Diversity and distribution of Symbiodiniaceae detected on coral reefs of Lombok, Indonesia using environmental DNA metabarcoding

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RT @beginersubhan: Our paper has been published today in @PeerJLife collaboration with @URI_fisheries @LaneLabURI https://t.co/3gKbAMczUt #…
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RT @thePeerJ: Pratomo et al. examine the diversity and distribution of #Symbiodiniaceae detected on #coral reefs of Lombok, Indonesia using…
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Pratomo et al. examine the diversity and distribution of #Symbiodiniaceae detected on #coral reefs of Lombok, Indonesia using environmental DNA #metabarcoding Read the full article https://t.co/0tOfVDgEBC @Beginersubhan #Biodiversity #MarineBio
Pratomo et al. examine the diversity and distribution of #Symbiodiniaceae detected on #coral reefs of Lombok, Indonesia using environmental DNA #metabarcoding Read the full article https://t.co/AuL2NjpBWH @Beginersubhan #Biodiversity #MarineBio
891 days ago
RT @XavPochon: An article I handled as editor has been published today @PeerJLife https://t.co/eGTXgeoXVR #Biodiversity #ConservationBiolog…
891 days ago
RT @XavPochon: An article I handled as editor has been published today @PeerJLife https://t.co/eGTXgeoXVR #Biodiversity #ConservationBiolog…
RT @XavPochon: An article I handled as editor has been published today @PeerJLife https://t.co/eGTXgeoXVR #Biodiversity #ConservationBiolog…
An article I handled as editor has been published today @PeerJLife https://t.co/eGTXgeoXVR #Biodiversity #ConservationBiology #Genetics #MarineBiology #BiologicalOceanography
Aquatic Biology

Main article text

 

Introduction

Methods

Study sites

eDNA sample collection

DNA extraction, amplification, and sequencing

Data processing and bioinformatic analyses

ASV identification

Statistical analyses

Results

Obtained sequences, ASVs, and eukaryote classification

Symbiodiniaceae detection and classification

Symbiodiniaceae distribution and diversity

Discussion

Conclusions

Supplemental Information

Count of sequences (raw data) per sample

DOI: 10.7717/peerj.14006/supp-1

OTU sequence data

DOI: 10.7717/peerj.14006/supp-2

Taxonomy of Eukaryote at 97 % and 99 % similarity and putative Symbiodiniaceae sequences

DOI: 10.7717/peerj.14006/supp-3

BLAST results from putative Symbiodiniaceae OTUs

DOI: 10.7717/peerj.14006/supp-4

Final compiling reference sequence database for phylogenetic reconstruction

DOI: 10.7717/peerj.14006/supp-5

Relative abundance data of putative Symbiodiniaceae

DOI: 10.7717/peerj.14006/supp-6

Detailed explanation of unique elements at Venn diagram of Symbiodiniaceae subclades around Lombok

DOI: 10.7717/peerj.14006/supp-7

Prensence of Symbiodiniaceae based on site-medium-fraction sample combination

DOI: 10.7717/peerj.14006/supp-8

Raw data for diversity

DOI: 10.7717/peerj.14006/supp-9

Additional Information and Declarations

Competing Interests

The authors declare there are no competing interests.

Author Contributions

Arief Pratomo conceived and designed the experiments, performed the experiments, analyzed the data, prepared figures and/or tables, authored or reviewed drafts of the article, and approved the final draft.

Dietriech G. Bengen analyzed the data, authored or reviewed drafts of the article, and approved the final draft.

Neviaty P. Zamani analyzed the data, authored or reviewed drafts of the article, and approved the final draft.

Christopher Lane conceived and designed the experiments, performed the experiments, authored or reviewed drafts of the article, and approved the final draft.

Austin T. Humphries conceived and designed the experiments, performed the experiments, authored or reviewed drafts of the article, and approved the final draft.

Erin Borbee conceived and designed the experiments, performed the experiments, analyzed the data, authored or reviewed drafts of the article, and approved the final draft.

Beginer Subhan performed the experiments, authored or reviewed drafts of the article, and approved the final draft.

Hawis Madduppa conceived and designed the experiments, performed the experiments, analyzed the data, prepared figures and/or tables, authored or reviewed drafts of the article, and approved the final draft.

Field Study Permissions

The following information was supplied relating to field study approvals (i.e., approving body and any reference numbers):

eDNA seawater sampling in this study was permitted within the framework of the United States Agency for International Development—Sustainable Higher Education Research Alliances (USAID-SHERA) program through the Centre for Collaborative Research Animal Biotechnology and Coral Reef Fisheries (CCR ANBIOCORE) of IPB University, award no. AID-497-A-16-00004. The field research permit was issued by IPB University Rector (Surat Tugas no. 403/IT3/KP/2019). Permits for this research were issued by the Indonesian Ministry of Research and Technology to EB (130/E5/E5.4/SIP/2019), CL and AH (455/SIP/FRP/E5/Dit.KI/XII/2017).

Data Availability

The following information was supplied regarding data availability:

The raw sequence data is available at GenBank: PRJNA768103.

The outative Symbiodiniaceae OTU sequence data is available at GenBank: SRP339775.

The code for this research analyses is available at GitHub: https://github.com/arief2021/Symbio_Qiime2.git.

Funding

This research was supported by the BPPDN scholarship and USAID through the Sustainable Higher Education Research Alliances (SHERA) Program—Centre for Collaborative Research on Animal Biotechnology and Coral Reef Fisheries (CCR ANBIOCORE) of IPB University. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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