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Chromosome-level assembly reveals extensive rearrangement in saker falcon and budgerigar, but not ostrich, genomes

O’Connor, Rebecca, Farré, Marta, Joseph, Sunitha, Damas, Joana, Kiazim, Lucas, Jennings, Rebecca, Bennett, Sophie, Slack, Eden A, Allanson, Emily, Larkin, Denis M, and others. (2018) Chromosome-level assembly reveals extensive rearrangement in saker falcon and budgerigar, but not ostrich, genomes. Genome Biology, 19 (1). ISSN 1474-760X. (doi:10.1186/s13059-018-1550-x) (KAR id:69780)

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https://doi.org/10.1186/s13059-018-1550-x

Abstract

Background: The number of de novo genome sequence assemblies is increasing exponentially; however, relatively few contain one scaffold/contig per chromosome. Such assemblies are essential for studies of genotype-to-phenotype association, gross genomic evolution, and speciation. Inter-species differences can arise from chromosomal changes fixed during evolution, and we previously hypothesized that a higher fraction of elements under negative selection contributed to avian-specific phenotypes and avian genome organization stability. The objective of this study is to generate chromosome-level assemblies of three avian species (saker falcon, budgerigar, and ostrich) previously reported as karyotypically rearranged compared to most birds. We also test the hypothesis that the density of conserved non-coding elements is associated with the positions of evolutionary breakpoint regions.

Results: We used reference-assisted chromosome assembly, PCR, and lab-based molecular approaches, to generate chromosome-level assemblies of the three species. We mapped inter- and intrachromosomal changes from the avian ancestor, finding no interchromosomal rearrangements in the ostrich genome, despite it being previously described as chromosomally rearranged. We found that the average density of conserved non-coding elements in evolutionary breakpoint regions is significantly reduced. Fission evolutionary breakpoint regions have the lowest conserved non-coding element density, and intrachromomosomal evolutionary breakpoint regions have the highest.

Conclusions: The tools used here can generate inexpensive, efficient chromosome-level assemblies, with > 80% assigned to chromosomes, which is comparable to genomes assembled using high-density physical or genetic mapping. Moreover, conserved non-coding elements are important factors in defining where rearrangements, especially interchromosomal, are fixed during evolution without deleterious effects.

Item Type: Article
DOI/Identification number: 10.1186/s13059-018-1550-x
Uncontrolled keywords: Chromosome-level genome assembly, Genome evolution, CNE, EBR
Subjects: Q Science > QR Microbiology
Divisions: Faculties > Sciences > School of Biosciences
Depositing User: Darren Griffin
Date Deposited: 25 Oct 2018 14:30 UTC
Last Modified: 06 Feb 2020 14:52 UTC
Resource URI: https://kar.kent.ac.uk/id/eprint/69780 (The current URI for this page, for reference purposes)
O’Connor, Rebecca: https://orcid.org/0000-0002-4270-970X
Farré, Marta: https://orcid.org/0000-0001-9170-5767
Griffin, Darren K.: https://orcid.org/0000-0001-7595-3226
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