전체메뉴 JMB
Advanced Search +

JMB Journal of Microbiolog and Biotechnology

QR Code QR Code

Research article

Molecular Biology and Omics

Development of Novel Microsatellite Markers for Strain-Specific Identification of Chlorella vulgaris

Beom-Ho Jo 1, Chang Soo Lee 2, Hae-Ryong Song 1, Hyung-Gwan Lee 2 and Hee-Mock Oh 2*

1Bureau of Ecological Conservation Research, National Institute of Ecology (NIE), Seocheon 325-813, Republic of Korea, 2Environmental Biotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 305-806, Republic of Korea

Received: May 20, 2014; Accepted: June 9, 2014

J. Microbiol. Biotechnol. 2014; 24(9): 1189-1195

Published September 28, 2014 https://doi.org/10.4014/jmb.1405.05047

Copyright © The Korean Society for Microbiology and Biotechnology.

Abstract

A strain-specific identification method is required to secure Chlorella strains with useful genetic traits, such as a fast growth rate or high lipid productivity, for application in biofuels, functional foods, and pharmaceuticals. Microsatellite markers based on simple sequence repeats can be a useful tool for this purpose. Therefore, this study developed five novel microsatellite markers (mChl-001, mChl-002, mChl-005, mChl-011, and mChl-012) using specific loci along the chloroplast genome of Chlorella vulgaris. The microsatellite markers were characterized based on their allelic diversities among nine strains of C. vulgaris with the same 18S rRNA sequence similarity. Each microsatellite marker exhibited 2~5 polymorphic allele types, and their combinations allowed discrimination between seven of the C. vulgaris strains. The two remaining strains were distinguished using one specific interspace region between the mChl-001 and mChl-005 loci, which was composed of about 27 single nucleotide polymorphisms, 13~15 specific sequence sites, and (T)n repeat sites. Thus, the polymorphic combination of the five microsatellite markers and one specific locus facilitated a clear distinction of C. vulgaris at the strain level, suggesting that the proposed microsatellite marker system can be useful for the accurate identification and classification of C. vulgaris.

Keywords

Chlorella vulgaris, chloroplast, microsatellite, marker, polymorphism, sequence repeat

