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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.
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1 Academia Sinica, Biodiversity Research Center, Taipei, Taiwan (GRID:grid.28665.3f) (ISNI:0000 0001 2287 1366); National Taiwan Normal University, Department of Life Science, Taipei, Taiwan (GRID:grid.412090.e) (ISNI:0000 0001 2158 7670); Academia Sinica and National Taiwan Normal University, Biodiversity Program, Taiwan International Graduate Program, Taipei, Taiwan (GRID:grid.412090.e) (ISNI:0000 0001 2158 7670)
2 Academia Sinica, Biodiversity Research Center, Taipei, Taiwan (GRID:grid.28665.3f) (ISNI:0000 0001 2287 1366); National Taiwan University, Bioinformatics Program, Taiwan International Graduate Program, Taipei, Taiwan (GRID:grid.19188.39) (ISNI:0000 0004 0546 0241); Academia Sinica, Bioinformatics Program, Institute of Information Science, Taiwan International Graduate Program, Taipei, Taiwan (GRID:grid.28665.3f) (ISNI:0000 0001 2287 1366)
3 Academia Sinica, Biodiversity Research Center, Taipei, Taiwan (GRID:grid.28665.3f) (ISNI:0000 0001 2287 1366); National Taiwan Normal University, Department of Life Science, Taipei, Taiwan (GRID:grid.412090.e) (ISNI:0000 0001 2158 7670); Academia Sinica and National Taiwan Normal University, Biodiversity Program, Taiwan International Graduate Program, Taipei, Taiwan (GRID:grid.412090.e) (ISNI:0000 0001 2158 7670); University of Copenhagen, Faculty of Science, Natural History Museum of Denmark, Copenhagen, Denmark (GRID:grid.5254.6) (ISNI:0000 0001 0674 042X)
4 Academia Sinica, Institute of Plant and Microbial Biology, Taipei, Taiwan (GRID:grid.28665.3f) (ISNI:0000 0001 2287 1366); National Chung-Hsing University, Graduate Institute of Biotechnology, Taichung, Taiwan (GRID:grid.260542.7) (ISNI:0000 0004 0532 3749); Academia Sinica and National Chung Hsing University, Molecular and Biological Agricultural Sciences, Taiwan International Graduate Program, Taipei, Taiwan (GRID:grid.469086.5) (ISNI:0000 0000 9360 4962)
5 Academia Sinica, Institute of Plant and Microbial Biology, Taipei, Taiwan (GRID:grid.28665.3f) (ISNI:0000 0001 2287 1366); National Chung Hsing University and Academia Sinica, Ph.D. Program in Microbial Genomics, Taipei, Taiwan (GRID:grid.469086.5) (ISNI:0000 0000 9360 4962)
6 Academia Sinica, Biodiversity Research Center, Taipei, Taiwan (GRID:grid.28665.3f) (ISNI:0000 0001 2287 1366)