Reference-Guided De Novo Genome Assembly of the Flour Beetle Tribolium freemani

Volarić, Marin; Despot-Slade, Evelin; Veseljak, Damira; Meštrović, Nevenka; Mravinac, Brankica

doi:10.3390/ijms23115869

Open AccessArticle

Reference-Guided De Novo Genome Assembly of the Flour Beetle Tribolium freemani

by

Marin Volarić

^†

,

Evelin Despot-Slade

^†

,

Damira Veseljak

,

Nevenka Meštrović

and

Brankica Mravinac

^*

Division of Molecular Biology, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia

^*

Author to whom correspondence should be addressed.

^†

These authors contributed equally to this work.

Int. J. Mol. Sci. 2022, 23(11), 5869; https://doi.org/10.3390/ijms23115869

Submission received: 22 April 2022 / Revised: 19 May 2022 / Accepted: 20 May 2022 / Published: 24 May 2022

(This article belongs to the Section Molecular Informatics)

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Abstract

The flour beetle Tribolium freemani is a sibling species of the model organism and important pest Tribolium castaneum. The two species are so closely related that they can produce hybrid progeny, but the genetic basis of their differences has not been revealed. In this work, we sequenced the T. freemani genome by applying PacBio HiFi technology. Using the well-assembled T. castaneum genome as a reference, we assembled 262 Mb of the T. freemani genomic sequence and anchored it in 10 linkage groups corresponding to nine autosomes and sex chromosome X. The assembly showed 99.8% completeness of conserved insect genes, indicating a high-quality reference genome. Comparison with the T. castaneum assembly revealed that the main differences in genomic sequence between the two sibling species come from repetitive DNA, including interspersed and tandem repeats. In this work, we also provided the complete assembled mitochondrial genome of T. freemani. Although the genome assembly needs to be ameliorated in tandemly repeated regions, the first version of the T. freemani reference genome and the complete mitogenome presented here represent useful resources for comparative evolutionary studies of related species and for further basic and applied research on different biological aspects of economically important pests.

Keywords: Tribolium freemani; de novo genome assembly; mitogenome; repetitive DNA; sibling species; the flour beetle; PacBio HiFi

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MDPI and ACS Style

Volarić, M.; Despot-Slade, E.; Veseljak, D.; Meštrović, N.; Mravinac, B. Reference-Guided De Novo Genome Assembly of the Flour Beetle Tribolium freemani. Int. J. Mol. Sci. 2022, 23, 5869. https://doi.org/10.3390/ijms23115869

AMA Style

Volarić M, Despot-Slade E, Veseljak D, Meštrović N, Mravinac B. Reference-Guided De Novo Genome Assembly of the Flour Beetle Tribolium freemani. International Journal of Molecular Sciences. 2022; 23(11):5869. https://doi.org/10.3390/ijms23115869

Chicago/Turabian Style

Volarić, Marin, Evelin Despot-Slade, Damira Veseljak, Nevenka Meštrović, and Brankica Mravinac. 2022. "Reference-Guided De Novo Genome Assembly of the Flour Beetle Tribolium freemani" International Journal of Molecular Sciences 23, no. 11: 5869. https://doi.org/10.3390/ijms23115869

APA Style

Volarić, M., Despot-Slade, E., Veseljak, D., Meštrović, N., & Mravinac, B. (2022). Reference-Guided De Novo Genome Assembly of the Flour Beetle Tribolium freemani. International Journal of Molecular Sciences, 23(11), 5869. https://doi.org/10.3390/ijms23115869

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Reference-Guided De Novo Genome Assembly of the Flour Beetle Tribolium freemani

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