DOI: 10.5061/dryad.9zw3r22k3
title: Barcode database of scleractinian corals (Cnidaria, Scleractinia) in two tropical marine protected areas (Perhentian and Redang Islands Marine Parks, Malaysia)

description: Coral reefs are particularly vulnerable to climate change as an elevation
 of sea surface temperatures would cause most coral species to bleach
 rapidly by expulsing their algal symbionts Symbiodiniaceae. Loss of these
 symbionts in coral species during stress-related “bleaching” events can
 lead to mass mortality of these corals and the collapse of the associated
 reef ecosystem. This makes the inventory of the diversity of coral species
 and their symbionts, in particular, genetic diversity, critical to the
 understanding of the assessment of coral reef resilience and ecosystem
 sustainability. The use of DNA barcoding has been proven useful in
 biodiversity assessments and monitoring schemes of marine ecosystems,
 particularly the highly diverse coral reef ecosystems. However, this
 information is lacking in Malaysia. Therefore, a comprehensive reference
 database of genetic sequences that represent the present coral reef
 biodiversity in the country would be needed. Here, we barcoded the
 scleractinian coral samples, the reef-building corals, collected from the
 two marine protected areas of Malaysia, Perhentian and Redang Islands
 Marine Parks, using the cytochrome c oxidase I (COI) marker. The data
 released from this project represent the first comprehensive reference
 database of the scleractinian coral diversity on the northeastern coasts
 of Malaysian coral reefs. A total of 62 nucleotide COI sequences of
 scleractinian corals collected from the two marine parks were obtained. Of
 these, a total of 34 taxa belonging to nine families were included in the
 dataset. This dataset added information on the occurrence and distribution
 of scleractinian coral species from the two tropical marine protected
 areas in the South China Sea (Western Pacific).
description: <strong><em>Study sites</em></strong> The coral specimens were collected from the Perhentian Marine Parks and Redang Marine Parks reef areas (Fig. 1) at 5–18 m depth. Sampling took place between 2017 and 2019. A list of sample details is in Table 1. The two marine parks harbored healthy diverse scleractinian corals (Fig. 2). Sample collection was conducted at a total of 23 sampling sites, the coordinates of the sites are listed in Table 2.  <strong><em>Sample collection </em></strong> Small coral skeletal fragments (~5 cm) were collected from the coral colony by SCUBA using a hammer and chisel and placed in a Ziplock plastic bag underwater. Coral colonies were photographed for coral morphological identification. The coral samples were transferred into cryotubes and preserved in 99% ethanol. The samples were transported back to the laboratory in a cooler box and were kept at -80°C until further DNA extraction. <strong><em>DNA extraction and barcode sequencing </em></strong> DNAs were extracted from the ethanol-preserved coral samples using the TOYOBO MagExtractor Genome extraction kit (TOYOBO, Osaka, Japan). Coral samples were grounded and homogenized by using mortar and pestle. The homogenized tissue was 3-1 treated with Proteinase K (0.5 mg/mL), and incubated at 55°C for 6 h prior to DNA extraction following the manufacturer’s protocol. The mitochondrial cytochrome c oxidase I gene (COI) was amplified using the universal primer pair LCO1490 (5′GGTCAACAAATCATAAAGATATTGG3′) and HCO2198 (5′TAAACTTCAGGGTGACCAAAAAATCA3′) (Folmer et al. 1994). PCR was performed in a 25 µL PCR mixture containing 0.1 mM of each primer, 0.25 mM dNTPs, 2 mM MgCl, 1× Invitrogen reaction buffer, 2.5 U Taq DNA Polymerase (Invitrogen, Life Technologies, Wisconsin, USA), and ~10 ng of DNA template.  PCR thermal cycling condition was as follows: 95°C for 2 min, followed by 40 cycles of 95°C for 30 s, 47°C for 90 s, and 72°C for 90 s, with a final extension of 72°C for 5 min (Shearer and Coffroth, 2006). The amplicons were purified with the TOYOBO MagExtractor PCR and Gel Clean-up Kit (TOYOBO). The purified amplicons were visualized on a 1% agarose gel stained with 1× SYBR Safe (Invitrogen, Carlsbad, CA). Single-pass DNA sequencing was performed on both strands using an ABI 3770XL automated sequencer (PE Applied Biosystems, Foster City, CA).  <strong><em>Sequence quality control</em></strong> The sequences were first examined with Sequence Scanner v1.0 (Applied Biosystems) to verify ambiguous bases and the forward and reverse sequences assembled by BioEdit Sequence Alignment Editor (Hall 1999). All COI barcode sequences were compared against the BOLD database using the BOLD Identification Systems (IDS) (Ratnasingham and Hebert 2007, https://www.boldsystems.org/index.php/IDS_OpenIdEngine), and the ninety-nine top hits were inspected to detect issues due to contamination or misidentifications. The sequences were then translated into amino acids with Expasy Translate tool (https://web.expasy.org/translate/ ), and only sequences confirmed as functional mitochondrial DNA were used (no nuclear pseudogenes).  <em><strong>Dataset</strong></em> The dataset consists of specimens and data details relating to 62 scleractinian coral specimens. All specimens were identified to at least the genus level. Overall, a total of 30 taxa are represented in the dataset in BOLD (http://www.boldsystems.org/index.php/Public_SearchTerms?) These taxa belong to 20 genera and nine families (Fig. 3). The species that were found belonged to the following families (see "Taxa included" below). Ten samples could not be identified to species level with 100% certainty. A list of taxonomic details of the coral specimens in this dataset is shown in Table 1.  The BOLD dataset can be downloaded from the Public Data Portal of BOLD (htt ps://www.boldsystems.org/) in various formats (data as dwc, xml or tsv, and sequences as fasta files). Alternatively, BOLD users can log in and access the dataset via the Workbench platform of BOLD. All records are also searchable within BOLD, using the search function of the database.
description: Data format: .csv