Genome-Wide Survey and Analysis of Microsatellite Sequences in Bovid Species
作者： Wen-Hua Qi , Xue-Mei Jiang , Lian-Ming Du , Guo-Sheng Xiao , Ting-Zhang Hu
DOI: 10.1371/JOURNAL.PONE.0133667
关键词: Capra hircus 、 Genome size 、 Bubalus 、 Biology 、 Genetics 、 Comparative genomics 、 Genome 、 Relative species abundance 、 Microsatellite 、 Genetic marker 、 General Biochemistry, Genetics and Molecular Biology 、 General Agricultural and Biological Sciences 、 General Medicine
摘要: Microsatellites or simple sequence repeats (SSRs) have become the most popular source of genetic markers, which are ubiquitously distributed in many eukaryotic and prokaryotic genomes. This is first study examining comparing SSRs completely sequenced genomes Bovidae. We analyzed compared number SSRs, relative abundance, density, guanine-cytosine (GC) content proportion six taxonomically different bovid species: Bos taurus, Bubalus bubalis, mutus, Ovis aries, Capra hircus, Pantholops hodgsonii. Our analysis revealed that, based on our search criteria, total perfect found ranged from 663,079 to 806,907 covered 0.44% 0.48% Relative abundance density these Bovinae were non-significantly correlated with genome size (Pearson, r 0.05). Perfect mononucleotide abundant, followed by pattern: di- > tri- penta- tetra- hexanucleotide SSRs. Generally, decreased as motif repeat length increased each species The GC-content was trinucleotide least GC-contents pentanucleotide showed a great deal similarity among chromosomes B. O. C. hircus. SSR all O.aries, hircus closely positively chromosome 0.980, p abundances same nucleotide type
harvard.edu
core.ac.uk 
sci-hub.se 参考文章(53)
Chang Pyo Hong, Beom-Seok Park, Yong Pyo Lim, Yoon-Kang Hur, David Edwards, Tae-Jin Yang, Jong Bhak, Zhong Yun Piao, Tae Wook Kang, Jacqueline Batley, Genomic distribution of simple sequence repeats in Brassica rapa. Molecules and Cells. ,vol. 23, pp. 349- 356 ,(2007)
A. E. Vinogradov, DNA helix: the importance of being GC-rich. Nucleic Acids Research. ,vol. 31, pp. 1838- 1844 ,(2003) , 10.1093/NAR/GKG296
Mukund V. Katti, Prabhakar K. Ranjekar, Vidya S. Gupta, Differential Distribution of Simple Sequence Repeats in Eukaryotic Genome Sequences Molecular Biology and Evolution. ,vol. 18, pp. 1161- 1167 ,(2001) , 10.1093/OXFORDJOURNALS.MOLBEV.A003903
Jun Qian, Haibin Xu, Jingyuan Song, Jiang Xu, Yingjie Zhu, Shilin Chen, Genome-wide analysis of simple sequence repeats in the model medicinal mushroom Ganoderma lucidum. Gene. ,vol. 512, pp. 331- 336 ,(2013) , 10.1016/J.GENE.2012.09.127
J. Mrazek, X. Guo, A. Shah, Simple sequence repeats in prokaryotic genomes. Proceedings of the National Academy of Sciences of the United States of America. ,vol. 104, pp. 8472- 8477 ,(2007) , 10.1073/PNAS.0702412104
Vladislav Victorovich Khrustalev, Eugene Victorovich Barkovsky, Research Article: Mutational pressure is a cause of inter- and intragenomic differences in GC-content of simplex and varicello viruses Computational Biology and Chemistry. ,vol. 33, pp. 295- 302 ,(2009) , 10.1016/J.COMPBIOLCHEM.2009.06.005
T. W. Hefferon, J. D. Groman, C. E. Yurk, G. R. Cutting, A variable dinucleotide repeat in the CFTR gene contributes to phenotype diversity by forming RNA secondary structures that alter splicing Proceedings of the National Academy of Sciences of the United States of America. ,vol. 101, pp. 3504- 3509 ,(2004) , 10.1073/PNAS.0400182101
Cheng-Yun Li, Lin Liu, Jing Yang, Jin-Bin Li, Yuan Su, Yue Zhang, Yun-Yue Wang, You-Yong Zhu, Genome-wide analysis of microsatellite sequence in seven filamentous fungi. Interdisciplinary Sciences: Computational Life Sciences. ,vol. 1, pp. 141- 150 ,(2009) , 10.1007/S12539-009-0014-5
Geoffrey K Chambers, Elizabeth S MacAvoy, Microsatellites: consensus and controversy Comparative Biochemistry and Physiology Part B: Biochemistry and Molecular Biology. ,vol. 126, pp. 455- 476 ,(2000) , 10.1016/S0305-0491(00)00233-9
Tae-Sung Kim, James G Booth, Hugh G Gauch, Qi Sun, Jongsun Park, Yong-Hwan Lee, Kwangwon Lee, Simple sequence repeats in Neurospora crassa : distribution, polymorphism and evolutionary inference BMC Genomics. ,vol. 9, pp. 31- 31 ,(2008) , 10.1186/1471-2164-9-31