The ferns, lycophytes and seed-free vascular plants commonly described as pteridophytes exhibit hyperdiversity in the insular vegetation that often characterizes Asian floras. Despite harboring biodiversity hotspots, these plants and their georegions have been poorly surveyed, particularly in Southeast Asia, where one third of the world's pteridophyte species are concentrated. More than 60 per cent of the approximately 4,500 species lack georeferenced records in GBIF and only 6 per cent have been DNA barcoded.
This project aims to increase the available knowledge on Asian pteridophytes by compiling a georeferenced occurrence dataset that includes images, DNA barcodes and other vouchering information from thousands of recent collections, building on the efforts of the Taiwan Pteridophyte Research Group and its Southeast Asian collaborators. The project team will set up a workflow incorporating next-generation sequencing for 1,500 Asian pteridophyte specimens from selected collections in Taiwan, Vietnam, the Philippines, Malaysia and other Southeast Asian countries that can fill in taxonomic and geographic gaps and represent Asian pteridophyte diversity.
Mobilization of and access to these vouchered and georeferenced DNA-derived records will advance further research into the biogeography of pteridophytes and other terrestrial vegetation and support the development of novel approaches to monitor biodiversity along the spatiotemporal scale, including metabarcoding of the invisible diversity held in soil and spore banks.
Project progress
The project began with the team focusing on molecular DNA work and computation in the laboratory, selecting rbcL and trnL-LF for the downstream works and by midterm reporting had already completed several activities and achieved new deliverables relating to methodology and findings of new species diversity.
Using the preliminary data of DNA barcodes, the project identified three undescribed fern species in Asian regions during its implementation: two Lomariopsis species and one Hymenophyllum species, and these have been documented in the two systematic papers published in the journal PhytoKeys:
- Wu, Y.‐H., C.‐Y. Sun, A. Ebihara, N. T. Lu, G. Rouhan, and L.‐Y. Kuo. 2021. Two new species in the fern genus Lomariopsis (Lomariopsidaceae) from East Asia. PhytoKeys 187: 161–176
- Chang Z-X, Hsu T-C, Kuo L-Y (2022) Hymenophyllum chamaecyparicola (Hymenophyllaceae), a new filmy fern species from Taiwan. PhytoKeys 204: 23-34
For new universal primer sets for fern DNA barcodes, the project wrote scripts and found conserve priming sites across 250 fern plastomes. For the trnL-F region, the project tested the newly designed primer set and published these primer sequences in Wu et al. (2022; "Integrating tissue‐direct PCR into genetic identification: an upgraded molecular ecology way to survey fern field gametophytes. Applications in Plant Sciences: e11462.")
By final reporting the project published three occurrence datasets with a total of 1536 vouchered specimens, including 828 from Taiwan, 302 from Vietnam, 224 from Malaysia, 184 from the Philippines, seven from China and one from India. China, one from India. All sequenced with rbcL.
In addition to this the project developed and generated a NGS pipeline “PowerBarcoder”, available at https://github.com/PowerBarcoder.
By incorporating these new datasets and workflow/pipeline, the project made a good process to carry out DNA identification works of fern gametophytes in the field, for example through the "Botany 2022" conference held in July 2022.
Furthermore, the project team demonstrated and introduced the newly developed NSG pipeline during their “Next generation DNA barcode” workshop held in October 2022 in Taiwan. Their study providing one of the best practices to "high throughput" DNA barcode sequences for fern collections, that will be very useful for DNA-based identifications for these organisms.
Despite the delays encountered by the project due to COVID-19 and it not being able to complete all its planned activities and deliverables, the project has been very successful. Post project the team envisage continuing work to improve identification results and testing of new pipelines. Furthermore, continuing to share their results and methods.
