Characterising planktonic dinoflagellate diversity in Singapore using DNA metabarcoding

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.

Searching for phylogenetic patterns of Symbiodiniaceae community structure among Indo-Pacific Merulinidae corals

“…The bioinformatics pipeline was based primarily on Sze et al (2018), Afiq-Rosli et al (2019) and Lim et al (2019) (but see Hume et al, 2019). Briefly, Paired-End reAd mergeR (PEAR) (version 0.9.8) (Zhang et al, 2014) was used to assemble paired-end sequences with a default minimum overlap of 100 bp; minimum and maximum lengths of 300 and 390 bp respectively, based on the expected amplicon size; and a minimum Phred quality score of 30 to ensure accurate base calls.…”

Endosymbiont diversity and community structure in Porites lutea from Southeast Asia are driven by a suite of environmental variables

“…Raw data were processed following the pipeline of Sze et al (2018). Briefly, the Paired-End reAd mergeR (PEAR) program was used to align and merge paired-end reads with overlapping regions of at least 100-bp (Zhang et al 2013).…”

Peer Review #3 of "Searching for phylogenetic patterns of Symbiodiniaceae community structure among Indo-Pacific Merulinidae corals (v0.2)"

“…The bioinformatics pipeline was based primarily on Sze et al (2018), Afiq-Rosli et al (2019) and Lim et al (2019) (but see Hume et al, 2019). Briefly, Paired-End reAd mergeR (PEAR) (version 0.9.8) (Zhang et al, 2014) was used to assemble paired-end sequences with a default minimum overlap of 10 bp; minimum and maximum lengths of 300 and 390 bp respectively, based on the expected amplicon size; and a minimum Phred quality score of 30 to ensure accurate base calls.…”