全部 标题 作者
关键词 摘要

OALib Journal期刊
ISSN: 2333-9721
费用:99美元

查看量下载量

相关文章

更多...

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, PP. 146-151

Keywords: 诸氏鲻虾虎鱼,转录组序列,微卫星,筛选,分布特征

Full-Text   Cite this paper   Add to My Lib

Abstract:

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47979条Unigenes,利用微卫星查找程序在47979条Unigenes中共获得6225个微卫星位点(12.97%),平均每7.02kb就出现1个微卫星位点。6225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。

References

[1]  Vukosavljev M, Esselink GD, Westende WPC, et al. Efficient development of highly polymorphic microsatellite markers based on polymorphic repeats in transcriptome sequences of multiple individuals[J]. Molecular Ecology Resources, 2014, 15(1). DOI:10.1111/1755-0998.1289.
[2]  李建军, 陈小曲, 林忠婷, 等. 诸氏鲻虾虎鱼的形态与生长特性分析[J]. 实验动物与比较医学, 2012, 32(4):334-340.
[3]  Luo RB, Liu BH, Xie YL, et al. SOAPdenovo2:an empirically improved memory-efficient short-read de novo assembler[J]. GigaScience, 2012, 1(18):1-6.
[4]  Edwards YJ, Elgar G, Clark MS, et al. The identicication and characteriction of microsatellites in the compact genome of the Japanese puffer fish, Fugu rubripes:Perspectives in functional and comparative genomic analysis[J]. Journal of Molecular Biology, 1998, 278:843-854.
[5]  Chen SL, Liu YG, Xu MY, et al. Isolation and characterization of polymorphic microsatellite loci from an EST library of red seabream(Chrysophrys major)and cross-species amplification[J]. Molecular Ecology Notes, 2005, 5:215-217.
[6]  谢芳静, 张子平, 邹志华, 等. 大黄鱼EST微卫星标记初步筛选[J]. 福建水产, 2011, 33(5):9-14.
[7]  陈松波, 龚丽, 刘海金. 牙鲆EST资源的SSR信息分析[J]. 东北农业大学学报, 2010, 41(10):82-86.
[8]  孙典巧, 孙悦娜, 王日昕, 等. 鮸鱼EST序列中微卫星标记的初步筛选及特性分析[J]. 水生生物学报, 2011, 35(5):753-760.
[9]  杨曦. 鲫鱼(Carassius auratus)表达序列标签资源的SSR构成与分布分析[J]. 生物技术通报, 2012(11):139-143.
[10]  Weber JL. Informativeness of human(dC-dA)n·(dG-dT)n polymorphisms[J]. Genomics, 1990, 7(4):524-530.
[11]  郭文久. 微卫星在基因组上的分布与功能及其计算方法初步研究[M]. 西安:陕西科学技术出版社, 2009:5-6.
[12]  Garg R, Patel RK, Tyagi AK, et al. De novo assembly of chickpea transcriptome using short reads for gene discovery and marker identification[J]. DNA Research, 2011, 18(1):53-63.
[13]  许晓军, 张海琪, 张超, 等. 中华鳖表达序列标签源中的微卫星信息分析[J]. 经济动物学报, 2013, 17(1):15-18.
[14]  Dor L, Shirak A, Gorshkov S, et al. Construction of a microsatellites-based linkage map for the white grouper(Epinephelus aeneus)[J]. Genomes, 2014, 45(5):699-708.
[15]  Grattapaglia D, Amaral D, Santos G. Performance of microsatellites for parentage assignment following mass controlled pollination in a clonal seed orchard of loblolly pine(Pinus taeda L.)[J]. Tree Genetics & Genomes, 2014, 10(6):1631-1643.
[16]  Norrell AE, Crawley D, Jones KL, et al. Development and characterization of eighty-four microsatellite markers for the red snapper(Lutjanus campechanus)using Illumina paired-end sequencing[J]. Aquaculture, 2014, 430:128-132.
[17]  李建军, 吴美慧, 叶慧欣, 等. 不同发育期诸氏鲻虾虎鱼对钻井液的敏感性比较[J]. 中国比较医学杂, 2013, 23:48-51.
[18]  Serapion J, Kucuktas H, Feng JN, et al. Bioinformation mining of type I microsatellites from expressed sequence tags of channel catfish(Ictalurus punctatus)[J]. Marine Biotechnology, 2004, 6(4):364-377.
[19]  懂迎辉, 吴国星, 姚韩韩, 等. 泥蚶34个EST-SSR标记的开发及在格粗饰蚶的通用性检测[J]. 水产学报, 2013, 37(1):70-77.
[20]  刘博, 邵艳卿, 滕爽爽, 等. 缢蛏(Sinonovacula constricta)EST-SSR分布特征及引物开发利用[J]. 海洋与湖沼, 2012, 43(1):133-137.
[21]  Blanca J, Ca?izares J, Roig C, et al. Transcriptome characterization and high throughput SSRs and SNPs discovery in Cucurbita pepo(Cucurbitaceae)[J]. BMC Genomics, 2011, 12:1-15.
[22]  Kantety RV, Rota ML, Matthews DE, et al. Data mining for simple sequence repeats in expressed sequence tags from barley, maize, rice, sorghum and wheat[J]. Plant Mol Biol, 2002, 48:501-510.

Full-Text

Contact Us

service@oalib.com

QQ:3279437679

WhatsApp +8615387084133