甘蓝型油菜ZF-HD基因家族的鉴定与系统进化分析

doi:10.11983/CBB19055

植物学报 ›› 2019, Vol. 54 ›› Issue (6): 699-710.DOI: 10.11983/CBB19055

甘蓝型油菜ZF-HD基因家族的鉴定与系统进化分析

宋敏(),张瑶,王丽莹,彭向永

曲阜师范大学生命科学学院, 曲阜 273165

收稿日期:2019-03-25 接受日期:2019-07-26 出版日期:2019-11-01 发布日期:2020-07-09
通讯作者: 宋敏
基金资助:
山东省高等学校科技计划(No.J15LE02);中国博士后基金(No.2018M632646);山东省高水平应用型立项建设专业群-生物工程专业群(No.[2016] 11-10)

Genome-wide Identification and Phylogenetic Analysis of Zinc Finger Homeodomain Family Genes in Brassica napus

Min Song(),Yao Zhang,Liying Wang,Xiangyong Peng

School of Life Sciences, Qufu Normal University, Qufu 273165, China

Received:2019-03-25 Accepted:2019-07-26 Online:2019-11-01 Published:2020-07-09
Contact: Min Song

摘要/Abstract

摘要： ZF-HD是一类植物特有的转录因子, 在植物生长发育及胁迫响应过程中发挥重要作用。利用生物信息学方法, 在甘蓝型油菜(Brassica napus)基因组中鉴定到62个ZF-HD基因, 其中83.9%的基因缺乏内含子, 93.5%的BnZF-HD等电点大于7, 预测定位于细胞核的蛋白大多由100个以上氨基酸组成。根据进化关系可将其分为6个亚群, 在每个亚群中, 甘蓝(B. oleracea)和白菜(B. rapa)的ZF-HD基因数量相等或近似相等, 而甘蓝型油菜的ZF-HD基因数量接近或等同于甘蓝和白菜的ZF-HD基因数量之和。同一亚群的motif数量和类型高度相似。共线性分析结果显示, 全基因组三倍体化使ZF-HD基因在二倍体祖先得到扩张, 而异源多倍体化又进一步使甘蓝型油菜ZF-HD基因家族扩张。K_a/K_s值说明大多数ZF-HD基因在进化过程中受到了纯化选择。所有BnZF-HD基因都具有光响应元件, 2/3的基因具有MeJA、ABA和厌氧诱导顺式作用元件, 推测这些基因可能参与相关生物学过程。研究结果为进一步挖掘该家族基因的生物学功能奠定基础, 同时为揭示多基因家族在异源多倍体中的进化式样提供借鉴。

关键词: 甘蓝型油菜, ZF-HD, 进化, 共线性分析, 顺式作用元件

Abstract: Zinc finger-homeodomain (ZF-HD) genes encode plant-specific transcription factors that participate in the regulation of plant growth, development and abiotic stress response. In this study, a total of 62 ZF-HD genes were identified in Brassica napus. Among them, 83.9% lack introns, 93.5% of deduced proteins have the isoelectric point greater than 7. Most of the BnZF-HD proteins with nuclear localization signal were predicted to be more than 100 amino acid residues. Based on phylogenetic analysis, this gene family can be divided into six subgroups. In each subgroup, the number of ZF-HD genes in B. oleracea and B. rapa was the same or nearly so, while the number of ZF-HD genes in B. napus was close to or equal to the sum of ZF-HD genes in B. oleracea and B. rapa. The number and type of motifs in each subgroup were highly conserved. Collinear analysis indicated that the whole genome triplication allowed the ZF-HD gene family to expand in diploid ancestors, and allopolyploidization made the ZF-HD gene family to reexpand in B. napus. K_a/K_s analysis showed that the ZF-HD gene family has experienced purification selection in the evolution process. All BnZF-HD genes have light response elements, and two-thirds of them have MeJA, ABA and anaerobic inducible cis-acting elements. It is speculated that they may participate in related biological processes. This study laid a foundation for further exploring the molecular mechanism of this family in regulating plant growth and stress responses, and provided more reference for future research on the evolution of plant polyploidization.

Key words: Brassica napus, ZF-HD, evolution, collinear analysis, cis-acting elements

宋敏,张瑶,王丽莹,彭向永. 甘蓝型油菜ZF-HD基因家族的鉴定与系统进化分析. 植物学报, 2019, 54(6): 699-710.

Min Song,Yao Zhang,Liying Wang,Xiangyong Peng. Genome-wide Identification and Phylogenetic Analysis of Zinc Finger Homeodomain Family Genes in Brassica napus. Chinese Bulletin of Botany, 2019, 54(6): 699-710.

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链接本文: https://www.chinbullbotany.com/CN/10.11983/CBB19055

https://www.chinbullbotany.com/CN/Y2019/V54/I6/699

图/表 4

图1 甘蓝型油菜、拟南芥、白菜和甘蓝ZF-HD蛋白的系统发生树利用MEGA 7.0软件构建邻接树, bootstrap值设为1 000。

Figure 1 Phylogenetic analysis of Brassica napus, Arabidopsis thaliana, B. rapa and B. oleracea ZF-HD proteins This phylogenetic unrooted tree was constructed by the neighbor-joining (NJ) method with MEGA 7.0, with 1 000 bootstrap replicates.

图2 甘蓝型油菜(A, B)、白菜(C)和甘蓝(D) ZF-HD基因在染色体上的分布基因名称后标注该基因所属亚群。

Figure 2 Chromosomal location of ZF-HD genes from Brassica napus (A, B), B. rapa (C) and B. oleracea (D) The gene name was followed by its subgroup.

图3 甘蓝型油菜ZF-HD蛋白家族的聚类(A)、motif结构(B)和顺式作用元件(C)

Figure 3 Phylogenetic analysis (A), motif structure (B) and cis-acting element (C) of different ZF-HD protein families in Brassica napus

图4 甘蓝型油菜、白菜、甘蓝与拟南芥ZF-HD基因的染色体共线性关系

Figure 4 Collinear relationship of ZF-HD genes among Brassica napus, B. rapa, B. oleracea, and Arabidopsis thaliana chromosomes

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甘蓝型油菜ZF-HD基因家族的鉴定与系统进化分析

Genome-wide Identification and Phylogenetic Analysis of Zinc Finger Homeodomain Family Genes in Brassica napus

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