References

  1. Anti V, Jan N, Craig RP. 2005. Expressed sequence tag-linked microsatellites as a source of gene-associated polymorphisms for detecting signatures of divergent selection in Atlantic salmon (Salmo salar L.). Mol. Biol. Evol. 22: 1067-1076.
  2. Bassam BJ, Caetano-Anollés G, Gresshoff PM. 1991. Fast and sensitive silver staining of DNA in polyacrylamide gels. Anal. Biochem. 196: 80-83.
  3. Bock C, Krienitz L, Pröeschold T. 2011. Taxonomic reassessment of the genus Chlorella (Trebouxiophyceae) using molecular signatures (barcodes), including description of seven new species. Fottea 11: 293-312.
  4. Boyle G. 2004. Renewable Energy. Oxford University Press, UK.
  5. Chambers GK, MacAvoy ES. 2000. Microsatellites: consensus and controversy. Comp. Biochem. Physiol. B Biochem. Mol. Biol. 126: 455-476.
  6. Chisti Y. 2007. Biodiesel from microalgae. Biotechnol. Adv. 25: 294-306.
  7. Cho SY, Nagai S, Han MS. 2009. Development of microsatellite markers in red-tide causative species Prorocentrum micans (Dinophyceae). Conserv. Genet. 10: 1151-1153.
  8. de Boer PA, Crossley RE, Rothfield LI. 1989. A division inhibitor and topological specificity factor coded for by the minicell locus determine proper placement of the division septum in E. coli. Cell 56: 641-649.
  9. Evans KM, Chepurnov VA, Mann DG. 2009. Ten microsatellite markers for the freshwater diatom Sellaphora capitata. Mol. Ecol. Resour. 9: 216-218.
  10. Kang TJ, Fawley MW. 1997. Variable (CA/GT)n simple sequence repeat DNA in the alga Chlamydomonas. Plant Mol. Biol. 35: 943-948.
  11. Kantety RV, La Rota M, Matthews DE, Sorrells ME. 2002. Data mining for simple sequence repeats in expressed sequence tags from barley, maize, rice, sorghum and wheat. Plant Mol. Biol. 48: 501-510.
  12. Kim J, Jo BH, Lee KL, Yoon ES, Ryu GH, Chung KW. 2007. Identification of new microsatellite markers in Panax ginseng. Mol. Cells 24: 60-68.
  13. Kim YO, Cho HK, Park EM, Nam BH, Hur YB, Lee SJ, Cheong J. 2008. Generation of expressed sequence tags for immune gene discovery and marker development in the sea squirt, Halocynthia roretzi. J. Microbiol. Biotechnol. 18: 1 5101517.
  14. Li S, Zhang X, Yin T. 2010. Characteristics of microsatellites in the transcript sequences of the Laccaria bicolor genome. J. Microbiol. Biotechnol. 20: 474-479.
  15. Mahmudul IN, Bian YB. 2010. Efficiency of RAPD and ISSR markers in differentiation of homo- and heterokaryotic protoclones of Agaricus bisporus. J. Microbiol. Biotechnol. 20:683-692.
  16. Mata TM, Martins A A, C aetano N S. 2 01 0. Microalgae for biodiesel production and other applications: a review. Renew. Sust. Energ. Rev. 14: 217-232.
  17. Nagai S, Lian C, Hamaguchi M, Matsuyama Y, Itakura S, Hogetsu T. 2004. Development of microsatellite markers in the toxic dinoflagellate Alexandrium tamarense (Dinophyceae). Mol. Ecol. Notes 4: 83-85.
  18. Nagai S, McCauley L, Yasuda N, Erdner DL, Kulis DM, Matsuyama Y, et al. 2006. Development of microsatellite markers in the toxic dinoflagellate Alexandrium minutum (Dinophyceae). Mol. Ecol. Notes 6: 756-758.
  19. Ohad I, Dal Bosco C, Herrmann RG, Meurer J. 2004. Photosystem II proteins PsbL and PsbJ regulate electron flow to the plastoquinone pool. Biochemistry 43: 2297-2308.
  20. Phukan MM, Chutia RS, Konwar BK, Kataki R. 2011. Microalgae Chlorella as a potential bio-energy feedstock. Appl. Energy 88: 3307-3312.
  21. Roder M S, Plaschke J, K önig S U, B örner A, S orrells ME, Tanksley SD, Ganal MW. 1995. Abundance, variability and chromosomal location of microsatellites in wheat. Mol. Gen. Genet. 246: 327-333.
  22. Semagn K, Bjørnstad Å, Ndjiondjop MN. 2007. An overview of molecular marker methods for plants. Afr. J. Biotechnol. 5:2540-2568.
  23. Shin SY, Jo BH, Lee HG, Oh HM. 2 01 3. P hysiological a nd ecological characteristics of lipid-producing Botryococcus isolated from the Korean freshwaters. Korean J. Environ. Biol. 31: 288-294.
  24. Stanier RY, Kunisawa R, Mandel M, Cohen-Bazire G. 1971. Purification and properties of unicellular blue-green algae (order Chroococcales). Bacteriol. Rev. 35: 171-205.
  25. Suorsa M, Regel RE, Paakkarinen V, Battchikova N, Herrmann RG, Aro EM. 2004. Protein assembly of photosystem II and accumulation of subcomplexes in the absence of low molecular mass subunits PsbL and PsbJ. Eur. J. Biochem. 271:96-107.
  26. Temnykh S, DeClerck G, Lukashova A, Lipovich L, Cartinhour S, McCouch S. 2001. Computational and experimental analysis of microsatellites in rice (Oryza sativa L.): frequency, length variation, transposon associations, and genetic marker potential. Genome Res. 11: 1441-1452.
  27. Ware D, Jaiswal P, Ji J, Pan X, Chang K, Clark K, et al. 2002. Gramene: a resource for comparative grass genomics. Nucleic Acids Res. 30: 103-105.

