Rattans are spiny climbing palms – their long, flexible stems are the source of rattan cane, which is harvested mainly from the wild. Rattan is the raw material on which a multibillion-dollar trade in cane furniture and other woven articles are built. Out of the ca. 500 species of rattan palms worldwide, numerous are reported to be utilised for cane products. The accurate identification of rattan species based on their morphology can be challenging because of the large number of species. In processed rattan articles, such as furniture, identification based on morphology is impossible because all required characters have been lost during processing.
The RattanID molecular identification toolkit enables the identification of rattan palms and furniture using genomic information. It is based on a near-complete genomic reference database of the palm subfamily Calamoideae, which contains all rattan palms. Particular attention has been paid to include economically important rattan species that are likely to be found in furniture.
This project is based on a collaboration between the Royal Botanic Gardens Kew and IKEA of Sweden AB to support a more sustainable rattan industry.
The workflow of rattan identification involves four steps:
| Step | Description |
|---|---|
| 1. Sampling | Sample collection, labelling and drying |
| 2. DNA extraction | Isolating genetic material from the sample |
| 3. DNA sequencing | Decoding genetic information for use in identification |
| 4. Identification | Species identification by comparing genetic information to a reference database |
Steps 1 to 3 (Sampling, DNA extraction and Sequencing) are covered in the laboratory protocol provided on Zenodo. Step 4 (Identification) is covered in detail on this webpage and requires the downloading of reference datasets deposited on Zenodo. We have developed two approaches for the identification of rattans:
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Skmer pipeline: Identification using genome skimming data
Shallow sequencing across the entire genome. Sample-specific genetic profiles are then computed using the composition of short stretches of DNA, so-called k-mers. Identification is based on the comparison of the k-mer profiles of the sample with the reference database. The reference species with the smallest genomic distance is considered the main identification. This procedure is fast, but identifications are slightly less accurate compared to the VSEARCH pipeline and genomic distances can be difficult to interpret.- Overview: Summary of the bioinformatic pipeline
- Tutorial: Step-by-step instructions for analysis of a single sample
- HPC instructions: Instructions for processing of multiple samples on a high performance computer (HPC) using our provided script.
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VSEARCH pipeline: Identification using target capture data
Targeted sequencing of hundreds of genes selected for their genetic informativeness. Retrieved genes are then compared one by one to the corresponding genes of the species in the reference database. The reference species identified by most genes is considered the main identification. This procedure is relatively complex but identifications are more accurate compared to the Skmer pipeline. The results are relatively easy to interpret, giving a good sense of the certainty of identification and plausible alternative identifications.- Overview: Summary of the bioinformatic pipeline
- Tutorial: Step-by-step instructions for analysis of a single sample
- HPC instructions: Instructions for processing of multiple samples on a high performance computer (HPC) using our provided script.
For interpretation of the results returned by both pipelines, please consult our Interpretation tutorial.
B.G. Kuhnhäuser, W. Baker & S. Bellot. 2023. RattanID – a molecular identification toolkit for rattan palms. Version 1.0. https://github.com/BenKuhnhaeuser/RattanID/.