| Issue |
BIO Web Conf.
Volume 186, 2025
The 2nd International Seminar on Tropical Bioresources Advancement and Technology (ISOTOBAT 2025)
|
|
|---|---|---|
| Article Number | 03007 | |
| Number of page(s) | 9 | |
| Section | Innovative Technologies in Bioresource Science and Engineering | |
| DOI | https://doi.org/10.1051/bioconf/202518603007 | |
| Published online | 22 August 2025 | |
Simple sequence repeats (SSRs) discovery, characterization and validation from de novo transcriptome assembly of Typhonium flagelliforme
1 Research Center for Applied Botany, BRIN, Bogor, West Java, Indonesia
2 Research Center for Pharmaceutical Ingredients and Traditional Medicine, BRIN, Bogor, West Java, Indonesia
3 Department of Agronomy and Horticulture, Faculty of Agriculture, IPB University, Bogor, Indonesia
* Corresponding author: sobir@apps.ipb.ac.id
Typhonium flagelliforme, a distinctive medicinal plant belonging to the Araceae family, is native Indonesian herb renowned for its anticancer properties. Despite of significant potential medicinal value, the availability of molecular markers for studying its genetic diversity and evolutionary background were limited. In this study, we performed the first transcriptome of T. flagelliforme leaf using paired-end Illumina NovaSeq 6000 PE150 which generated 10.79 GB of raw data. De novo assembly using rnaSpades resulted in a total of 11,521 transcripts with contigs length and longest contigs respectively 123,909,948 bp and 28,917,662 bp. The analysis succesfully identified 20,960 genic SSR loci from the transcriptome sequencing data using the Microsatellite (MISA) tool. The perfect motifs showed the following distribution of motif types: mononucleotides (32.1%), dinucleotides (40.8%), trinucleotides (24.9%), tetranucleotides (1.5%), pentanucleotides (0.2%), and hexanucleotides (0.4%). From these, 161 primer pairs were designed and 40 selected primers were validated. To the best of our knowledge, this is the first study to identify and characterize EST- SSR markers in T. flagelliforme. These markers are potential for genetic diversity assessment, marker-assisted selection (MAS), cultivar identification, kinship analysis, and genetic mapping.
© The Authors, published by EDP Sciences, 2025
This is an Open Access article distributed under the terms of the Creative Commons Attribution License 4.0, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
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