Determination of the Optimum Number of Short Reads to Obtain the Mitogenome in some Insect Orders
Abstract
Sanger sequencing is frequently used as the final step in time-consuming extraction and enrichment processes for examining the mitochondrial genome (mitogenome). The development of next-generation or massively parallel sequencing has made it possible to consistently gather data at the nucleotide level with comparatively little difficulty. Additionally, reference-based genome assembly is now achievable thanks to the growing amount of mt genome data in databases. Consequently, acquiring the genome with fewer short-read counts reduces the financial load on research projects. The use of mitogenomes, particularly in the studies of systematic and population genetics of insects, have increased, and sequencing mitogenomes in non-model animals have become critical. Twelve species from four insect orders, each having a different-sized genome, were employed in the study. Short reads of these species, used in the study, were acquired from the SRA (The Sequence Read Archive) database. Alignments to the reference genome were carried out in triplicate for five different short read counts. It was observed that 0.092 (Chrysotoxum bicinctum) to 14.04 (Anopheles coluzzii) sequencing depth was needed to obtain the mitogenome with 100X coverage. This work aims to give researchers a better understanding of how much sequencing depth is necessary for mitogenome investigations.
Keywords
Next-generation sequencing, Mitogenome, Short-reads, Coverage, Insects.
References
- [1] Ladoukakis, E. D., Zouros, E., Evolution and inheritance of animal mitochondrial DNA: Rules and exceptions, Journal of Biological Research-Thessaloniki, 24 (2) (2017) 1–7.
- [2] Carlucci, A., Lignitto, L., Feliciello, A., Control of mitochondria dynamics and oxidative metabolism by cAMP, AKAPs and the proteasome, Trends in Cell Biology, 18 (12) (2008) 604–613.
- [3] Cameron, S. L., Insect mitochondrial genomics: Implications for evolution and phylogeny, Annual Review of Entomology, 59 (2014) 95–117.
- [4] Aydemir, M. N., Korkmaz, E. M., Comparative mitogenomics of hymenoptera reveals evolutionary differences in structure and composition, International Journal of Biological Macromolecules, 144 (2020) 460–472.
- [5] Ballard, J. W. O., Pichaud, N., Mitochondrial DNA: More than an evolutionary bystander, Functional Ecology, 28 (1) (2014) 218–231.
- [6] Okamura, Y., Sato, A., Kawaguchi, L., Nagano, A. J., Murakami, M., Vogel, H., Kroymann, J., Microevolution of pieris butterfly genes involved in host plant adaptation along a host plant community cline, Molecular Ecology, 31 (11) (2022) 3083–3097.
- [7] González-Tokman, D., Córdoba-Aguilar, A., Dáttilo, W., Lira-Noriega, A., Sánchez-Guillén, R. A., Villalobos, F., Insect responses to heat: Physiological mechanisms, evolution and ecological implications in a warming world, Biological Reviews, 95 (3) (2020) 802–821.
- [8] Boore, J. L., Animal mitochondrial genomes, Nucleic Acids Research, 27 (8) (1999) 1767–1780.
- [9] Güler, M., Güler, F. T., Korkmaz, E. M., Budak, M., Böcek dokularından DNA İzolasyonu yöntemlerinin kalite, verim ve maliyet açısından karşılaştırılması, Selçuk Üniversitesi Fen Fakültesi Fen Dergisi, 44 (2018) 135–148.
- [10] Budak, M., Korkmaz, E. M., Basibuyuk, H. H., A molecular phylogeny of the cephinae (hymenoptera, cephidae) based on mtDNA COI gene: A test of traditional classification, ZooKeys, 130 (2011) 363–378.