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

Mahir Budak

doi:10.17776/csj.1221192

EN

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

References

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Details

Primary Language

English

Subjects

Structural Biology

Journal Section

Research Article

Authors

Mahir Budak ^*
0000-0001-5610-486X
Türkiye

Publication Date

March 26, 2023

Submission Date

December 19, 2022

Acceptance Date

March 16, 2023

Published in Issue

Year 2023 Volume: 44 Number: 1

DOI

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

IZ

https://izlik.org/JA22RS45CR

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RIS / Bibtex

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

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

Öz

Anahtar Kelimeler

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

Abstract

Keywords

References

Details

Primary Language

Subjects

Journal Section

Authors

Publication Date

Submission Date

Acceptance Date

Published in Issue

DOI

IZ

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