诸氏鲻虾虎鱼转录组序列中微卫星标记的初步筛选及特征分析

doi:10.13560/j.cnki.biotech.bull.1985.2015.09.020

生物技术通报 ›› 2015, Vol. 31 ›› Issue (9): 146-151.doi: 10.13560/j.cnki.biotech.bull.1985.2015.09.020

诸氏鲻虾虎鱼转录组序列中微卫星标记的初步筛选及特征分析

蔡磊, 余露军, 陈小曲, 叶惠欣, 陈琳, 李建军

(广东省实验动物监测所广东省实验动物重点实验室，广州 510663)

收稿日期:2014-12-13 出版日期:2015-09-15 发布日期:2015-09-16
作者简介:蔡磊，男，硕士研究生，研究方向：水生实验动物遗传质量控制；E-mail：cailei17@163.com
基金资助:
广东省中国科学院全面战略合作项目(2011B090300099)，广东省科技计划项目(2012A020602008)，国家科技支撑计划项目(2013BAK11B902)

A Preliminary Screening and Characteristic Analysis of Microsatellite Markers from Transcriptome Sequences in Mugilogobius chulae

Cai Lei, Yu Lujun, Chen Xiaoqu, Ye Huixin, Chen Lin, Li Jianjun

(Key Laboratory of Guangdong Laboratory Animals，Guangdong Laboratory Animals Monitoring Institute，Guangzhou 510663)

Received:2014-12-13 Published:2015-09-15 Online:2015-09-16

摘要/Abstract

摘要： 旨在为大规模开发诸氏鲻虾虎鱼微卫星标记，采用高通量测序技术，对诸氏鲻虾虎鱼肝脏转录组进行了测序。结果共获得47 979条Unigenes，利用微卫星查找程序在47 979条Unigenes中共获得6 225个微卫星位点(12.97%)，平均每7.02 kb就出现1个微卫星位点。6 225个微卫星位点由226种重复基序组成，主要分布在三、四和五碱基重复类型中。在数量上，单碱基重复类型微卫星位点最多，占42.49%，二碱基和三碱基重复类型所占比例相似，分别为25.22%和26.27%，四、五、六重复类型较少，合计占6.03%。单碱基重复序列中最多的类型为A/T，二碱基重复序列中以AG/CT重复单元为主，三碱基重复序列中以AGC/TCG为优势类型。挑选部分二、三和四单元重复类型微卫星序列，共设计76对引物，可稳定扩增出目的条带的有55对，其中32对具有多态性。结果表明，利用诸氏鲻虾虎鱼转录组数据可快速大量开发微卫星标记。

关键词: 诸氏鲻虾虎鱼, 转录组序列, 微卫星, 筛选, 分布特征

Abstract: In order to explore microsatellite markers in large-scale, the liver transcriptome of Mugilogobius chulae was sequenced by high-throughput sequencing technology. A total of 6 225(12.97%)microsatellite markers were screened from 47 979 Unigenes by microsatellite software, averagely 1 microsatellite marker in every 7.02 kb. The 6 225 microsatellite markers consisted of 226 repeat motifs, which mainly distributed in tri-nucleotide, quad-nucleotide and penta-nucleotide repeats. The mono-nucleotide repeats were of the most by number, accounting for 42.49% of all the microsatellite markers, the di-nucleotide repeats and tri-nucleotide repeats had the similar proportion(25.22% and 26.27% of all the markers, respectively), the rest were the quad-nucleotide, penta-nucleotide and hexa-nucleotide repeats, together accounting for 6.03%. A/T, AG/CT and AGC/TCG were the most frequent motifs in mono-nucleotide, di-nucleotide and tri-nucleotide repeats, respectively. In this research, 76 pairs of primers were designed and synthesized, by 55 pairs of them the target bands were successfully amplified, and 32 loci were of polymorphism. The results suggested that it was feasible to explore a number of microsatellite markers quickly based on the transcriptome sequences of M. chulae.

Key words: Mugilogobius chulae, transcriptome sequence, microsatellites, screening, distribution characteristic

蔡磊, 余露军, 陈小曲, 叶惠欣, 陈琳, 李建军. 诸氏鲻虾虎鱼转录组序列中微卫星标记的初步筛选及特征分析[J]. 生物技术通报, 2015, 31(9): 146-151.

Cai Lei, Yu Lujun, Chen Xiaoqu, Ye Huixin, Chen Lin, Li Jianjun. A Preliminary Screening and Characteristic Analysis of Microsatellite Markers from Transcriptome Sequences in Mugilogobius chulae[J]. Biotechnology Bulletin, 2015, 31(9): 146-151.

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诸氏鲻虾虎鱼转录组序列中微卫星标记的初步筛选及特征分析

A Preliminary Screening and Characteristic Analysis of Microsatellite Markers from Transcriptome Sequences in Mugilogobius chulae

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