Table of Contents Author Guidelines Submit a Manuscript
International Journal of Genomics
Volume 2015, Article ID 679548, 7 pages
http://dx.doi.org/10.1155/2015/679548
Research Article

Expressed Sequence Tags Analysis and Design of Simple Sequence Repeats Markers from a Full-Length cDNA Library in Perilla frutescens (L.)

1Bioherb Research Institute, Kangwon National University, Chuncheon 200-701, Republic of Korea
2Department of Bioconvergence Science and Technology, College of Agriculture and Life Sciences, Kangwon National University, Chuncheon 200-701, Republic of Korea
3Hwajin Cosmetics, Hongcheon 250-807, Republic of Korea
4Department of Agricultural Life Sciences, Kangwon National University, Chuncheon 200-701, Republic of Korea
5Department of Applied Bioscience, Konkuk University, Seoul 143-701, Republic of Korea

Received 27 July 2015; Accepted 21 October 2015

Academic Editor: Xiaohan Yang

Copyright © 2015 Eun Soo Seong 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.

Linked References

  1. Y.-J. Park, A. Dixit, K.-H. Ma et al., “Evaluation of genetic diversity and relationships within an on-farm collection of Perilla frutescens (L.) Britt. using microsatellite markers,” Genetic Resources and Crop Evolution, vol. 55, no. 4, pp. 523–535, 2008. View at Publisher · View at Google Scholar · View at Scopus
  2. A. K. Pandey and K. C. Bhatt, “Diversity distribution and collection of genetic resources of cultivated and weedy type in Perilla frutescens (L.) Britton var. frutescens and their uses in Indian Himalaya,” Genetic Resources and Crop Evolution, vol. 55, no. 6, pp. 883–892, 2008. View at Publisher · View at Google Scholar · View at Scopus
  3. C. X. You, K. Yang, Y. Wu et al., “Chemical composition and insecticidal activities of the essential oil of Perilla frutescens (L.) Britt. aerial parts against two stored product insects,” European Food Research and Technology, vol. 239, pp. 481–490, 2014. View at Publisher · View at Google Scholar · View at Scopus
  4. H.-S. Shin and S.-W. Kim, “Lipid composition of perilla seed,” Journal of the American Oil Chemists' Society, vol. 71, no. 6, pp. 619–622, 1994. View at Publisher · View at Google Scholar · View at Scopus
  5. T. Longvah and Y. G. Deosthale, “Chemical and nutritional studies on Hanshi (Perilla frutescens), a traditional oilseed from northeast India,” Journal of the American Oil Chemists Society, vol. 68, no. 10, pp. 781–784, 1991. View at Publisher · View at Google Scholar · View at Scopus
  6. S. J. Kim, E. Y. Kang, S. E. Won et al., “Chemical composition and comparison of essential oil contents of Perilla frutescens Britton var. japonica HARA leaves,” Korean Journal of Medicinal Crop Science, vol. 16, pp. 242–254, 2008. View at Google Scholar
  7. M. Nitta, H. Kobayashi, M. Ohnishi-Kameyama, T. Nagamine, and M. Yoshida, “Essential oil variation of cultivated and wild Perilla analyzed by GC/MS,” Biochemical Systematics and Ecology, vol. 34, no. 1, pp. 25–37, 2006. View at Publisher · View at Google Scholar · View at Scopus
  8. H. Ueda, C. Yamazaki, and M. Yamazaki, “Luteolin as an anti-inflammatory and anti-allergic constituent of Perilla frutescens,” Biological and Pharmaceutical Bulletin, vol. 25, no. 9, pp. 1197–1202, 2002. View at Publisher · View at Google Scholar · View at Scopus
  9. M.-K. Kim, H.-S. Lee, E.-J. Kim et al., “Protective effect of aqueous extract of Perilla frutescens on tert-butyl hydroperoxide-induced oxidative hepatotoxicity in rats,” Food and Chemical Toxicology, vol. 45, no. 9, pp. 1738–1744, 2007. View at Publisher · View at Google Scholar · View at Scopus
  10. M. D. Adams, M. B. Soares, A. R. Kerlavage, C. Fields, and J. C. Venter, “Rapid cDNA sequencing (expressed sequence tags) from a directionally cloned human infant brain cDNA library,” Nature Genetics, vol. 4, no. 4, pp. 373–380, 1993. View at Publisher · View at Google Scholar · View at Scopus
