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

• Published in: Tree genetics & genomes Vol. 15; no. 3; pp. 1 - 12
• Main Authors: Eum, Sang Mi, Kim, Soo-Yong, Hong, Jin Sung, Roy, Neha Samir, Choi, Sangho, Paik, Jinhyup, Lee, Sang Woo, Tran, The Bach, Do, Van Hai, Kim, Kyoung Su, Seong, Eun-Soo, Park, Kyong-Cheul, Yu, Chang Yeon, Eom, Seok Hyun, Choi, Ki-Young, Kim, Jong-Hwa, Na, Jong-Kuk
• Format: Journal Article
• Language: English
• Published: Berlin/Heidelberg Springer Berlin Heidelberg 01.06.2019; Springer Nature B.V
• Subjects: Biomedical and Life Sciences; Biosynthesis; Biotechnology; Encyclopedias; Forestry; Gene Expression; Gene polymorphism; Genomes; Genotypes; Leaves; Life Sciences; Markers; Metabolic pathways; Metabolites; Original Article; Orthology; Plant Breeding/Biotechnology; Plant Genetics and Genomics; Polymorphism; Ribonucleic acid; RNA; Secondary metabolites; Simple sequence repeats; Sterculia; Tree Biology; Genomics; SSR markers; Medicinal plant
• ISSN: 1614-2942; 1614-2950
• DOI: 10.1007/s11295-019-1348-3

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 .