- About this Journal
- Abstracting and Indexing
- Aims and Scope
- Annual Issues
- Article Processing Charges
- Articles in Press
- Author Guidelines
- Bibliographic Information
- Citations to this Journal
- Contact Information
- Editorial Board
- Editorial Workflow
- Free eTOC Alerts
- Publication Ethics
- Reviewers Acknowledgment
- Submit a Manuscript
- Subscription Information
- Table of Contents
BioMed Research International
Volume 2014 (2014), Article ID 281912, 10 pages
Microsatellites in the Genome of the Edible Mushroom, Volvariella volvacea
1National Engineering Research Center of Edible Fungi and Key Laboratory of Applied Mycological Resources and Utilization, Ministry of Agriculture and Shanghai Key Laboratory of Agricultural Genetics and Breeding and Institute of Edible Fungi, Shanghai Academy of Agriculture Science, Shanghai 201403, China
2Key Laboratory of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China
Received 2 October 2013; Revised 23 October 2013; Accepted 23 October 2013; Published 19 January 2014
Academic Editor: Yudong Cai
Copyright © 2014 Ying Wang et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
- D. Bao, M. Gong, H. Zheng, et al., “Sequencing and comparative analysis of the straw mushroom (Volvariella volvacea) genome,” PLoS ONE, vol. 8, no. 3, Article ID e58294, 2013.
- G. Thiribhuvanamala, S. Krishnamoorthy, K. Manoranjitham, V. Praksasm, and S. Krishnan, “Improved techniques to enhance the yield of paddy straw mushroom (Volvariella volvacea) for commercial cultivation,” African Journal of Biotechnology, vol. 11, no. 64, pp. 12740–12748, 2012.
- Y. J. Cai, S. J. Chapman, J. A. Buswell, and S.-T. Chang, “Production and distribution of endoglucanase, cellobiohydrolase, and β- glucosidase components of the cellulolytic system of Volvariella volvacea, the edible straw mushroom,” Applied and Environmental Microbiology, vol. 65, no. 2, pp. 553–559, 1999.
- S. T. Chang, “Mushroom research and development-equality and mutual benefit,” Mushroom Biology and Mushroom Products, pp. 1–10, 1996.
- S. V. Kalava and S. G. Menon, “Protective efficacy of the extract of volvariella volvacea (bulliard ex fries) singer. against carbon tetrachloride induced hepatic injury,” International Journal of Pharmaceutical Sciences and Research, vol. 3, no. 8, pp. 2849–2856, 2012.
- L. Ramkumar, T. Ramanathan, and J. Johnprabagaran, “Evaluation of nutrients, trace metals and antioxidant activity in Volvariella volvacea (Bull. Ex. Fr.) Sing,” Emirates Journal of Food and Agriculture, vol. 24, no. 2, pp. 113–119, 2012.
- B. Z. Chen, F. Gui, B. G. Xie, F. Zou, Y. J. Jiang, and Y. J. Deng, “Sequence and comparative analysis of the MIP gene in Chinese straw mushroom, Volvariella volvacea,” Genome, vol. 55, no. 9, pp. 667–672, 2012.
- D. Field and C. Wills, “Long, polymorphic microsatellites in simple organisms,” Proceedings of the Royal Society B, vol. 263, no. 1367, pp. 209–215, 1996.
- G. Tóth, Z. Gáspári, and J. Jurka, “Microsatellites in different eukaryotic genomes: surveys and analysis,” Genome Research, vol. 10, no. 7, pp. 967–981, 2000.
- S. Rufai, M. M. Hanafi, M. Y. Rafii, S. Ahmad, I. W. Arolu, and J. Ferdous, “Genetic dissection of new genotypes of drumstick tree (Moringa oleifera Lam.) using random amplified polymorphic DNA marker,” BioMed Research International, vol. 2013, Article ID 604598, 6 pages, 2013.
- H. Ellegren, “Microsatellites: simple sequences with complex evolution,” Nature Reviews Genetics, vol. 5, no. 6, pp. 435–445, 2004.
