Savu Sea-Indonesia eDNA Dataset

Study Extent

Taman Nasional Perairan Laut Sawu or Savu Sea National Marine Park is located in East Nusa Tenggara Indonesia covering an area of more than three million hectares. The hallmark of the marine park is its unique feature as a migratory area for whale species and is a home for a variety of marine megafauna. It houses 11 whale species, 7 dolphin species, 5 manta, and Turtle species and includes two sunfish and dugongs. For this study, we specifically choose areas from Solor, Rote, Adonara, Manggarai, and West Manggarai to collect the water samples. The areas have never been studied before and hence the biodiversity information from the area will important for biodiversity management and conservation

Sampling

The sampling collection event summarized the collection event across 4 locations in Savu Sea waters. We collected surface seawater samples at 5 sites from each location. eDNA samples from seawater sample were collected across 4 designated locations across the Sawu Sea, with 5 sites in each location. 2 liters of seawater samples were collected with sterile Nalgene bottle from the sea surface in every site. Water sample than filtered through a 0.22-133 micron Sterivex™ filter. eDNA samples and blanks will be extracted using the DNeasy Blood & Tissue Kit (QIAGEN, Hilden, 143 Germany). Extracted DNA was then sent to a sequencing facility for the NGS metabarcoding method using the Illumina platform.

Method steps

1. 1. For each of the sampling sites, one water samples were collected an homogenized 2. DNA was extracted from each of the samples with a modified protocol based on PowerMax soil kit (MoBio, now Qiagen) 3. For each DNA extract 1 µl, the COI region was amplified in triplicates with the primers mlCOIintF and jgCOIR, using Amplitaq Gold. 4. All PCR products were built into Illumina sequencing libraries with the TruSeq PCR free kit. 5. Sequencing of the 10 samples was done with the Illumina MiSeq platform using the V2 kit 250 bp paired end sequencing. 6. Paired reads were demultiplexed and analyzed with Metaworks https://github.com/terrimporter/MetaWorks using cutadapt, vsearch and dada2, and vsearch. 7. Sequences were annotated by comparison with the Ribosomal Database classifier v2.13 (RDP classifier)

DNA sequences from water samples will be identified to species whenever possible. When sequences were unable to be assigned to a taxonomic name, a dedicated OTU (Operational Taxonomic Name)/occurenceID will be given to the sequences

1. Metazoan
2. Bacteria
   rank: kingdom

The Savu Sea is a small sea within Indonesia named for the island of Savu (Sawu) on its southern boundary. It is bounded by Savu and Rai Jua to the south, the islands of Rote and Timor (split between East Timor and Indonesia) to the east, Flores and the Alor archipelago to the north/northwest, and the island of Sumba to the west/northwest. Between these islands, it flows into the Indian Ocean to the south and west, the Flores Sea to the north, and the Banda Sea to the northeast.