Utilisation of Oxford Nanopore sequencing to generate six complete gastropod mitochondrial genomes as part of a biodiversity curriculum
Abstract High-throughput sequencing has enabled genome skimming approaches to produce complete mitochondrial genomes (mitogenomes) for species identification and phylogenomics purposes. In particular, the portable sequencing device from Oxford Nanopore Technologies (ONT) has the potential to facilit...
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| Format: | Article |
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Nature Portfolio
2022-06-01
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| Series: | Scientific Reports |
| Online Access: | https://doi.org/10.1038/s41598-022-14121-0 |
| _version_ | 1818236887220879360 |
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| author | Mattia De Vivo Hsin-Han Lee Yu-Sin Huang Niklas Dreyer Chia-Ling Fong Felipe Monteiro Gomes de Mattos Dharmesh Jain Yung-Hui Victoria Wen John Karichu Mwihaki Tzi-Yuan Wang Ryuji J. Machida John Wang Benny K. K. Chan Isheng Jason Tsai |
| author_facet | Mattia De Vivo Hsin-Han Lee Yu-Sin Huang Niklas Dreyer Chia-Ling Fong Felipe Monteiro Gomes de Mattos Dharmesh Jain Yung-Hui Victoria Wen John Karichu Mwihaki Tzi-Yuan Wang Ryuji J. Machida John Wang Benny K. K. Chan Isheng Jason Tsai |
| author_sort | Mattia De Vivo |
| collection | DOAJ |
| description | Abstract High-throughput sequencing has enabled genome skimming approaches to produce complete mitochondrial genomes (mitogenomes) for species identification and phylogenomics purposes. In particular, the portable sequencing device from Oxford Nanopore Technologies (ONT) has the potential to facilitate hands-on training from sampling to sequencing and interpretation of mitogenomes. In this study, we present the results from sampling and sequencing of six gastropod mitogenomes (Aplysia argus, Cellana orientalis, Cellana toreuma, Conus ebraeus, Conus miles and Tylothais aculeata) from a graduate level biodiversity course. The students were able to produce mitogenomes from sampling to annotation using existing protocols and programs. Approximately 4 Gb of sequence was produced from 16 Flongle and one MinION flow cells, averaging 235 Mb and N50 = 4.4 kb per flow cell. Five of the six 14.1–18 kb mitogenomes were circlised containing all 13 core protein coding genes. Additional Illumina sequencing revealed that the ONT assemblies spanned over highly AT rich sequences in the control region that were otherwise missing in Illumina-assembled mitogenomes, but still contained a base error of one every 70.8–346.7 bp under the fast mode basecalling with the majority occurring at homopolymer regions. Our findings suggest that the portable MinION device can be used to rapidly produce low-cost mitogenomes onsite and tailored to genomics-based training in biodiversity research. |
| first_indexed | 2024-12-12T12:17:00Z |
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| institution | Directory Open Access Journal |
| issn | 2045-2322 |
| language | English |
| last_indexed | 2024-12-12T12:17:00Z |
| publishDate | 2022-06-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj.art-f5abb87570844389b1bb58b21d86c5042022-12-22T00:24:45ZengNature PortfolioScientific Reports2045-23222022-06-0112111110.1038/s41598-022-14121-0Utilisation of Oxford Nanopore sequencing to generate six complete gastropod mitochondrial genomes as part of a biodiversity curriculumMattia De Vivo0Hsin-Han Lee1Yu-Sin Huang2Niklas Dreyer3Chia-Ling Fong4Felipe Monteiro Gomes de Mattos5Dharmesh Jain6Yung-Hui Victoria Wen7John Karichu Mwihaki8Tzi-Yuan Wang9Ryuji J. Machida10John Wang11Benny K. K. Chan12Isheng Jason Tsai13Biodiversity Research Center, Academia SinicaBiodiversity Research Center, Academia SinicaBiodiversity Research Center, Academia SinicaBiodiversity Research Center, Academia SinicaBiodiversity Research Center, Academia SinicaBiodiversity Research Center, Academia SinicaInstitute of Plant and Microbial Biology, Academia SinicaInstitute of Plant and Microbial Biology, Academia SinicaBiodiversity Research Center, Academia SinicaBiodiversity Research Center, Academia SinicaBiodiversity Research Center, Academia SinicaBiodiversity Research Center, Academia SinicaBiodiversity Research Center, Academia SinicaBiodiversity Research Center, Academia SinicaAbstract High-throughput sequencing has enabled genome skimming approaches to produce complete mitochondrial genomes (mitogenomes) for species identification and phylogenomics purposes. In particular, the portable sequencing device from Oxford Nanopore Technologies (ONT) has the potential to facilitate hands-on training from sampling to sequencing and interpretation of mitogenomes. In this study, we present the results from sampling and sequencing of six gastropod mitogenomes (Aplysia argus, Cellana orientalis, Cellana toreuma, Conus ebraeus, Conus miles and Tylothais aculeata) from a graduate level biodiversity course. The students were able to produce mitogenomes from sampling to annotation using existing protocols and programs. Approximately 4 Gb of sequence was produced from 16 Flongle and one MinION flow cells, averaging 235 Mb and N50 = 4.4 kb per flow cell. Five of the six 14.1–18 kb mitogenomes were circlised containing all 13 core protein coding genes. Additional Illumina sequencing revealed that the ONT assemblies spanned over highly AT rich sequences in the control region that were otherwise missing in Illumina-assembled mitogenomes, but still contained a base error of one every 70.8–346.7 bp under the fast mode basecalling with the majority occurring at homopolymer regions. Our findings suggest that the portable MinION device can be used to rapidly produce low-cost mitogenomes onsite and tailored to genomics-based training in biodiversity research.https://doi.org/10.1038/s41598-022-14121-0 |
| spellingShingle | Mattia De Vivo Hsin-Han Lee Yu-Sin Huang Niklas Dreyer Chia-Ling Fong Felipe Monteiro Gomes de Mattos Dharmesh Jain Yung-Hui Victoria Wen John Karichu Mwihaki Tzi-Yuan Wang Ryuji J. Machida John Wang Benny K. K. Chan Isheng Jason Tsai Utilisation of Oxford Nanopore sequencing to generate six complete gastropod mitochondrial genomes as part of a biodiversity curriculum Scientific Reports |
| title | Utilisation of Oxford Nanopore sequencing to generate six complete gastropod mitochondrial genomes as part of a biodiversity curriculum |
| title_full | Utilisation of Oxford Nanopore sequencing to generate six complete gastropod mitochondrial genomes as part of a biodiversity curriculum |
| title_fullStr | Utilisation of Oxford Nanopore sequencing to generate six complete gastropod mitochondrial genomes as part of a biodiversity curriculum |
| title_full_unstemmed | Utilisation of Oxford Nanopore sequencing to generate six complete gastropod mitochondrial genomes as part of a biodiversity curriculum |
| title_short | Utilisation of Oxford Nanopore sequencing to generate six complete gastropod mitochondrial genomes as part of a biodiversity curriculum |
| title_sort | utilisation of oxford nanopore sequencing to generate six complete gastropod mitochondrial genomes as part of a biodiversity curriculum |
| url | https://doi.org/10.1038/s41598-022-14121-0 |
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