De novo genome sequencing for endangered bird of prey species
2024
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Аутори:
Erić, PavleTanasković, Marija
Patenković, Aleksandra
Erić, Katarina
Hribšek, Irena
Ovari, Kristijan
Davidović, Slobodan
Остала ауторства
Morić, IvanaĐorđević, Valentina
Тип документа:
Конференцијски прилог (Објављена верзија)
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© 2024 by the Institute of Molecular Genetics and Genetic Engineering, University of Belgrade
Метаподаци
Приказ свих података о документуАпстракт:
The Eastern Imperial Eagle (Aquila heliaca) is a large migratory bird of prey, with breeding sites spanning from eastern Czechia and Austria to Northwestern China and Mongolia. Due to the decline of its populations throughout its area of distribution, the IUCN Red List categorized species as vulnerable. Thus, it has become a subject of numerous conservation efforts. To develop effective conservation strategies, it is crucial to have a comprehensive understanding of the genetic variability of these populations. Establishing a reference genome serves as a cornerstone for conservationists, offering a starting tool to assess population dynamics, adaptive potential and evolutionary history with further analyses. Therefore, we performed the whole genome sequencing of A. heliaca
The genome sequencing of a male A. heliaca was conducted using Illumina paired-end
150bp short reads, and de novo assembly was conducted as there is no reference genome available. After the use of paired-end information for scaffolding the assembly remained very fragmented, with the genome being represented with hundreds of thousands of contigs, primarily due to the inherent limitations of short-read sequencing in resolving repetitive regions and regions with strong nucleotide composition bias. To enhance scaffolding, we used a chromosome-level assembly of a closely related species, Aquila chrysaetos, available in the GenBank. BLAST analysis revealed high sequence similarity (~94%) between sequences from our assembly compared to the A. chrysaetos reference genome. The absence of major rearrangements or inversions in the selected contigs supported the usage of the A. chrysaetos reference genome for scaffolding. Thus, we generated a chromosome-level assembly for A. heliaca, encompassing 26 autosomes and the Z sex chromosome. Even though our assembly contained a few thousand unplaced scaffolds ranging in size from over 700Kb to very small fragments, the vast majority (>98%) of the assembly was assigned to 27 chromosomal-level scaffolds. The assembly demonstrated a completeness score of 97.2% according to the BUSCO assessment.
Кључне речи:
Aquila heliaca; WGS; De-novo genome assembly; conservationФинансирање / пројекти:
- Министарство науке, технолошког развоја и иновација Републике Србије, институционално финансирање - 200007 (Универзитет у Београду, Институт за биолошка истраживања 'Синиша Станковић') (RS-MESTD-inst-2020-200007)
У:
- Morić I, Đorđević V, editors. Book of Abstracts: 5th Belgrade Bioinfromatics Conference: BELBI 2024; 2024 Jun 17-20; Belgrade, Serbia. Belgrade: Institute of Molecular Genetics and Genetic Engineering, University of Belgrade; 2024. p. 122.