) are different from that, and genes with the same node colors indicate in the same subgroup of the Wang et al. (2018).

Figure 2 Structural analysis of PLATZ family genes in foxtail millet (A) Evolutionary tree of PLATZ family in foxtail millet; (B) The gene structure of PLATZ family in foxtail millet (CDS: Coding sequences; PLATZ: Plant AT-rich sequence and zinc-binding protein domains; UTR: Untranslated regions; SP: Signal peptide; BBOX: B-Box-type zinc finger domains); (C) The conserved motif of PLATZ family in foxtail millet; (D) Analysis of cis-acting elements in the promoter of PLATZ family gene in foxtail millet

Table 2 Calculation of Ka/Ks value of SiPLATZ collinear gene pair in foxtail millet genome by NG method

Homologous gene	K_a	K_s	K_a/K_s
SiPLATZ10-SiPLATZ4 segmental duplication	0.434473	0.577238	0.752677
SiPLATZ14-SiPLATZ8 segmental duplication	0.164238	0.394477	0.416344
SiPLATZ1-SiPLATZ2 tandem repeats	0.471405	1.482013	0.318084
SiPLATZ1-SiPLATZ3 tandem repeats	0.415490	0.958245	0.433595
SiPLATZ1-SiPLATZ4 tandem repeats	0.173058	0.550660	0.314274
SiPLATZ2-SiPLATZ3 tandem repeats	0.516098	0.872575	0.591465
SiPLATZ2-SiPLATZ4 tandem repeats	0.614008	1.027812	0.597393
SiPLATZ3-SiPLATZ4 tandem repeats	0.352090	0.772969	0.455503

Figure 3 Collinear analysis of PLATZ family genes (A) The internal collinearity of the PLATZ family in foxtail millet; (B) The collinearity of the PLATZ family in maize, foxtail millet, rice and Arabidopsis

Figure 4 Local network of genes related to the PLATZ family of foxtail millet (A) The related gene network diagram of the foxtail millet PLATZ family in the blue module; (B) The related gene network diagram of the foxtail millet PLATZ family in the turquoise module. Red indicates the core gene, blue indicates the candidate gene, yellow indicates the transcription factor, and green indicates other co-expressed genes with high connectivity. The size of the circle represented the level of gene connectivity. The larger the circle, the higher the connectivity, and vice versa.

Figure 5 Expression patterns of SiPLATZ family members in different tissue and development stages of foxtail millet (A) The expression levels of SiPLATZ family members in different tissue stages of foxtail millet (it consists of 15 tissue stages, J2: Stem-top-second_filling-stage; D4Y: Leaf-top-fourth_filling-stage; D4sh: Leaf-sheath-top-fourth_filling-stage; R: Root_filling- stage; P1: Panicle_primary-panicle-branch-differentiation-stage; P3: Panicle_third-panicle-branch-differentiation-stage; PS2: Immature-spikelet_S2; PS4: Immature-spikelet_S4; S1-S5: Immature-seed_S1-S5; Lv: Leaf-veins_S3; M: Mesophyll_S3); (B) qPCR verification of part of the SiPLATZ genes.

Figure 6 Heat map of gene expression of SiPLATZ6, SiPLATZ8, SiPLATZ9 and SiPLATZ11

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