Utilisation of Oxford Nanopore sequencing to generate six complete gastropod mitochondrial genomes as part of a biodiversity curriculum

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

doi:10.1038/s41598-022-14121-0

Utilisation of Oxford Nanopore sequencing to generate six complete gastropod mitochondrial genomes as part of a biodiversity curriculum

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^*

^*Corresponding author af dette arbejde

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Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › peer review

22 Citationer (Scopus)

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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.

Originalsprog	Engelsk
Artikelnummer	9973
Tidsskrift	Scientific Reports
Vol/bind	12
Udgave nummer	1
Antal sider	11
ISSN	2045-2322
DOI	https://doi.org/10.1038/s41598-022-14121-0
Status	Udgivet - 2022

Bibliografisk note

Funding Information:
We thank Pei-Chen Tsai, Yao-Feng Tsao and the staff of Green Island Marine Research Station, Marine Science Center (Academia Sinica) for help with specimen collection and field trip logistics, Vanessa Chen (Academia Sinica) for helping with organising both the class and the trip to Green Island. We are grateful to the National Center for High-Performance Computing for its computer time and for letting us use its facilities. We kindly acknowledge support from Tzu-Ching Meng (Department of International Affairs, Academia Sinica), who started this first Academia Sinica TIGP signature course, Ecology Master Class Taiwan (EMT) and whose support was very important to the completion of this work. We thank the two reviewers for their suggestions on the manuscript. This study was supported by the Taiwan International Graduate Program (TIGP) and Biodiversity Research Center, Academia Sinica (Taipei, Taiwan). ND was jointly sponsored by a double-degree graduate grant from TIGP and the Natural History Museum of Denmark. This is EMT paper #2.

Publisher Copyright:
© 2022, The Author(s).

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Citationsformater

De Vivo, M., Lee, H.-H., Huang, Y.-S., Dreyer, N., Fong, C.-L., de Mattos, F. M. G., Jain, D., Wen, Y.-H. V., Mwihaki, J. K., Wang, T.-Y., Machida, R. J., Wang, J., Chan, B. K. K., & Tsai, I. J. (2022). Utilisation of Oxford Nanopore sequencing to generate six complete gastropod mitochondrial genomes as part of a biodiversity curriculum. Scientific Reports, 12(1), Artikel 9973. https://doi.org/10.1038/s41598-022-14121-0

De Vivo, M, Lee, H-H, Huang, Y-S, Dreyer, N, Fong, C-L, de Mattos, FMG, Jain, D, Wen, Y-HV, Mwihaki, JK, Wang, T-Y, Machida, RJ, Wang, J, Chan, BKK & Tsai, IJ 2022, 'Utilisation of Oxford Nanopore sequencing to generate six complete gastropod mitochondrial genomes as part of a biodiversity curriculum', Scientific Reports, bind 12, nr. 1, 9973. https://doi.org/10.1038/s41598-022-14121-0

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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.",

author = "{De Vivo}, Mattia and Hsin-Han Lee and Yu-Sin Huang and Niklas Dreyer and Chia-Ling Fong and {de Mattos}, {Felipe Monteiro Gomes} and Dharmesh Jain and Wen, {Yung-Hui Victoria} and Mwihaki, {John Karichu} and Tzi-Yuan Wang and Machida, {Ryuji J.} and John Wang and Chan, {Benny K. K.} and Tsai, {Isheng Jason}",

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AU - Dreyer, Niklas

AU - Fong, Chia-Ling

AU - de Mattos, Felipe Monteiro Gomes

AU - Jain, Dharmesh

AU - Wen, Yung-Hui Victoria

AU - Mwihaki, John Karichu

AU - Wang, Tzi-Yuan

AU - Machida, Ryuji J.

AU - Wang, John

AU - Chan, Benny K. K.

AU - Tsai, Isheng Jason

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