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引用本文:曹广勇,张志勇,张志伟,陈淑吟,祝斐,贾超峰,陈自强,曾海峰,汤晓建.黑鲷、真鲷及其杂交子代基因编码区微卫星序列及密码子偏好性分析.海洋与湖沼,2019,50(5):1108-1115.
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黑鲷、真鲷及其杂交子代基因编码区微卫星序列及密码子偏好性分析
曹广勇1,2, 张志勇2, 张志伟2, 陈淑吟2, 祝斐2, 贾超峰2, 陈自强1,2, 曾海峰2, 汤晓建2
1.上海海洋大学水产与生命学院 上海 201306;2.江苏省海洋水产研究所 江苏省海水鱼类遗传育种重点实验室 南通 226007
摘要:
本研究采用生物信息学方法分析比较了黑鲷、真鲷及其两种杂交子代基因编码区(Coding sequence,CDS)中微卫星序列(简单重复序列,SSR)的分布规律及密码子偏好性。结果表明:(1)黑鲷、真鲷及其两种杂交子代微卫星序列均以三碱基重复类型为主,其次为二碱基重复,片段长度大多数在12-20bp之间。(2)黑鲷与反交(黑鲷♀×真鲷)在三、五碱基中优势基元类型相同,真鲷与正交(真鲷♀×黑鲷)在三碱基中优势基元类型相同,而黑鲷与正交在四碱基中优势基元类型相同。(3)UUC、UAC等28个密码子为黑鲷、真鲷及其两种杂交子代基因编码区的偏好性密码子,偏爱使用以C或G结尾的密码子,且第三位密码子碱基的GC含量(GC3s)均高于基因编码区平均GC含量。(4)真鲷与正交的密码子使用的偏好性相似,一定程度上说明黑鲷、真鲷杂交子代偏母系遗传。分析结果将为研究鲷科鱼类微卫星标记、研究其群体遗传多样性、构建转基因表达系统和开展分子遗传育种提供理论基础。
关键词:  黑鲷  真鲷  CDS序列  微卫星  密码子偏好性
DOI:10.11693/hyhz20190200038
分类号:Q953;S931
基金项目:江苏省重点研发计划(现代农业)项目,BE2016326号;江苏省农业科技自主创新资金项目,CX(17)2021号;江苏省农业重大新品种创制项目,PZCZ201744号;江苏省自然科学基金项目,BK20181202号。
ANALYSIS OF THE MICROSATELLITE SEQUENCES AND CODON BIAS OF THE CODING SEQUENCE IN ACANTHOPAGRUS SCHLEGELII, PAGRUS MAJOR AND THEIR HYBRID PROGENIES
CAO Guang-Yong1,2, ZHANG Zhi-Yong2, ZHANG Zhi-Wei2, CHEN Shu-Yin2, ZHU Fei2, JIA Chao-Feng2, CHEN Zi-Qiang1,2, ZENG Hai-Feng2, TANG Xiao-Jian2
1.Fishery and Life Science College, Shanghai Ocean University, Shanghai 201306, China;2.Jiangsu Marine Fisheries Research Institute, Nantong 226007, China
Abstract:
The microsatellite sequences (simple sequence repeats, SSR) and codon bias in the coding regions (CDS) of black porgy (Acanthopagrus schlegelii), red porgy (Pagrus major), and their offspring (orthogonal and reciprocal ones) were analyzed and compared using the method of bio-informatics. The results are followed. The microsatellite sequence is mainly composed of the three-base repeat type, followed by the two-base repeat, and the most fragment length of repeat sequences is between 12bp and 20bp. The black porgy and the reciprocal cross (black porgy♀×red porgy ) have the same dominant primitive type in the three and five bases, and the red porgy and the orthogonal (red porgy♀×black porgy ) dominant base types in the three bases as well, while the black porgy and the orthogonal are the same in the four bases. Twenty-eight pieces of genetic codons such as UUC and UAC are the preferred codons in gene coding regions of the four sea bream species, preferring to use the codons ended in C or G, and the GC content of the third codon base (GC3s). Both are higher than the average GC content of the coding region of the gene. The preference of codon use of the red porgy and the orthogonal is similar, which to some degree shows that black porgy and red porgy hybrids are of maternal hereditary characteristics. This research may provide a theoretical basis for the study of microsatellite markers of sea bream, their population genetic diversity, the construction of a transgenic expression system, and molecular genetic breeding.
Key words:  Acanthopagrus schlegelii  Pagrus major  coding sequence  microsatellite  codon usage bias
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