  11. R. K. Varshney, A. Graner, and M. E. Sorrells, “Genic microsatellite markers in plants: features and applications,” Trends in Biotechnology, vol. 23, no. 1, pp. 48–55, 2005. View at Publisher · View at Google Scholar · View at Scopus
  12. R. K. Varshney, R. Sigmund, A. Börner et al., “Interspecific transferability and comparative mapping of barley EST-SSR markers in wheat, rye and rice,” Plant Science, vol. 168, no. 1, pp. 195–202, 2005. View at Publisher · View at Google Scholar · View at Scopus
  13. R. Peakall, S. Gilmore, W. Keys, M. Morgante, and A. Rafalski, “Cross-species amplification of soybean (Glycine max) simple sequence repeats (SSRs) within the genus and other legume genera: implications for the transferability of SSRs in plants,” Molecular Biology and Evolution, vol. 15, no. 10, pp. 1275–1287, 1998. View at Publisher · View at Google Scholar · View at Scopus
  14. 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. View at Publisher · View at Google Scholar · View at Scopus
  15. T. Thiel, W. Michalek, R. K. Varshney, and A. Graner, “Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.),” Theoretical and Applied Genetics, vol. 106, no. 3, pp. 411–422, 2003. View at Publisher · View at Google Scholar · View at Scopus
  16. J.-K. Yu, T. M. Dake, S. Singh et al., “Development and mapping of EST-derived simple sequence repeat markers for hexaploid wheat,” Genome, vol. 47, no. 5, pp. 805–818, 2004. View at Publisher · View at Google Scholar · View at Scopus
  17. J.-K. Yu, M. La Rota, R. V. Kantety, and M. E. Sorrells, “EST derived SSR markers for comparative mapping in wheat and rice,” Molecular Genetics and Genomics, vol. 271, no. 6, pp. 742–751, 2004. View at Google Scholar · View at Scopus
  18. A. Heesacker, V. K. Kishore, W. Gao et al., “SSRs and INDELs mined from the sunflower EST database: abundance, polymorphisms, and cross-taxa utility,” Theoretical and Applied Genetics, vol. 117, no. 7, pp. 1021–1029, 2008. View at Publisher · View at Google Scholar · View at Scopus
  19. J. R. Ellis and J. M. Burke, “EST-SSRs as a resource for population genetic analyses,” Heredity, vol. 99, no. 2, pp. 125–132, 2007. View at Publisher · View at Google Scholar · View at Scopus
  20. 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. View at Publisher · View at Google Scholar · View at Scopus
  21. C. H. Pashley, J. R. Ellis, D. E. McCauley, and J. M. Burke, “EST databases as a source for molecular markers: lessons from Helianthus,” Journal of Heredity, vol. 97, no. 4, pp. 381–388, 2006. View at Publisher · View at Google Scholar · View at Scopus
  22. M. A. Chapman, J. Hvala, J. Strever et al., “Development, polymorphism, and cross-taxon utility of EST-SSR markers from safflower (Carthamus tinctorius L.),” Theoretical and Applied Genetics, vol. 120, no. 1, pp. 85–91, 2009. View at Publisher · View at Google Scholar · View at Scopus
  23. A. Depeiges, C. Goubely, A. Lenoir et al., “Identification of the most represented repeated motifs in Arabidopsis thaliana microsatellite loci,” Theoretical and Applied Genetics, vol. 91, no. 1, pp. 160–168, 1995. View at Publisher · View at Google Scholar · View at Scopus
  24. G. M. Cordeiro, R. Casu, C. L. McIntyre, J. M. Manners, and R. J. Henry, “Microsatellite markers from sugarcane (Saccharum spp.) ESTs cross transferable to Erianthus and sorghum,” Plant Science, vol. 160, no. 6, pp. 1115–1123, 2001. View at Publisher · View at Google Scholar · View at Scopus
  25. L. S. Lima, K. P. Gramacho, A. S. Gesteira et al., “Characterization of microsatellites from cacao-Moniliophthora perniciosa interaction expressed sequence tags,” Molecular Breeding, vol. 22, no. 2, pp. 315–318, 2008. View at Publisher · View at Google Scholar · View at Scopus
  26. E. De Keyser, J. de Riek, and E. van Bockstaele, “Discovery of species-wide EST-derived markers in Rhododendron by intron-flanking primer design,” Molecular Breeding, vol. 23, no. 1, pp. 171–178, 2009. View at Publisher · View at Google Scholar · View at Scopus
