MinION-in-ARMS: Nanopore Sequencing to Expedite Barcoding of Specimen-Rich Macrofaunal Samples From Autonomous Reef Monitoring Structures
Autonomous Reef Monitoring Structure (ARMS) are standardized devices for sampling biodiversity in complex marine benthic habitats such as coral reefs. When coupled with DNA sequencing, these devices greatly expand our ability to document marine biodiversity. Unfortunately, the existing workflow for...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2020-06-01
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| Series: | Frontiers in Marine Science |
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| Online Access: | https://www.frontiersin.org/article/10.3389/fmars.2020.00448/full |
| _version_ | 1819064237242187776 |
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| author | Jia Jin Marc Chang Yin Cheong Aden Ip Andrew G. Bauman Danwei Huang Danwei Huang |
| author_facet | Jia Jin Marc Chang Yin Cheong Aden Ip Andrew G. Bauman Danwei Huang Danwei Huang |
| author_sort | Jia Jin Marc Chang |
| collection | DOAJ |
| description | Autonomous Reef Monitoring Structure (ARMS) are standardized devices for sampling biodiversity in complex marine benthic habitats such as coral reefs. When coupled with DNA sequencing, these devices greatly expand our ability to document marine biodiversity. Unfortunately, the existing workflow for processing macrofaunal samples (>2-mm) in the ARMS pipeline—which involves Sanger sequencing—is expensive, laborious, and thus prohibitive for ARMS researchers. Here, we propose a faster, more cost-effective alternative by demonstrating a successful application of the MinION-based barcoding approach on the >2 mm-size fraction of ARMS samples. All data were available within 3.5–4 h, and sequencing costs relatively low at approximately US$3 per MinION barcode. We sequenced the 313-bp fragment of the cytochrome c oxidase subunit I (COI) for 725 samples on both MinION and Illumina platforms, and retrieved 507–584 overlapping barcodes. MinION barcodes were highly accurate (∼99.9%) when compared with Illumina reference barcodes. Molecular operational taxonomic units inferred between MinION and Illumina barcodes were consistently stable, and match ratios demonstrated highly congruent clustering patterns (≥0.96). Our method would make ARMS more accessible to researchers, and greatly expedite the processing of macrofaunal samples; it can also be easily applied to other small-to-moderate DNA barcoding projects (<10,000 specimens) for rapid species identification and discovery. |
| first_indexed | 2024-12-21T15:27:22Z |
| format | Article |
| id | doaj.art-5004058719864530842a02c0bb65b3da |
| institution | Directory Open Access Journal |
| issn | 2296-7745 |
| language | English |
| last_indexed | 2024-12-21T15:27:22Z |
| publishDate | 2020-06-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Marine Science |
| spelling | doaj.art-5004058719864530842a02c0bb65b3da2022-12-21T18:58:52ZengFrontiers Media S.A.Frontiers in Marine Science2296-77452020-06-01710.3389/fmars.2020.00448546596MinION-in-ARMS: Nanopore Sequencing to Expedite Barcoding of Specimen-Rich Macrofaunal Samples From Autonomous Reef Monitoring StructuresJia Jin Marc Chang0Yin Cheong Aden Ip1Andrew G. Bauman2Danwei Huang3Danwei Huang4Department of Biological Sciences, National University of Singapore, Singapore, SingaporeDepartment of Biological Sciences, National University of Singapore, Singapore, SingaporeDepartment of Biological Sciences, National University of Singapore, Singapore, SingaporeDepartment of Biological Sciences, National University of Singapore, Singapore, SingaporeTropical Marine Science Institute, National University of Singapore, Singapore, SingaporeAutonomous Reef Monitoring Structure (ARMS) are standardized devices for sampling biodiversity in complex marine benthic habitats such as coral reefs. When coupled with DNA sequencing, these devices greatly expand our ability to document marine biodiversity. Unfortunately, the existing workflow for processing macrofaunal samples (>2-mm) in the ARMS pipeline—which involves Sanger sequencing—is expensive, laborious, and thus prohibitive for ARMS researchers. Here, we propose a faster, more cost-effective alternative by demonstrating a successful application of the MinION-based barcoding approach on the >2 mm-size fraction of ARMS samples. All data were available within 3.5–4 h, and sequencing costs relatively low at approximately US$3 per MinION barcode. We sequenced the 313-bp fragment of the cytochrome c oxidase subunit I (COI) for 725 samples on both MinION and Illumina platforms, and retrieved 507–584 overlapping barcodes. MinION barcodes were highly accurate (∼99.9%) when compared with Illumina reference barcodes. Molecular operational taxonomic units inferred between MinION and Illumina barcodes were consistently stable, and match ratios demonstrated highly congruent clustering patterns (≥0.96). Our method would make ARMS more accessible to researchers, and greatly expedite the processing of macrofaunal samples; it can also be easily applied to other small-to-moderate DNA barcoding projects (<10,000 specimens) for rapid species identification and discovery.https://www.frontiersin.org/article/10.3389/fmars.2020.00448/fullamplicon sequencingcytochrome c oxidase subunit I (COI)DNA barcodingmetazoanext-generation sequencingOxford Nanopore Technologies |
| spellingShingle | Jia Jin Marc Chang Yin Cheong Aden Ip Andrew G. Bauman Danwei Huang Danwei Huang MinION-in-ARMS: Nanopore Sequencing to Expedite Barcoding of Specimen-Rich Macrofaunal Samples From Autonomous Reef Monitoring Structures Frontiers in Marine Science amplicon sequencing cytochrome c oxidase subunit I (COI) DNA barcoding metazoa next-generation sequencing Oxford Nanopore Technologies |
| title | MinION-in-ARMS: Nanopore Sequencing to Expedite Barcoding of Specimen-Rich Macrofaunal Samples From Autonomous Reef Monitoring Structures |
| title_full | MinION-in-ARMS: Nanopore Sequencing to Expedite Barcoding of Specimen-Rich Macrofaunal Samples From Autonomous Reef Monitoring Structures |
| title_fullStr | MinION-in-ARMS: Nanopore Sequencing to Expedite Barcoding of Specimen-Rich Macrofaunal Samples From Autonomous Reef Monitoring Structures |
| title_full_unstemmed | MinION-in-ARMS: Nanopore Sequencing to Expedite Barcoding of Specimen-Rich Macrofaunal Samples From Autonomous Reef Monitoring Structures |
| title_short | MinION-in-ARMS: Nanopore Sequencing to Expedite Barcoding of Specimen-Rich Macrofaunal Samples From Autonomous Reef Monitoring Structures |
| title_sort | minion in arms nanopore sequencing to expedite barcoding of specimen rich macrofaunal samples from autonomous reef monitoring structures |
| topic | amplicon sequencing cytochrome c oxidase subunit I (COI) DNA barcoding metazoa next-generation sequencing Oxford Nanopore Technologies |
| url | https://www.frontiersin.org/article/10.3389/fmars.2020.00448/full |
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