Nanopore-based metabarcoding of protist communities and using 18S rRNA V4 region in upland and coastal environments of La Union, Philippines
This study generates metabarcoding data targeting the V4 region of the 18S rRNA gene to characterize protist communities, including Amoebozoa composition against contrasting ecosystems in La Union, Philippines.Water samples were collected from upland freshwater and coastal marine sites. Environmental DNA was obtained using two sampling approaches: filtration of water samples and centrifugation to produce pellet fractions. These complementary methods were used to capture a broad representation of protist diversity.Amplicon libraries of the 18S rRNA V4 region were prepared and sequenced using Oxford Nanopore Technologies MinION Mk1D. The dataset enables analysis of protist taxonomic diversity and community structure across contrasting environmental conditions and sample processing methods.All raw sequencing data are provided in FASTQ format, with accompanying metadata describing sample origin, collection method, and environmental context.