Environmental DNA metabarcoding of freshwater fish in Malaysian tropical rivers using short-read nanopore sequencing as a potential biomonitoring tool
The approach of combining cost-effective nanopore sequencing and emerging environmental DNA (eDNA) metabarcoding could prove to be a promising tool for biodiversity documentation, especially in Malaysia. Given the substantial funding constraints in recent years, especially in relation to the countr...
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Wiley
2024
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| Online Access: | http://eprints.uthm.edu.my/11134/1/J17625_63b7a8f72b27f3662866a4fdd9b7ab24.pdf http://eprints.uthm.edu.my/11134/ https://doi.org/10.1111/1755-0998.13936 |
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| author | Kaviarasu Munian, Kaviarasu Munian Ramli, Farah Farhana Othman, Nursyuhada Mahyudin, Nur Aina Amira Sariyati, Nur Hartini Abdullah-Fauzi, Nurfatiha Akmal Fawwazah Haris, Hidayah Norhakim, Mohd Lokman Ilham Abdul-Latiff, Muhammad Abu Bakar |
| author_facet | Kaviarasu Munian, Kaviarasu Munian Ramli, Farah Farhana Othman, Nursyuhada Mahyudin, Nur Aina Amira Sariyati, Nur Hartini Abdullah-Fauzi, Nurfatiha Akmal Fawwazah Haris, Hidayah Norhakim, Mohd Lokman Ilham Abdul-Latiff, Muhammad Abu Bakar |
| author_sort | Kaviarasu Munian, Kaviarasu Munian |
| building | UTHM Library |
| collection | Institutional Repository |
| content_provider | Universiti Tun Hussein Onn Malaysia |
| content_source | UTHM Institutional Repository |
| continent | Asia |
| country | Malaysia |
| description | The approach of combining cost-effective nanopore sequencing and emerging environmental DNA (eDNA) metabarcoding could prove to be a promising tool for
biodiversity documentation, especially in Malaysia. Given the substantial funding constraints in recent years, especially in relation to the country's biodiversity, many researchers have been limited to conduct restricted research without extended
monitoring periods, potentially hindering comprehensive surveys and could compromise the conservation efforts. Therefore, the present study aimed to evaluate the application of eDNA metabarcoding on freshwater fish using short reads generated through nanopore sequencing. This assessment focused on species detection in three selected rivers within the Endau Rompin Landscape in Malaysia.
Additionally, the study compared levels of species detection between eDNA metabarcoding and conventional sampling methods, examined the effectiveness of primer choice, and applied both metabarcoding and shotgun sequencing to the
eDNA approach. We successfully identified a total of 22 and 71 species with an identification threshold of >97% and >90%, respectively, through the MinION platform. The eDNA metabarcoding approach detected over 13% more freshwater fish species than when the conventional method was used. Notably, the distinction in freshwater fish detection between eDNA primers for 12S rRNA and cytochrome oxidase I was insignificant. The cost for eDNA metabarcoding proved to be more effective compared to conventional sampling with cost reduction at 33.4%. With favourable cost-effectiveness and increased species detection, eDNA metabarcoding could complement existing methods, enhance holistic diversity documentation for targeted habitats and facilitate effective conservation planning. |
| format | Article |
| id | my.uthm.eprints-11134 |
| institution | Universiti Tun Hussein Onn Malaysia |
| language | en |
| publishDate | 2024 |
| publisher | Wiley |
| record_format | eprints |
