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引用本文:许净,刘慧敏,林筱钧,郑江,江兴龙,鄢庆枇,范云庭,汤学敏.鳗弧菌(Vibrio anguillarum)核酸适配体筛选中高频序列的进化多样性研究.海洋与湖沼,2021,52(5):1315-1322.
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鳗弧菌(Vibrio anguillarum)核酸适配体筛选中高频序列的进化多样性研究
许净1,2,3,4, 刘慧敏1, 林筱钧1, 郑江1,2,3, 江兴龙1,2, 鄢庆枇1, 范云庭1, 汤学敏2
1.集美大学水产学院 厦门 361021;2.鳗鲡现代产业技术教育部工程研究中心 厦门 361021;3.福建省水产生物育种与健康养殖工程研究中心 厦门 361021;4.福建省特种水产配合饲料重点实验室 福清 350308
摘要:
核酸适配体是采用分子进化技术从随机寡核苷酸文库中筛选得到的对靶目标有较高亲和力的寡核苷酸序列。研究核酸适配体筛选过程中高频序列的进化多样性,对于提高筛选效率,掌握核酸适配体的进化规律具有重要意义。利用Margalef丰富度指数、Shannon-Wiener多样性指数、Pielou均匀度指数、Berger-Parker优势度指数,研究了鳗弧菌(Vibrio anguillarum)核酸适配体筛选产物中高频序列的进化多样性,结果表明,随着筛选进行,高频序列的种类数、丰富度、多样性、优势度和均匀度在前六轮都呈现较为剧烈的波动,之后种类数、丰富度、多样性、优势度呈现逐步增加的趋势,而均匀度则呈逐步下降的趋势,说明竞争力强的序列在筛选竞争中逐渐占据优势,其种类数量不断增加;利用相对重要性指数(IRI)对高频序列进行了计算分析,根据IRI值可将高频序列分为5类:优势序列,重要序列,常见序列,一般序列和少见序列,其中前三种序列是筛选进化中的相对优势种群;最后对IRI较高的7种核酸适配体进行了二级结构预测,结果显示其二级结构中存在着大小、数量不等的环状结构,这些环的大小数量可能与其结合位点相关。相关研究结果对于鳗弧菌的病害防控及核酸适配体的筛选都具有重要意义。
关键词:  核酸适配体  高频序列  鳗弧菌  多样性  相对重要性  进化
DOI:10.11693/hyhz20210100027
分类号:Q939;S917.1
基金项目:福建省自然科学基金,2018J01455号;鳗鲡现代产业技术教育部工程研究中心开放基金,RE201808号,RE202104号;福建省水产生物育种与健康养殖工程研究中心开放基金课题,DF201901号;福建省特种水产配合饲料重点实验室开放课题,TMKJZ1909号。
附件
STUDY ON Evolutionary Diversity of SEQUENCES WITH high frequency DURING SELECTION OF APTAMERS against vibrio anguillarum
XU Jing1,2,3,4, LIU Hui-Min1, LIN Xiao-Jun1, ZHENG Jiang1,2,3, JIANG Xing-Long1,2, YAN Qing-Pi1, FAN Yun-Ting1, TANG Xue-Min2
1.Fisheries College of Jimei University, Xiamen 361021, China;2.Engineering Research Center of the Modern Technology for Eel Industry, Ministry of Education, Xiamen 361021, China;3.Engineering Research Center of Aquaculture Breeding and Healthy of Fujian, Xiamen 361021, China;4.Fujian Province Key Laboratory of Special Aquatic Formula Feed, Fuqing 350308, China
Abstract:
Aptamers are oligonucleotides in high affinity to target compounds selected from random oligonucleotide libraries by molecular evolutionary techniques. It is of great significance to study the diversity of those sequences with high frequency in the selection evolution for improving the selection efficiency and understanding the evolutionary rules of aptamers. The Margalef richness index, Shannon-Wiener diversity index, Pielou evenness index, and Berger-Parker dominance index were applied to explore the evolution diversity of the high-frequency sequences obtained from the selection of the aptamers against Vibrio anguillarum. The results show that the numbers of the high-frequency sequences species, and their richness, diversity, dominance, and evenness index fluctuated drastically in the first six selection rounds, and the evenness index declined gradually and other items increased gradually after the 6th selection round, suggesting that the highly competitive sequences gradually occupied the advantage in the selection competition, and their species and numbers kept increasing. The index of relative importance (IRI) was used to calculate and analyze the high-frequency sequences. According to the IRI value, the high-frequency sequences could be divided into five types:dominant, important, common, general, and rare sequences. The first three types were relatively dominant in the selection evolution. Finally, the secondary structures of seven aptamers with high IRI values were predicted, and found that their secondary structures were composed of the rings with different sizes and numbers. The size and number of these rings could be related to their binding sites. These findings are of great significance for disease control and aptamer selection of Vibrio anguillarum.
Key words:  aptamer  high-frequency sequence  Vibrio anguillarum  diversity  index of relative importance  evolution
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