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首页> 美国卫生研究院文献>Evolutionary Bioinformatics Online >AP2/ERF Transcription Factor in Rice: Genome-Wide Canvas and Syntenic Relationships between Monocots and Eudicots
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AP2/ERF Transcription Factor in Rice: Genome-Wide Canvas and Syntenic Relationships between Monocots and Eudicots

机译：水稻AP2 / ERF转录因子：全基因组画布和单子叶植物与双子叶植物之间的同义关系

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摘要

The transcription factor family intimately regulates gene expression in response to hormones, biotic and abiotic factors, symbiotic interactions, cell differentiation, and stress signalling pathways in plants. In this study, 170 AP2/ERF family genes are identified by phylogenetic analysis of the rice genome (Oryza sativa l. japonica) and they are divided into a total of 11 groups, including four major groups (AP2, ERF, DREB, and RAV), 10 subgroups, and two soloists. Gene structure analysis revealed that, at position-6, the amino acid threonine (Thr-6) is conserved in the double domain AP2 proteins compared to the amino acid arginine (Arg-6), which is preserved in the single domain of ERF proteins. In addition, the histidine (His) amino acid is found in both domains of the double domain AP2 protein, which is missing in single domain ERF proteins. Motif analysis indicates that most of the conserved motifs, apart from the AP2/ERF domain, are exclusively distributed among the specific clades in the phylogenetic tree and regulate plausible functions. Expression analysis reveals a widespread distribution of the rice AP2/ERF family genes within plant tissues. In the vegetative organs, the transcripts of these genes are found most abundant in the roots followed by the leaf and stem; whereas, in reproductive tissues, the gene expression of this family is observed high in the embryo and lemma. From chromosomal localization, it appears that repetition and tandem-duplication may contribute to the evolution of new genes in the rice genome. In this study, interspecies comparisons between rice and wheat reveal 34 rice loci and unveil the extent of collinearity between the two genomes. It was subsequently ascertained that chromosome-9 has more orthologous loci for CRT/DRE genes whereas chromosome-2 exhibits orthologs for ERF subfamily members. Maximum conserved synteny is found in chromosome-3 for AP2 double domain subfamily genes. Macrosynteny between rice and Arabidopsis, a distant, related genome, uncovered 11 homologs/orthologs loci in both genomes. The distribution of AP2/ERF family gene paralogs in Arabidopsis was most frequent in chromosome-1 followed by chromosome-5. In Arabidopsis, ERF subfamily gene orthologs are found on chromosome-1, chromosome-3, and chromosome-5, whereas DRE subfamily genes are found on chromosome-2 and chromosome-5. Orthologs for RAV and AP2 with double domains in Arabidopsis are located on chromosome-1 and chromosome-3, respectively. In conclusion, the data generated in this survey will be useful for conducting genomic research to determine the precise role of the AP2/ERF gene during stress responses with the ultimate goal of improving crops.
机译：转录因子家族响应激素，生物和非生物因子，共生相互作用，细胞分化以及植物的胁迫信号通路，密切调节基因表达。在这项研究中，通过对水稻基因组（Oryza sativa l。japonica）的系统进化分析鉴定了170个AP2 / ERF家族基因，它们共分为11个组，包括四个主要组（AP2，ERF，DREB和RAV） ），10个小组和两名独奏者。基因结构分析表明，与氨基酸精氨酸（Arg-6）保留在ERF蛋白的单个域相比，氨基酸苏氨酸（Thr-6）在第6位保留在双域AP2蛋白中。此外，在双结构域AP2蛋白的两个结构域中都发现了组氨酸（His）氨基酸，而在单结构域ERF蛋白中则没有。母题分析表明，除AP2 / ERF结构域外，大多数保守基序都专门分布在系统发育树中的特定进化枝之间，并调节合理的功能。表达分析显示水稻AP2 / ERF家族基因在植物组织中的广泛分布。在营养器官中，发现这些基因的转录本在根部最丰富，其次是叶和茎。而在生殖组织中，该家族的基因表达在胚胎和外中较高。从染色体定位看来，重复和串联重复可能有助于水稻基因组中新基因的进化。在这项研究中，水稻和小麦之间的种间比较揭示了34个水稻基因座，并揭示了两个基因组之间的共线性程度。随后确定9号染色体对CRT / DRE基因具有更多的直系同源基因座，而2号染色体对ERF亚家族成员表现出直系同源基因。在AP3双结构域亚家族基因的3号染色体中发现了最大的保守同义。水稻和拟南芥（一个遥远的相关基因组）之间的大同化在两个基因组中均发现了11个同源/直系同源基因座。 AP2 / ERF家族基因旁系同源物在拟南芥中的分布最常见于1号染色体，其次是5号染色体。在拟南芥中，在1号染色体，3号染色体和5号染色体上发现了ERF亚家族基因直系同源物，而在2号染色体和5号染色体上发现了DRE亚家族基因。 RAV和AP2在拟南芥中具有双结构域的直系同源物分别位于1号染色体和3号染色体上。总之，本次调查产生的数据将有助于进行基因组研究，确定AP2 / ERF基因在胁迫响应过程中的精确作用，最终目的是改善作物。

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