Related articles in JMB

Article

Research article

J. Microbiol. Biotechnol. 2014; 24(9): 1189-1195

Published online September 28, 2014 https://doi.org/10.4014/jmb.1405.05047

Copyright © The Korean Society for Microbiology and Biotechnology.

Development of Novel Microsatellite Markers for Strain-Specific Identification of Chlorella vulgaris

Beom-Ho Jo 1, Chang Soo Lee 2, Hae-Ryong Song 1, Hyung-Gwan Lee 2 and Hee-Mock Oh 2*

1Bureau of Ecological Conservation Research, National Institute of Ecology (NIE), Seocheon 325-813, Republic of Korea, 2Environmental Biotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 305-806, Republic of Korea

Received: May 20, 2014; Accepted: June 9, 2014

Abstract

A strain-specific identification method is required to secure Chlorella strains with useful
genetic traits, such as a fast growth rate or high lipid productivity, for application in biofuels,
functional foods, and pharmaceuticals. Microsatellite markers based on simple sequence
repeats can be a useful tool for this purpose. Therefore, this study developed five novel
microsatellite markers (mChl-001, mChl-002, mChl-005, mChl-011, and mChl-012) using
specific loci along the chloroplast genome of Chlorella vulgaris. The microsatellite markers were
characterized based on their allelic diversities among nine strains of C. vulgaris with the same
18S rRNA sequence similarity. Each microsatellite marker exhibited 2~5 polymorphic allele
types, and their combinations allowed discrimination between seven of the C. vulgaris strains.
The two remaining strains were distinguished using one specific interspace region between
the mChl-001 and mChl-005 loci, which was composed of about 27 single nucleotide
polymorphisms, 13~15 specific sequence sites, and (T)n repeat sites. Thus, the polymorphic
combination of the five microsatellite markers and one specific locus facilitated a clear
distinction of C. vulgaris at the strain level, suggesting that the proposed microsatellite marker
system can be useful for the accurate identification and classification of C. vulgaris.

Keywords: Chlorella vulgaris, chloroplast, microsatellite, marker, polymorphism, sequence repeat