- E. Guichoux, L. Lagache, S. Wagner et al., “Current trends in microsatellite genotyping,” Molecular Ecology Resources, vol. 11, no. 4, pp. 591–611, 2011.
- N. Mittal and A. K. Dubey, “Microsatellite markers—a new practice of DNA based markers in molecular genetics,” Pharmacognosy Reviews, vol. 3, no. 6, pp. 235–246, 2009.
- C. Spampinato and D. Leonardi, “Molecular fingerprints to identify Candida species,” BioMed Research International, vol. 2013, Article ID 923742, 10 pages, 2013.
- J. Labbé, C. Murat, E. Morin, F. Le Tacon, and F. Martin, “Survey and analysis of simple sequence repeats in the Laccaria bicolor genome, with development of microsatellite markers,” Current Genetics, vol. 57, no. 2, pp. 75–88, 2011.
- M. J. Lawson and L. Zhang, “Distinct patterns of SSR distribution in the Arabidopsis thaliana and rice genomes,” Genome Biology, vol. 7, no. 2, article R14, 2006.
- J. J. Rudd, J. Antoniw, R. Marshall, J. Motteram, B. Fraaije, and K. Hammond-Kosack, “Identification and characterisation of Mycosphaerella graminicola secreted or surface-associated proteins with variable intragenic coding repeats,” Fungal Genetics and Biology, vol. 47, no. 1, pp. 19–32, 2010.
- C. Murat, C. Riccioni, B. Belfiori et al., “Distribution and localization of microsatellites in the Perigord black truffle genome and identification of new molecular markers,” Fungal Genetics and Biology, vol. 48, no. 6, pp. 592–601, 2011.
- J. G. Gibbons and A. Rokas, “Comparative and functional characterization of intragenic tandem repeats in 10 Aspergillus genomes,” Molecular Biology and Evolution, vol. 26, no. 3, pp. 591–602, 2009.
- K. J. Verstrepen, A. Jansen, F. Lewitter, and G. R. Fink, “Intragenic tandem repeats generate functional variability,” Nature Genetics, vol. 37, no. 9, pp. 986–990, 2005.
- Y. C. Li, A. B. Korol, T. Fahima, and E. Nevo, “Microsatellites within genes: structure, function, and evolution,” Molecular Biology and Evolution, vol. 21, no. 6, pp. 991–1007, 2004.
- S. Feng, H. Tong, Y. Chen, et al., “Development of pineapple microsatellite markers and germplasm genetic diversity analysis,” BioMed Research International, vol. 2013, Article ID 317912, 11 pages, 2013.
- C. Dutech, J. Enjalbert, E. Fournier et al., “Challenges of microsatellite isolation in fungi,” Fungal Genetics and Biology, vol. 44, no. 10, pp. 933–949, 2007.
- J. Qian, H. Xu, J. Song, J. Xu, Y. Zhu, and S. Chen, “Genome-wide analysis of simple sequence repeats in the model medicinal mushroom Ganoderma lucidum,” Gene, vol. 512, no. 2, pp. 331–336, 2013.
- J. Jurka and C. Pethiyagoda, “Simple repetitive DNA sequences from primates: compilation and analysis,” Journal of Molecular Evolution, vol. 40, no. 2, pp. 120–126, 1995.
- C. Y. Li, L. Liu, J. Yang, et al., “Genome-wide analysis of microsatellite sequence in seven filamentous fungi,” Interdisciplinary Sciences, vol. 1, no. 2, pp. 141–150, 2009.
- H. Karaoglu, C. M. Y. Lee, and W. Meyer, “Survey of simple sequence repeats in completed fungal genomes,” Molecular Biology and Evolution, vol. 22, no. 3, pp. 639–649, 2005.
- J. Ye, L. Fang, H. Zheng et al., “WEGO: a web tool for plotting GO annotations,” Nucleic Acids Research, vol. 34, pp. W293–W297, 2006.
- P. Jarne and P. J. L. Lagoda, “Microsatellites, from molecules to populations and back,” Trends in Ecology and Evolution, vol. 11, no. 10, pp. 424–429, 1996.
