Jurassic spark: Mapping the genomes of birds and other dinosaurs

Griffin, Darren K. and O'Connor, Rebecca and Romanov, Michael N and Damas, J and Farré, Marta and Martell, Henry and Kiazim, Lucas and Jennings, R and Mandawala, A and Joseph, S and Fowler, Katie E and Slack, Eden A and Allanson, Emily and Ferguson-Smith, Malcolm and Barrett, Paul M and Valenzuela, Nicole and Larkin, Denis M (2018) Jurassic spark: Mapping the genomes of birds and other dinosaurs. Comparative Cytogenetics, 12 (3). 322-323, Abstract L13. ISSN 1993-0771. E-ISSN 1993-078X. (doi:https://doi.org/10.3897/CompCytogen.v12i3.27748) (The full text of this publication is not currently available from this repository. You may be able to access a copy if URLs are provided)

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Official URL
https://doi.org/10.3897/CompCytogen.v12i3.27748

Abstract

The ultimate aim of a genome assembly is to create a contiguous length of sequence from the p- to q- terminus of each chromosome. Most assemblies are however highly fragmented, limiting their use in studies of gene mapping, phylogenomics and genomic organisation. To overcome these limitations, we developed a novel scaffold-to-chromosome anchoring method combining reference-assisted chromosome assembly (RACA) and fluorescence in situ hybridisation (FISH) to position scaffolds from de novo genomes onto chromosomes. Using RACA, scaffolds were ordered and orientated into ‘predicted chromosome fragments’ (PCFs) against a reference and outgroup genome. PCFs were verified using PCR prior to FISH mapping. A universal set of FISH probes developed through the selection of conserved regions were then used to map PCFs of peregrine falcon (Falco peregrinus Tunstall, 1771), pigeon (Columba livia Gmelin, 1789), ostrich (Struthio camelus Linnaeus, 1758), saker falcon (Falco cherrug Gray, 1834) the budgerigar (Melopsittacus undulatus Shaw, 1805). Using this approach, we were able to improve the N50 of genomes seven-fold. Results revealed that Interchromosomal breakpoint regions are limited to regions with low sequence conservation, shedding light on why most avian species have very stable karyotypes. Our combined FISH and bioinformatics approach represents a step-change in the mapping of genome assemblies, allowing comparative genomic research at a higher resolution than was previously possible. The universal probe set facilitates research into avian karyotype evolution and the role of chromosome rearrangements in adaptation and phenotypic diversity in birds. Indeed, they have been used on over 20 avian species plus non-avian reptiles (including turtles), shedding light into the evolution of dinosaur species. Non-avian dinosaurs remain subjects of intense biological enquiry while pervading popular culture and the creative arts. While organismal studies focus primarily on their morphology, relationships, likely behaviour, and ecology there have been few academic studies that have made extensive extrapolations about the nature of non-avian dinosaur genome structure prior to the emergence of modern birds. We have used multiple avian whole genome sequences assembled at a chromosomal level, to reconstruct the most likely gross genome organization of the overall genome structure of the diapsid ancestor and reconstruct the sequence of inter and intrachromosomal events that most likely occurred along the Archosauromorpha-Archosauria-Avemetatarsalia-Dinosauria-Theropoda-Maniraptora-Avialae lineage from the lepidosauromorph-archosauromorph divergence ~275 million years ago through to extant neornithine birds.

Item Type: Article
Subjects: Q Science > QH Natural history > QH426 Genetics
Divisions: Faculties > Sciences > School of Biosciences
Faculties > Sciences > School of Biosciences > Biomedical Research Group
Depositing User: M. Romanov
Date Deposited: 17 Sep 2018 10:17 UTC
Last Modified: 13 Nov 2018 10:18 UTC
Resource URI: https://kar.kent.ac.uk/id/eprint/69112 (The current URI for this page, for reference purposes)
O'Connor, Rebecca: https://orcid.org/0000-0002-4270-970X
Romanov, Michael N: https://orcid.org/0000-0003-3584-4644
Farré, Marta: https://orcid.org/0000-0001-9170-5767
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