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Year 2023, Volume: 44 Issue: 1, 36 - 40, 26.03.2023

Mahir Budak

https://doi.org/10.17776/csj.1221192

Abstract

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.
  • [11] Hu, M., Jex, A. R., Campbell, B. E., Gasser, R. B., Long PCR amplification of the entire mitochondrial genome from individual helminths for direct sequencing, Nature Protocols, 2 (10) (2007) 2339–2344.
  • [12] Jex, A. R., Hall, R. S., Littlewood, D. T. J., Gasser, R. B., An integrated pipeline for next-generation sequencing and annotation of mitochondrial genomes, Nucleic Acids Research, 38 (2) (2010) 522–533.
  • [13] Ye, F., Samuels, D. C., Clark, T., Guo, Y., High-throughput sequencing in mitochondrial DNA research, Mitochondrion, 17 (2014) 157–163.
  • [14] Al-Nakeeb, K., Petersen, T. N., Sicheritz-Pontén, T., Norgal: Extraction and de novo assembly of mitochondrial DNA from whole-genome sequencing data, BMC Bioinformatics, 18 (1) (2017) 1–7.
  • [15] Langmead, B., Salzberg, S. L., Fast gapped-read alignment with bowtie 2, Nature Methods, 9 (2012) 357–359.
  • [16] R Core Team, R: A language and environment for statistical computing, R Foundation for Statistical Computing, Vienna, Austria (2022).
  • [17] Wickham, H., ggplot2: Elegant graphics for data analysis. 2nd ed., New York: Springer-Verlag (2016) 18 – 30.
  • [18] Reinhold, K., Energetically costly behaviour and the evolution of resting metabolic rate in insects, Functional Ecology, 13 (1999) 217–224.
  • [19] Li, F., Zhao, X., Li, M., He, K., Huang, C., Zhou, Y., Li, Z., Walters, J. R., Insect genomes: Progress and challenges, Insect Molecular Biology, 28 (6) (2019) 739–758.
  • [20] Cameron, S. L., How to sequence and annotate insect mitochondrial genomes for systematic and comparative genomics research, Systematic Entomology, 39 (3) (2014) 400–411.
  • [21] Gómez-Rodríguez, C., Intraspecific genetic variation in complex assemblages from mitochondrial metagenomics: Comparison with DNA barcodes, Methods in Ecology and Evolution, 8 (2) (2017) 248–256.
  • [22] Patzold, F., Zilli, A., Hundsdoerfer, A. K., Advantages of an easy-to-use DNA extraction method for minimal-destructive analysis of collection specimens, PloS one, 15 (7) (2020) e0235222.

Determination of the Optimum Number of Short Reads to Obtain the Mitogenome in some Insect Orders

Year 2023, Volume: 44 Issue: 1, 36 - 40, 26.03.2023

Mahir Budak

https://doi.org/10.17776/csj.1221192

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.
  • [11] Hu, M., Jex, A. R., Campbell, B. E., Gasser, R. B., Long PCR amplification of the entire mitochondrial genome from individual helminths for direct sequencing, Nature Protocols, 2 (10) (2007) 2339–2344.
  • [12] Jex, A. R., Hall, R. S., Littlewood, D. T. J., Gasser, R. B., An integrated pipeline for next-generation sequencing and annotation of mitochondrial genomes, Nucleic Acids Research, 38 (2) (2010) 522–533.
  • [13] Ye, F., Samuels, D. C., Clark, T., Guo, Y., High-throughput sequencing in mitochondrial DNA research, Mitochondrion, 17 (2014) 157–163.
  • [14] Al-Nakeeb, K., Petersen, T. N., Sicheritz-Pontén, T., Norgal: Extraction and de novo assembly of mitochondrial DNA from whole-genome sequencing data, BMC Bioinformatics, 18 (1) (2017) 1–7.
  • [15] Langmead, B., Salzberg, S. L., Fast gapped-read alignment with bowtie 2, Nature Methods, 9 (2012) 357–359.
  • [16] R Core Team, R: A language and environment for statistical computing, R Foundation for Statistical Computing, Vienna, Austria (2022).
  • [17] Wickham, H., ggplot2: Elegant graphics for data analysis. 2nd ed., New York: Springer-Verlag (2016) 18 – 30.
  • [18] Reinhold, K., Energetically costly behaviour and the evolution of resting metabolic rate in insects, Functional Ecology, 13 (1999) 217–224.
  • [19] Li, F., Zhao, X., Li, M., He, K., Huang, C., Zhou, Y., Li, Z., Walters, J. R., Insect genomes: Progress and challenges, Insect Molecular Biology, 28 (6) (2019) 739–758.
  • [20] Cameron, S. L., How to sequence and annotate insect mitochondrial genomes for systematic and comparative genomics research, Systematic Entomology, 39 (3) (2014) 400–411.
  • [21] Gómez-Rodríguez, C., Intraspecific genetic variation in complex assemblages from mitochondrial metagenomics: Comparison with DNA barcodes, Methods in Ecology and Evolution, 8 (2) (2017) 248–256.
  • [22] Patzold, F., Zilli, A., Hundsdoerfer, A. K., Advantages of an easy-to-use DNA extraction method for minimal-destructive analysis of collection specimens, PloS one, 15 (7) (2020) e0235222.
There are 22 citations in total.

Details

Primary Language English
Subjects Structural Biology
Journal Section Natural Sciences
Authors

Mahir Budak 0000-0001-5610-486X

Publication Date March 26, 2023
Submission Date December 19, 2022
Acceptance Date March 16, 2023
Published in Issue Year 2023Volume: 44 Issue: 1

Cite

APA Budak, M. (2023). Determination of the Optimum Number of Short Reads to Obtain the Mitogenome in some Insect Orders. Cumhuriyet Science Journal, 44(1), 36-40. https://doi.org/10.17776/csj.1221192
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