The auxin response factor gene family in allopolyploid Brassica napus
The auxin response factor gene family in allopolyploid Brassica napus
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异源多倍体甘蓝型油菜生长素反应因子基因家族
DOI：
10.1371/journal.pone.0214885
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发表时间：
2019-04
期刊：
影响因子：
3.7
通讯作者：
Du Hai
中科院分区：
文献类型：
--
作者：
Wen Jing;Guo Pengcheng;Ke Yunzhuo;Liu Mingming;Li Pengfeng;Wu Yunwen;Ran Feng;Wang Mangmang;Li Jiana;Du Hai
生长素反应因子（ARF）是植物特异性B3 DNA结合超家族的成员。本文报道了对异源四倍体甘蓝型油菜（2n = 38，AACC）ARF基因的综合分析结果。在B中鉴定出67个ARF基因。napus（BnARFs），分为四个亚科（I-IV）。61个BnARF分布在除C 02外的所有染色体上;其余的分布在Ann和Cnn上。BnARF蛋白的全长高度保守，尤其是在每个亚家族中，所有成员共享N端DNA结合结构域（DBD）和中间区域（MR），并且大多数包含C端二聚化结构域（PBI）。21名成员有一个谷氨酰胺丰富的MR，这可能是一个激活剂，其余的是阻遏物。因此，内含子模式在每个亚家族或进化枝中高度保守，特别是在DBD和PBI结构域中。亚家族III中的几个成员是miR 167的潜在靶点。许多假定的顺式元件参与植物激素，光信号响应，生物和非生物胁迫被确定在BnARF启动子，这意味着他们可能的作用。大多数ARF蛋白可能与生长素/吲哚乙酸（Aux/IAA）相关蛋白相互作用，并且不同亚家族的成员通常具有许多共同的相互作用蛋白。芜菁与甘蓝杂交产生的全基因组复制和片段复制导致了基因扩增。WGD后的基因丢失是有偏向的，An-亚基因组比Cn-亚基因组保留更多的祖先基因。BnARF在不同发育阶段的营养和生殖器官中具有广泛的表达谱。An-和Cn-亚基因组之间没有观察到明显的表达偏倚。大多数同线性对基因具有相似的表达模式，表明它们的功能冗余。BnARF对外源IAA和6-BA处理敏感，尤其是亚家族III。本研究为了解ARF基因家族的分布、发生和进化提供了新的思路。
Auxin response factor (ARF) is a member of the plant-specific B3 DNA binding superfamily. Here, we report the results of a comprehensive analysis of ARF genes in allotetraploid Brassica napus (2n = 38, AACC). Sixty-seven ARF genes were identified in B. napus (BnARFs) and divided into four subfamilies (I–IV). Sixty-one BnARFs were distributed on all chromosomes except C02; the remaining were on Ann and Cnn. The full length of the BnARF proteins was highly conserved especially within each subfamily with all members sharing the N-terminal DNA binding domain (DBD) and the middle region (MR), and most contained the C-terminal dimerization domain (PBI). Twenty-one members had a glutamine-rich MR that may be an activator and the remaining were repressors. Accordingly, the intron patterns are highly conserved in each subfamily or clade, especially in DBD and PBI domains. Several members in subfamily III are potential targets for miR167. Many putative cis-elements involved in phytohormones, light signaling responses, and biotic and abiotic stress were identified in BnARF promoters, implying their possible roles. Most ARF proteins are likely to interact with auxin/indole-3-acetic acid (Aux/IAA) -related proteins, and members from different subfamilies generally shared many common interaction proteins. Whole genome-wide duplication (WGD) by hybridization between Brassica rapa and Brassica oleracea and segmental duplication led to gene expansion. Gene loss following WGD is biased with the An-subgenome retaining more ancestral genes than the Cn-subgenome. BnARFs have wide expression profiles across vegetative and reproductive organs during different developmental stages. No obvious expression bias was observed between An- and Cn-subgenomes. Most synteny-pair genes had similar expression patterns, indicating their functional redundancy. BnARFs were sensitive to exogenous IAA and 6-BA treatments especially subfamily III. The present study provides insights into the distribution, phylogeny, and evolution of ARF gene family.
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