- G. Luikart, P. R. England, D. Tallmon, S. Jordan, and P. Taberlet, “The power and promise of population genomics: from genotyping to genome typing,” Nature Reviews Genetics, vol. 4, no. 12, pp. 981–994, 2003.
- F. Martin, A. Kohler, C. Murat, et al., “Perigord black truffle genome uncovers evolutionary origins and mechanisms of symbiosis,” Nature, vol. 464, no. 7291, pp. 1033–1038, 2010.
- V. Albanèse, N. F. Biguet, H. Kiefer, E. Bayard, J. Mallet, and R. Meloni, “Quantitative effects on gene silencing by allelic variation at a tetranucleotide microsatellite,” Human Molecular Genetics, vol. 10, no. 17, pp. 1785–1792, 2001.
- Y. D. Kelkar, N. Strubczewski, S. E. Hile, F. Chiaromonte, K. A. Eckert, and K. D. Makova, “What is a microsatellite: a computational and experimental definition based upon repeat mutational behavior at A/T and GT/AC repeats,” Genome Biology and Evolution, vol. 2, no. 1, pp. 620–635, 2010.
- C. E. Pearson, K. N. Edamura, and J. D. Cleary, “Repeat instability: mechanisms of dynamic mutations,” Nature Reviews Genetics, vol. 6, no. 10, pp. 729–742, 2005.
- E. Meglecz, G. Nève, E. Biffin, and M. G. Gardner, “Breakdown of phylogenetic signal: a survey of microsatellite densities in 454 shotgun sequences from 154 non model eukaryote species,” PLoS ONE, vol. 7, no. 7, Article ID e40861, 2012.
- O. Rose and D. Falush, “A threshold size for microsatellite expansion,” Molecular Biology and Evolution, vol. 15, no. 5, pp. 613–615, 1998.
- K. J. Dechering, K. Cuelenaere, R. N. H. Konings, and J. A. M. Leunissen, “Distinct frequency-distributions of homopolymeric DNA tracts in different genomes,” Nucleic Acids Research, vol. 26, no. 17, pp. 4056–4062, 1998.
- Y. Lai and F. Sun, “The relationship between microsatellite slippage mutation rate and the number of repeat units,” Molecular Biology and Evolution, vol. 20, no. 12, pp. 2123–2131, 2003.
- D. Metzgar, J. Bytof, and C. Wills, “Selection against frameshift mutations limits microsatellite expansion in coding DNA,” Genome Research, vol. 10, no. 1, pp. 72–80, 2000.
- S. Temnykh, G. DeClerck, A. Lukashova, L. Lipovich, S. Cartinhour, and S. McCouch, “Computational and experimental analysis of microsatellites in rice (Oryza sativa L.): frequency, length variation, transposon associations, and genetic marker potential,” Genome Research, vol. 11, no. 8, pp. 1441–1452, 2001.
- Y. C. Li, A. B. Korol, T. Fahima, A. Beiles, and E. Nevo, “Microsatellites: genomic distribution, putative functions and mutational mechanisms: a review,” Molecular Ecology, vol. 11, no. 12, pp. 2453–2465, 2002.
- S. Subramanian, R. K. Mishra, and L. Singh, “Genome-wide analysis of microsatellite repeats in humans: their abundance and density in specific genomic regions,” Genome Biology, vol. 4, no. 2, p. R13, 2003.
- D. E. Riley and J. N. Krieger, “UTR dinucleotide simple sequence repeat evolution exhibits recurring patterns including regulatory sequence motif replacements,” Gene, vol. 429, no. 1-2, pp. 80–86, 2009.
- M. D. Vinces, M. Legendre, M. Caldara, M. Hagihara, and K. J. Verstrepen, “Unstable tandem repeats in promoters confer transcriptional evolvability,” Science, vol. 324, no. 5931, pp. 1213–1216, 2009.
- T. D. Murphy and G. H. Karpen, “Localization of centromere function in a Drosophila minichromosome,” Cell, vol. 82, no. 4, pp. 599–609, 1995.