  27. E. S. Seong, J. H. Yoo, J. H. Choi et al., “Construction and classification of a cDNA Library from Miscanthus sinenesis (Eulalia) treated with UV-B,” Plant Omics Journal, vol. 8, pp. 264–269, 2015. View at Google Scholar
  28. F. C. Peixoto and J. M. Ortega, “On the pursuit of optimal sequence trimming parameters for EST projects,” in Proceedings of the 1st Brazilian Symposium/Workshop on Bioinformatics (BSB/WOB '02), pp. 48–55, Gramado, Brazil, October 2002.
  29. X. Huang and A. Madan, “CAP3: a DNA sequence assembly program,” Genome Research, vol. 9, no. 9, pp. 868–877, 1999. View at Publisher · View at Google Scholar · View at Scopus
  30. L. Shangguan, J. Han, E. Kayesh et al., “Evaluation of genome sequencing quality in selected plant species using expressed sequence tags,” PLoS ONE, vol. 8, no. 7, Article ID e69890, 2013. View at Publisher · View at Google Scholar · View at Scopus
  31. E. S. Lander, L. M. Linton, B. Birren, C. Nusbaum, and M. C. Zody, “Initial sequencing and analysis of the human genome,” Nature, vol. 409, pp. 860–921, 2001. View at Google Scholar
  32. R. Versteeg, B. D. C. van Schaik, M. F. van Batenburg et al., “The human transcriptome map reveals extremes in gene dentistry, intron length, GC content, and repeat pattern for domains of highly and weakly expressed genes,” Genome Research, vol. 13, no. 9, pp. 1998–2004, 2003. View at Publisher · View at Google Scholar · View at Scopus
  33. S. K. Arasan, J.-I. Park, N. U. Ahmed et al., “Gene ontology based characterization of expressed sequence tags (ESTs) of Brassica rapa cv. Osome,” Indian Journal of Experimental Biology, vol. 51, no. 7, pp. 522–530, 2013. View at Google Scholar · View at Scopus
  34. The Gene Ontology Consortium, “Gene ontology annotations and resources,” Nucleic Acids Research, vol. 41, pp. 530–535, 2013. View at Google Scholar
  35. H. J. Kim, K. H. Baek, S. W. Lee et al., “Pepper EST database: comprehensive in silico tool for analyzing the chili pepper (Capsicum annuum) transcriptome,” BMC Plant Biology, vol. 8, article 101, 7 pages, 2008. View at Publisher · View at Google Scholar
  36. A. Conesa and S. Götz, “Blast2GO: a comprehensive suite for functional analysis in plant genomics,” International Journal of Plant Genomics, vol. 2008, Article ID 619832, 12 pages, 2008. View at Publisher · View at Google Scholar · View at Scopus
  37. K. D. Scott, P. Eggler, G. Seaton et al., “Analysis of SSRs derived from grape ESTs,” Theoretical and Applied Genetics, vol. 100, no. 5, pp. 723–726, 2000. View at Publisher · View at Google Scholar · View at Scopus
  38. P. Bajgain, B. A. Richardson, J. C. Price, R. C. Cronn, and J. A. Udall, “Transcriptome characterization and polymorphism detection between subspecies of big sagebrush (Artemisia tridentata),” BMC Genomics, vol. 12, article 370, 2011. View at Publisher · View at Google Scholar · View at Scopus
  39. T. S. Wu, C. Liang, H. B. Li, and Z. Y. Piao, “Development of unigene derived microsatellite (UGMS) markers in Panax ginseng,” Scientia Agricultura Sinica, vol. 44, pp. 2650–2660, 2011. View at Google Scholar
  40. K.-J. Deng, Y. Zhang, B.-Q. Xiong et al., “Identification, characterization and utilization of simple sequence repeat markers derived from Salvia miltiorrhiza expressed sequence tags,” Acta Pharmacologica Sinica, vol. 44, no. 10, pp. 1165–1172, 2009. View at Google Scholar · View at Scopus
  41. Y. Yuan, P. Long, C. Jiang, M. Li, and L. Huang, “Development and characterization of simple sequence repeat (SSR) markers based on a full-length cDNA library of Scutellaria baicalensis,” Genomics, vol. 105, no. 1, pp. 61–67, 2015. View at Publisher · View at Google Scholar · View at Scopus
  42. M. Seki, M. Narusaka, A. Kamiya et al., “Functional annotation of a full-length Arabidopsis cDNA collection,” Science, vol. 296, no. 5565, pp. 141–145, 2002. View at Publisher · View at Google Scholar · View at Scopus