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Transcriptome analysis and development of SSR markers of ethnobotanical plant Sterculia lanceolata

  • Sang Mi Eum
  • Soo-Yong Kim
  • Jin Sung Hong
  • Neha Samir Roy
  • Sangho Choi
  • Jinhyup Paik
  • Sang Woo Lee
  • The Bach Tran
  • Van Hai Do
  • Kyoung Su Kim
  • Eun-Soo Seong
  • Kyong-Cheul Park
  • Chang Yeon Yu
  • Seok Hyun Eom
  • Ki-Young Choi
  • Jong-Hwa Kim
  • Jong-Kuk NaEmail author
Original Article
Part of the following topical collections:
  1. Gene Expression

Abstract

Several members of the genus Sterculia have a great potential as a candidate for the identification of new drug lead molecules, but lack of their genomic information can be a hindrance for the verification of the genetic background for future use. To obtain genomic resources, RNA-seq transcriptome analysis was conducted using leaves of Sterculia lanceolata, a member of the genus Sterculia, resulting in a total of 28,088,794 clear reads with a length of 3,692,930,973 bp. De novo assembly generated 7857 (3,559,905 bp) non-redundant unigenes with an average length of 453 bp. Among 1893 unigenes assigned by the Kyoto Encyclopedia of Genes and Genomes (KEGG) Orthology (KO) database, a total of 1158 were mapped into 328 different metabolic pathways. The biosynthesis of secondary metabolites (KO01110) pathway was the second highest hits with 159 unigenes, of which 72 are known to be involved in terpenoid, phenylpropanoid, and flavonoid biosynthesis. The search for simple sequence repeats (SSRs) identified a total of 899 SSRs. Nineteen polymorphic SSR markers were developed, of which polymorphism information content (PIC) values ranging from 0.10 to 0.49. Both Principal Coordinates Analysis (PCoA) and neighbor joining analysis using allelic data formed three clusters among 15 Sterculia species. The cluster of genotypes formed in the PCoA shows the genotypes in close proximity to those in neighbor joining tree. Taken together, our results provide a valuable source for genetic studies and also for molecular studies to unravel underlying mechanisms involved in medicinal properties of Sterculia L.

Keywords

Sterculia Genomics Medicinal plant SSR markers 

Notes

Acknowledgments

This work was supported by grants from the KRIBB Research Initiative Program (KGM4581811, 2018) and the Cooperative Research Program for Agricultural Science & Technology Development (PJ012266012018, 2018) of Rural Development Administration, Republic of Korea.

Data archiving statement

This transcriptome shotgun assembly project has been deposited at DDBJ/EMBL/GenBank under the accession GGIS00000000. The version described in this paper is the first version, GGIS01000000. SRA accession number is SRP133819.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interests.

Supplementary material

11295_2019_1348_MOESM1_ESM.docx (93 kb)
ESM 1 (DOCX 92.5 kb)

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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2019

Authors and Affiliations

  • Sang Mi Eum
    • 1
  • Soo-Yong Kim
    • 1
  • Jin Sung Hong
    • 2
  • Neha Samir Roy
    • 3
  • Sangho Choi
    • 1
  • Jinhyup Paik
    • 1
  • Sang Woo Lee
    • 1
  • The Bach Tran
    • 4
  • Van Hai Do
    • 4
  • Kyoung Su Kim
    • 2
  • Eun-Soo Seong
    • 5
  • Kyong-Cheul Park
    • 3
  • Chang Yeon Yu
    • 6
  • Seok Hyun Eom
    • 7
  • Ki-Young Choi
    • 8
  • Jong-Hwa Kim
    • 9
  • Jong-Kuk Na
    • 8
    Email author
  1. 1.International Biological Material Research CenterKRIBBDaejeonRepublic of Korea
  2. 2.Division of Bioresource SciencesKangwon National UniversityChuncheonRepublic of Korea
  3. 3.Department of Agricultural Life ScienceKangwon National UniversityChuncheonRepublic of Korea
  4. 4.Institute of Ecology and Biological Resources (IEBR)Vietnam Academy of Science and Technology (VAST)Cay GiayVietnam
  5. 5.Department of Medicinal PlantsSuwon Women’s UniversitySuwonRepublic of Korea
  6. 6.Department of Applied Plant ScienceKangwon National UniversityChuncheonRepublic of Korea
  7. 7.Department of Horticultural BiotechnologyKyung Hee UniversityYonginRepublic of Korea
  8. 8.Department of Controlled AgricultureKangwon National UniversityChuncheonRepublic of Korea
  9. 9.Department of HorticultureKangwon National UniversityChuncheonRepublic of Korea

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