Please use this identifier to cite or link to this item: https://doi.org/10.3897/mbmg.2.25136
Title: Characterising planktonic dinoflagellate diversity in Singapore using DNA metabarcoding
Authors: Sze, Y.
Miranda, L.N. 
Sin, T.M. 
Huang, D. 
Keywords: High-throughput sequencing
Johor Strait
Molecular operational taxonomic unit
Phytoplankton
Singapore Strait
Issue Date: 2018
Publisher: Pensoft Publishers
Citation: Sze, Y., Miranda, L.N., Sin, T.M., Huang, D. (2018). Characterising planktonic dinoflagellate diversity in Singapore using DNA metabarcoding. Metabarcoding and Metagenomics 2 : e25136. ScholarBank@NUS Repository. https://doi.org/10.3897/mbmg.2.25136
Rights: Attribution 4.0 International
Abstract: Dinoflagellates are traditionally identified morphologically using microscopy, which is a time-consuming and labour-intensive process. Hence, we explored DNA metabarcoding using high-throughput sequencing as a more efficient way to study planktonic dinoflagellate diversity in Singapore's waters. From 29 minimally pre-sorted water samples collected at four locations in western Singapore, DNA was extracted, amplified and sequenced for a 313-bp fragment of the V4-V5 region in the 18S ribosomal RNA gene. Two sequencing runs generated 2,847,170 assembled paired-end reads, corresponding to 573,176 unique sequences. Sequences were clustered at 97% similarity and analysed with stringent thresholds (≥150 bp, ≥20 reads, ≥95% match to dinoflagellates), recovering 28 dinoflagellate taxa. Dinoflagellate diversity captured includes parasitic and symbiotic groups which are difficult to identify morphologically. Richness is similar between the inner and outer West Johor Strait, but variations in community structure are apparent, likely driven by environmental differences. None of the taxa detected in a recent phytoplankton bloom along the West Johor Strait have been recovered in our samples, suggesting that background communities are distinct from bloom communities. The voluminous data obtained in this study contribute baseline information for Singapore's phytoplankton communities and prompt future research and monitoring to adopt the approach established here. © 2018 Pensoft Publishers. All right reserved.
Source Title: Metabarcoding and Metagenomics
URI: https://scholarbank.nus.edu.sg/handle/10635/210879
ISSN: 25349708
DOI: 10.3897/mbmg.2.25136
Rights: Attribution 4.0 International
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