| spelling | my.uthm.eprints-111342024-06-10T02:02:55Z http://eprints.uthm.edu.my/11134/ Environmental DNA metabarcoding of freshwater fish in Malaysian tropical rivers using short-read nanopore sequencing as a potential biomonitoring tool Kaviarasu Munian, Kaviarasu Munian Ramli, Farah Farhana Othman, Nursyuhada Mahyudin, Nur Aina Amira Sariyati, Nur Hartini Abdullah-Fauzi, Nurfatiha Akmal Fawwazah Haris, Hidayah Norhakim, Mohd Lokman Ilham Abdul-Latiff, Muhammad Abu Bakar T Technology (General) The approach of combining cost-effective nanopore sequencing and emerging environmental DNA (eDNA) metabarcoding could prove to be a promising tool for biodiversity documentation, especially in Malaysia. Given the substantial funding constraints in recent years, especially in relation to the country's biodiversity, many researchers have been limited to conduct restricted research without extended monitoring periods, potentially hindering comprehensive surveys and could compromise the conservation efforts. Therefore, the present study aimed to evaluate the application of eDNA metabarcoding on freshwater fish using short reads generated through nanopore sequencing. This assessment focused on species detection in three selected rivers within the Endau Rompin Landscape in Malaysia. Additionally, the study compared levels of species detection between eDNA metabarcoding and conventional sampling methods, examined the effectiveness of primer choice, and applied both metabarcoding and shotgun sequencing to the eDNA approach. We successfully identified a total of 22 and 71 species with an identification threshold of >97% and >90%, respectively, through the MinION platform. The eDNA metabarcoding approach detected over 13% more freshwater fish species than when the conventional method was used. Notably, the distinction in freshwater fish detection between eDNA primers for 12S rRNA and cytochrome oxidase I was insignificant. The cost for eDNA metabarcoding proved to be more effective compared to conventional sampling with cost reduction at 33.4%. With favourable cost-effectiveness and increased species detection, eDNA metabarcoding could complement existing methods, enhance holistic diversity documentation for targeted habitats and facilitate effective conservation planning. Wiley 2024 Article PeerReviewed text en http://eprints.uthm.edu.my/11134/1/J17625_63b7a8f72b27f3662866a4fdd9b7ab24.pdf Kaviarasu Munian, Kaviarasu Munian and Ramli, Farah Farhana and Othman, Nursyuhada and Mahyudin, Nur Aina Amira and Sariyati, Nur Hartini and Abdullah-Fauzi, Nurfatiha Akmal Fawwazah and Haris, Hidayah and Norhakim, Mohd Lokman Ilham and Abdul-Latiff, Muhammad Abu Bakar (2024) Environmental DNA metabarcoding of freshwater fish in Malaysian tropical rivers using short-read nanopore sequencing as a potential biomonitoring tool. MOLECULAR ECOLOGY. pp. 1-14. https://doi.org/10.1111/1755-0998.13936 |
| spellingShingle | T Technology (General) Kaviarasu Munian, Kaviarasu Munian Ramli, Farah Farhana Othman, Nursyuhada Mahyudin, Nur Aina Amira Sariyati, Nur Hartini Abdullah-Fauzi, Nurfatiha Akmal Fawwazah Haris, Hidayah Norhakim, Mohd Lokman Ilham Abdul-Latiff, Muhammad Abu Bakar Environmental DNA metabarcoding of freshwater fish in Malaysian tropical rivers using short-read nanopore sequencing as a potential biomonitoring tool |
| title | Environmental DNA metabarcoding of freshwater fish in
Malaysian tropical rivers using short-read nanopore sequencing as a potential biomonitoring tool |
| title_full | Environmental DNA metabarcoding of freshwater fish in
Malaysian tropical rivers using short-read nanopore sequencing as a potential biomonitoring tool |
| title_fullStr | Environmental DNA metabarcoding of freshwater fish in
Malaysian tropical rivers using short-read nanopore sequencing as a potential biomonitoring tool |
| title_full_unstemmed | Environmental DNA metabarcoding of freshwater fish in
Malaysian tropical rivers using short-read nanopore sequencing as a potential biomonitoring tool |
| title_short | Environmental DNA metabarcoding of freshwater fish in
Malaysian tropical rivers using short-read nanopore sequencing as a potential biomonitoring tool |
| title_sort | environmental dna metabarcoding of freshwater fish in
malaysian tropical rivers using short-read nanopore sequencing as a potential biomonitoring tool |
| topic | T Technology (General) |
| url | http://eprints.uthm.edu.my/11134/1/J17625_63b7a8f72b27f3662866a4fdd9b7ab24.pdf http://eprints.uthm.edu.my/11134/ https://doi.org/10.1111/1755-0998.13936 |
| url_provider | http://eprints.uthm.edu.my/ |