References

  1. Anti V, Jan N, Craig RP. 2005. Expressed sequence tag-linked microsatellites as a source of gene-associated polymorphisms for detecting signatures of divergent selection in Atlantic salmon (Salmo salar L.). Mol. Biol. Evol. 22: 1067-1076.
  2. Bassam BJ, Caetano-Anollés G, Gresshoff PM. 1991. Fast and sensitive silver staining of DNA in polyacrylamide gels. Anal. Biochem. 196: 80-83.
  3. Bock C, Krienitz L, Pröeschold T. 2011. Taxonomic reassessment of the genus Chlorella (Trebouxiophyceae) using molecular signatures (barcodes), including description of seven new species. Fottea 11: 293-312.
  4. Boyle G. 2004. Renewable Energy. Oxford University Press, UK.
  5. Chambers GK, MacAvoy ES. 2000. Microsatellites: consensus and controversy. Comp. Biochem. Physiol. B Biochem. Mol. Biol. 126: 455-476.
  6. Chisti Y. 2007. Biodiesel from microalgae. Biotechnol. Adv. 25: 294-306.
  7. Cho SY, Nagai S, Han MS. 2009. Development of microsatellite markers in red-tide causative species Prorocentrum micans (Dinophyceae). Conserv. Genet. 10: 1151-1153.
  8. de Boer PA, Crossley RE, Rothfield LI. 1989. A division inhibitor and topological specificity factor coded for by the minicell locus determine proper placement of the division septum in E. coli. Cell 56: 641-649.
  9. Evans KM, Chepurnov VA, Mann DG. 2009. Ten microsatellite markers for the freshwater diatom Sellaphora capitata. Mol. Ecol. Resour. 9: 216-218.
  10. Kang TJ, Fawley MW. 1997. Variable (CA/GT)n simple sequence repeat DNA in the alga Chlamydomonas. Plant Mol. Biol. 35: 943-948.
  11. Kantety RV, La Rota M, Matthews DE, Sorrells ME. 2002. Data mining for simple sequence repeats in expressed sequence tags from barley, maize, rice, sorghum and wheat. Plant Mol. Biol. 48: 501-510.
  12. Kim J, Jo BH, Lee KL, Yoon ES, Ryu GH, Chung KW. 2007. Identification of new microsatellite markers in Panax ginseng. Mol. Cells 24: 60-68.
  13. Kim YO, Cho HK, Park EM, Nam BH, Hur YB, Lee SJ, Cheong J. 2008. Generation of expressed sequence tags for immune gene discovery and marker development in the sea squirt, Halocynthia roretzi. J. Microbiol. Biotechnol. 18: 1 5101517.
  14. Li S, Zhang X, Yin T. 2010. Characteristics of microsatellites in the transcript sequences of the Laccaria bicolor genome. J. Microbiol. Biotechnol. 20: 474-479.
  15. Mahmudul IN, Bian YB. 2010. Efficiency of RAPD and ISSR markers in differentiation of homo- and heterokaryotic protoclones of Agaricus bisporus. J. Microbiol. Biotechnol. 20:683-692.
  16. Mata TM, Martins A A, C aetano N S. 2 01 0. Microalgae for biodiesel production and other applications: a review. Renew. Sust. Energ. Rev. 14: 217-232.
  17. Nagai S, Lian C, Hamaguchi M, Matsuyama Y, Itakura S, Hogetsu T. 2004. Development of microsatellite markers in the toxic dinoflagellate Alexandrium tamarense (Dinophyceae). Mol. Ecol. Notes 4: 83-85.
  18. Nagai S, McCauley L, Yasuda N, Erdner DL, Kulis DM, Matsuyama Y, et al. 2006. Development of microsatellite markers in the toxic dinoflagellate Alexandrium minutum (Dinophyceae). Mol. Ecol. Notes 6: 756-758.
  19. Ohad I, Dal Bosco C, Herrmann RG, Meurer J. 2004. Photosystem II proteins PsbL and PsbJ regulate electron flow to the plastoquinone pool. Biochemistry 43: 2297-2308.
  20. Phukan MM, Chutia RS, Konwar BK, Kataki R. 2011. Microalgae Chlorella as a potential bio-energy feedstock. Appl. Energy 88: 3307-3312.
  21. Roder M S, Plaschke J, K önig S U, B örner A, S orrells ME, Tanksley SD, Ganal MW. 1995. Abundance, variability and chromosomal location of microsatellites in wheat. Mol. Gen. Genet. 246: 327-333.
  22. Semagn K, Bjørnstad Å, Ndjiondjop MN. 2007. An overview of molecular marker methods for plants. Afr. J. Biotechnol. 5:2540-2568.
  23. Shin SY, Jo BH, Lee HG, Oh HM. 2 01 3. P hysiological a nd ecological characteristics of lipid-producing Botryococcus isolated from the Korean freshwaters. Korean J. Environ. Biol. 31: 288-294.
  24. Stanier RY, Kunisawa R, Mandel M, Cohen-Bazire G. 1971. Purification and properties of unicellular blue-green algae (order Chroococcales). Bacteriol. Rev. 35: 171-205.
  25. Suorsa M, Regel RE, Paakkarinen V, Battchikova N, Herrmann RG, Aro EM. 2004. Protein assembly of photosystem II and accumulation of subcomplexes in the absence of low molecular mass subunits PsbL and PsbJ. Eur. J. Biochem. 271:96-107.
  26. Temnykh S, DeClerck G, Lukashova A, Lipovich L, Cartinhour S, McCouch S. 2001. Computational and experimental analysis of microsatellites in rice (Oryza sativa L.): frequency, length variation, transposon associations, and genetic marker potential. Genome Res. 11: 1441-1452.
  27. Ware D, Jaiswal P, Ji J, Pan X, Chang K, Clark K, et al. 2002. Gramene: a resource for comparative grass genomics. Nucleic Acids Res. 30: 103-105.
Clarivate Analytics PubMed PubMed Central Crossref Similarity Check Crossref Cited-by Crossref KMB MBL Clarivate Analytics PubMed PubMed Central Crossref Similarity Check Crossref Cited-by Crossref KMB MBL

AltStyle によって変換されたページ (->オリジナル) /

[フレーム]