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甘薯基因组R2R3-MYB转录因子鉴定与分析 被引量:2

Identification and Analysis of R2R3-MYB Transcription Factor in Sweet Potato Genome
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摘要 MYB是植物中数量众多且功能重要的转录因子家族。本研究通过生物信息学方法从未经注释的甘薯全基因组序列中筛选鉴定出MYB家族基因,分析了R2R3-MYB类基因的结构与功能。结果发现,甘薯基因组中含有R2R3-MYB转录因子基因88个,均含有完整的R2、R3保守结构域,且R2、R3保守结构域中分别含有8个和9个高度保守的碱性氨基酸。MEME分析结果表明,甘薯R2R3-MYB蛋白序列中含有10个保守基序,其中80%以上的R2R3-MYB序列中含有motif 1、motif 2、motif 3、motif 4、motif 5以及motif 7;利用circos软件定位R2R3-MYB序列在染色体上的分布情况,发现甘薯88个R2R3-MYB基因不均匀分布在15条染色体上,其中5号染色体上数量最多,达15个,4号和13号数量最少,仅2个,经序列比对分析,发现它们在染色体内和染色体间均存在复制关系,其中存在于染色体间潜在复制关系的基因有6对,染色体内有20对,且这20个基因对中有19对在染色体上成簇状分布。经序列功能预测与归类,有44个R2R3-MYB转录因子基因可归入拟南芥R2R3-MYB基因分类的13个亚组中,分别参与响应生物与非生物胁迫、花青素合成、花药发育等途径。进一步分析发现,甘薯中有36个R2R3-MYB转录因子基因可能在响应生物和非生物胁迫上发挥重要功能,其中9个基因在尖孢镰刀菌(Fusarium oxysporum f.sp.batatas,Fob)胁迫下表达量出现明显上调/下调变化,27个在低温胁迫下表达量出现明显上调/下调变化。甘薯R2R3-MYB转录因子结构域高度保守,R2和R3结构域中均含有较高的保守基序;进化树及转录组测序分析显示部分基因可能参与植物生长发育、代谢调控以及生物与非生物胁迫等途径,可为甘薯抗性育种提供参考。 The plant MYB is a transcription factor family large in number and with important functions. In this study, the MYB family genes were screened and identified via bioinformatic methods from the raw sequence of sweet potato(Ipomoea batatas) genome and the gene structure and function of R2R3-MYB were analyzed. The results showed that there were 88 R2R3-MYB genes with intact R2 and R3 conservative domains, which contained 8 and 9 highly conserved basic amino acids. The results of MEME analysis showed that there were 10 conserved motifs within the I. batatas R2R3-MYB protein sequences. For the I. batatas R2R3-MYB protein sequences, over80% contained motif 1, motif 2, motif 3, motif 4, motif 5 and motif 7. The R2R3-MYB genes were distributed unevenly across the 15 chromosomes. The number of R2R3-MYB genes in chromosome No.5 was 15, which was the largest;the numbers of R2R3-MYB genes in chromosome No. 4 and 13 were both only 2, which was the smallest. Analysis of the sequence alignment showed that there were 6 pairs of interchromosomal duplication and there were 20 pairs of intrachromosomal duplication, 19 of which existed in clusters. The function prediction and categorization via sequence analysis showed that 44 R2R3-MYB genes of the I. batatas could be categorized to the13 subgroups of the A. thaliana R2R3-MYB genes, which were involved in the responses to biotic stress and abiotic stress, anthocyanin biosynthesis, anther development, etc. Further analysis showed that 36 R2R3-MYB genes might play important roles in dealing with biotic stress and abiotic stress, 9 of which showed significant up/down-regulation under Fusarium oxysporum f. sp. batatas stress and 27 of which showed significant up/down-regulation under low temperature stress. The domains of I. batatas R2R3-MYB transcription factors were highly conservative, which contained highly conserved motifs within R2 and R3 domains. The phylogenetic tree and transcriptomics data analysis showed that some R2R3-MYB genes might play roles in growth and development, metabolism regulation, biotic stress and abiotic stress, which lent support to I. batatas breeding.
作者 黄小芳 毕楚韵 黄碧芳 许明 杨志坚 林世强 陈选阳 Huang Xiaofang;Bi Chuyun;Huang Bifang;Xu Ming;Yang Zhijian;Lin Shiqiang;Chen Xuanyang(Key Laboratory of Crop Biotechnology,Fujian Agriculture and Forestry University,Fuzhou,350002;College of Agriculture,Fujian Agriculture and Forestry University,Fuzhou,350002;College of Life Science,Fujian Agriculture and Forestry University,Fuzhou,350002;Key Lab of Genetics,Breeding and Multiple Application of Crops,Ministry of Education,Fujian Agriculture and Forestry University,Fuzhou,350002)
出处 《分子植物育种》 CAS 北大核心 2021年第21期7000-7011,共12页 Molecular Plant Breeding
基金 福建省科技厅项目(2019N0050)资助。
关键词 甘薯 R2R3-MYB 转录因子 生物信息学 Ipomoea batatas R2R3-MYB Transcription factor Bioinformatics
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