Upgrading short-read animal genome assemblies to chromosome level using comparative genomics and a universal probe set
- Joana Damas1,5,
- Rebecca O'Connor2,5,
- Marta Farré1,
- Vasileios Panagiotis E. Lenis3,
- Henry J. Martell2,
- Anjali Mandawala2,4,
- Katie Fowler4,
- Sunitha Joseph2,
- Martin T. Swain3,
- Darren K. Griffin2,6 and
- Denis M. Larkin1,6
- 1Department of Comparative Biomedical Sciences, Royal Veterinary College, University of London, London, NW1 0TU, United Kingdom;
- 2School of Biosciences, University of Kent, Canterbury, CT2 7NY, United Kingdom;
- 3Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, SY23 3DA, United Kingdom;
- 4School of Human and Life Sciences, Canterbury Christ Church University, Canterbury, CT1 1QU, United Kingdom
- Corresponding author: dlarkin{at}rvc.ac.uk
Abstract
Most recent initiatives to sequence and assemble new species’ genomes de novo fail to achieve the ultimate endpoint to produce contigs, each representing one whole chromosome. Even the best-assembled genomes (using contemporary technologies) consist of subchromosomal-sized scaffolds. To circumvent this problem, we developed a novel approach that combines computational algorithms to merge scaffolds into chromosomal fragments, PCR-based scaffold verification, and physical mapping to chromosomes. Multigenome-alignment-guided probe selection led to the development of a set of universal avian BAC clones that permit rapid anchoring of multiple scaffolds to chromosomes on all avian genomes. As proof of principle, we assembled genomes of the pigeon (Columbia livia) and peregrine falcon (Falco peregrinus) to chromosome levels comparable, in continuity, to avian reference genomes. Both species are of interest for breeding, cultural, food, and/or environmental reasons. Pigeon has a typical avian karyotype (2n = 80), while falcon (2n = 50) is highly rearranged compared to the avian ancestor. By using chromosome breakpoint data, we established that avian interchromosomal breakpoints appear in the regions of low density of conserved noncoding elements (CNEs) and that the chromosomal fission sites are further limited to long CNE “deserts.” This corresponds with fission being the rarest type of rearrangement in avian genome evolution. High-throughput multiple hybridization and rapid capture strategies using the current BAC set provide the basis for assembling numerous avian (and possibly other reptilian) species, while the overall strategy for scaffold assembly and mapping provides the basis for an approach that (provided metaphases can be generated) could be applied to any animal genome.
Footnotes
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[Supplemental material is available for this article.]
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Article published online before print. Article, supplemental material, and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.213660.116.
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Freely available online through the Genome Research Open Access option.
- Received August 1, 2016.
- Accepted November 16, 2016.
This article, published in Genome Research, is available under a Creative Commons License (Attribution 4.0 International), as described at http://creativecommons.org/licenses/by/4.0/.
