谷子PLATZ转录因子基因家族的鉴定和分析

doi:10.11983/CBB22147

摘要/Abstract

摘要： PLATZ转录因子家族是一类植物特异性锌依赖DNA结合蛋白, 在植物生长发育和抗逆过程中发挥不可或缺的作用。然而, 对于谷子(Setaria italica) PLATZ家族基因尚未进行系统研究。在谷子基因组中鉴定出17个PLATZ基因并对其进行系统命名。通过系统发育分析将SiPLATZ基因划分为5个亚家族, 同一亚家族成员具有相似的基因结构和保守基序。顺式作用元件分析表明, SiPLATZ基因可能在籽粒胚乳发育和多种抗逆反应中发挥作用。K_a/K_s分析表明, 重复基因受到纯化选择。SiPLATZ基因在不同组织和发育阶段的表达存在显著差异, 主要包括在根、叶和茎中高表达, 以及在穗和籽粒中高表达两类, 这体现出SiPLATZ基因生理功能的复杂性, 其可能参与调节籽粒生长和多种抗逆反应。此外, 结合WGCNA分析构建的共表达网络, 发现SiPLATZ6、SiPLATZ8、SiPLATZ9和SiPLATZ11可能是谷子产量遗传改良和功能基因研究的候选基因。研究结果为深入揭示PLATZ转录因子在谷子生长发育中的生物学功能奠定了基础。

关键词: PLATZ, 谷子, 全基因组鉴定, 组织特异性表达, WGCNA

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

孙蓉, 杨宇琭, 李亚军, 张会, 李旭凯. 谷子PLATZ转录因子基因家族的鉴定和分析. 植物学报, 2023, 58(4): 548-559.

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

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链接本文: https://www.chinbullbotany.com/CN/10.11983/CBB22147

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

图/表 8

表1 谷子SiPLATZ基因家族编码蛋白理化性质

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

图1 谷子、水稻、玉米和拟南芥PLATZ家族蛋白系统发育关系 PLATZ基因家族的亚组通过系统发育树的分支颜色及填充底色区分, 分支长度表示基因的遗传距离。圆形节点的基因与Wang等(2018)的研究分组一致, 方形节点的基因(4个)则与其不同, 节点颜色一致的基因表示在Wang等(2018)的研究中为同一亚组。

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).

图2 谷子PLATZ家族基因结构分析 (A) 谷子PLATZ家族进化树; (B) 谷子PLATZ家族基因结构(CDS: 蛋白质编码区; PLATZ: Plant AT-rich sequence and zinc-bind- ing proteins结构域; UTR: 非翻译区; SP: 信号肽; BBOX: B-Box-type zinc finger结构域); (C) 谷子PLATZ家族保守基序; (D) 谷子PLATZ家族基因启动子顺式作用元件分析

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

表2 NG法计算谷子基因组内SiPLATZ共线性基因对Ka/Ks值

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

图3 PLATZ家族基因共线性分析 (A) 谷子PLATZ家族内部共线性关系; (B) 玉米、谷子、水稻和拟南芥PLATZ家族共线性关系

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

图4 谷子PLATZ家族相关基因局部网络图 (A) Blue模块中谷子PLATZ家族相关基因网络图; (B) Turquoise模块中谷子PLATZ家族相关基因网络图。红色表示核心基因, 蓝色表示候选基因, 黄色表示转录因子, 绿色表示其它连通度较高的共表达基因。圆圈的大小代表基因连通度的高低。圆圈越大连通度越高, 反之越低。

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.

图5 SiPLATZ家族成员在谷子不同组织和发育时期的表达模式 (A) SiPLATZ家族成员在谷子不同组织和发育时期的表达谱(共包括15个组织时期, J2: 谷子灌浆期S3的倒2节茎秆; D4Y: 灌浆期倒4叶; D4sh: 灌浆期倒4叶叶鞘; R: 灌浆期根; P1: 初生分枝分化期小穗; P3: 第3级分枝分化期小穗; PS2: 灌浆期S2小穗; PS4: 灌浆期S4小穗; S1-S5: 灌浆期S1-S5籽粒; Lv: S3期叶脉; M: S3期叶肉); (B) 部分SiPLATZ基因籽粒灌浆S3时期的qPCR验证。

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.

图6 SiPLATZ6、SiPLATZ8、SiPLATZ9及SiPLATZ11基因表达热图

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

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