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Park NI, Choi IY, Choi BS, et al. EST sequencing and gene expression profiling in Scutellaria baicalensis. EXCLI J. 2014;13:392-400
Park, N. I., Choi, I. Y., Choi, B. S., Kim, Y. S., Lee, M. Y., & Park, S. U. (2014). EST sequencing and gene expression profiling in Scutellaria baicalensis. EXCLI journal, 13392-400.
Park, Nam Il, et al. "EST sequencing and gene expression profiling in Scutellaria baicalensis." EXCLI journal vol. 13 (2014): 392-400.
Park NI, Choi IY, Choi BS, Kim YS, Lee MY, Park SU. EST sequencing and gene expression profiling in Scutellaria baicalensis. EXCLI J. 2014 Apr 07;13:392-400. eCollection 2014. PMID: 26417266; PMCID: PMC4464476.
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EXCLI J. 2014 Apr 07;13:392-400. eCollection 2014.

EST sequencing and gene expression profiling in Scutellaria baicalensis.

EXCLI journal

Nam Il Park, Ik Young Choi, Beom-Soon Choi, Young Seon Kim, Mi Young Lee, Sang Un Park

Affiliations

  1. Department of Plant Science, Gangneung-Wonju National University, 7 Jukheon-gil, Gangneung-si, Gangwon-do, 210-702, Korea.
  2. National Instrumentation Center for Environmental Management, Seoul National University, 599 Gwanangno, Daehak-dong, Gwanak-gu, Seoul, 151-921, Korea.
  3. KM-Based Herbal Drug Research Group, Korea Institute of Oriental Medicine, Daejeon, 305-811, Korea.
  4. Department of Crop Science, Chungnam National University, 99 Daehak-ro, Yuseong-Gu, Daejeon, 305-764, Korea.

PMID: 26417266 PMCID: PMC4464476

Abstract

Scutellaria baicalensis is an important medicinal plant, but few genomic resources are available for this species, as well as for other non-model plants. One of the major new directions in genome research is to discover the full spectrum of genes transcribed from the whole genome. Here, we report extensive transcriptome data of the early growth stage of S. baicalensis. This transcriptome consensus sequence was constructed by de novo assembly of shotgun sequencing data, obtained using multiple next-generation DNA sequencing (NGS) platforms (Roche/454 GS_FLX+ and Illumina/Solexa HiSeq2000). We show that this new approach to obtain extensive mRNA is an efficient strategy for genome-wide transcriptome analysis. We obtained 1,226,938 and 161,417,646 reads using the GS_FLX and the Illumina/Solexa HiSeq2000, respectively. De novo assembly of the high-quality GS_FLX and Illumina reads (95 % and 75 %) resulted in more than 82 Mb of mRNA consensus sequence, which we assembled into 51,188 contigs, with at least 500 bp per contig. Of these contigs, 39,581 contained known genes, as determined by BLASTX searches against non-redundant NCBI database. Of these, 20,498 different genes were expressed during the early growth stage of S. baicalensis. We have made the expressed sequences available on a public database. Our results demonstrate the utility of combining NGS technologies as a basis for the development of genomic tools in non-model, medicinal plant species. Knowledge of all described genes and quantitation of the expressed genes, including the transcription factors involved, will be useful in studies of the biology of S. baicalensis gene regulation.

Keywords: Scutellaria baicalensis; de novo assembly; expression profiling; next generation sequencing

References

  1. BMC Genomics. 2012 Jan 25;13:45 - PubMed
  2. Gene. 2012 Apr 15;497(2):256-62 - PubMed
  3. Nat Methods. 2008 Jul;5(7):621-8 - PubMed
  4. Plant Physiol. 2005 Jun;138(2):1083-96 - PubMed
  5. Mol Ecol Resour. 2012 Mar;12(2):333-43 - PubMed
  6. BMC Genomics. 2011 Jul 12;12:360 - PubMed
  7. Genome Biol. 2010;11(12):220 - PubMed
  8. BMC Plant Biol. 2012 Apr 02;12 :46 - PubMed
  9. Bioresour Technol. 2010 Dec;101(24):9715-22 - PubMed
  10. BMC Genomics. 2011 Jan 13;12:30 - PubMed
  11. Funct Integr Genomics. 2011 Sep;11(3):491-6 - PubMed
  12. BMC Genomics. 2010 Mar 16;11:180 - PubMed
  13. BMC Genet. 2011 Dec 15;12:104 - PubMed
  14. BMC Genomics. 2010 Apr 01;11:219 - PubMed
  15. Curr Opin Biotechnol. 1998 Dec;9(6):609-14 - PubMed
  16. BMC Genomics. 2010 Feb 08;11:94 - PubMed
  17. BMC Plant Biol. 2011 Nov 23;11:167 - PubMed
  18. Phytochemistry. 2005 Oct;66(20):2399-407 - PubMed
  19. PLoS One. 2010 Aug 06;5(8):e12010 - PubMed
  20. Curr Opin Plant Biol. 2004 Apr;7(2):202-9 - PubMed
  21. Biochemistry (Mosc). 2009 Jan;74(1):1-11 - PubMed
  22. BMC Genomics. 2010 Oct 16;11:571 - PubMed

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