Upgrading short read animal genome assemblies to chromosome level using comparative genomics and a universal probe set
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 sub-chromosomal sized scaffolds. To circum...
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Cold Spring Harbour
2016
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Online Access: | https://kar.kent.ac.uk/60239/ https://kar.kent.ac.uk/60239/19/Genome%20Res.-2017-Damas-875-84.pdf https://kar.kent.ac.uk/60239/1/Damas%20et%20al%202016%20-%20accepted%20manuscript.pdf https://doi.org/10.1101/gr.213660.116 |
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ftkentuniv:oai:kar.kent.ac.uk:60239 2023-05-15T16:10:01+02:00 Upgrading short read animal genome assemblies to chromosome level using comparative genomics and a universal probe set Damas, J. O'Connor, Rebecca Farré, Marta Lenis, V.P.E. Martell, H.J. Mandawala, A. Fowler, K. Joseph, S. Swain, M.T. Griffin, Darren K. Larkin, D.M. 2016-11-30 application/pdf https://kar.kent.ac.uk/60239/ https://kar.kent.ac.uk/60239/19/Genome%20Res.-2017-Damas-875-84.pdf https://kar.kent.ac.uk/60239/1/Damas%20et%20al%202016%20-%20accepted%20manuscript.pdf https://doi.org/10.1101/gr.213660.116 en eng Cold Spring Harbour https://kar.kent.ac.uk/60239/19/Genome%20Res.-2017-Damas-875-84.pdf https://kar.kent.ac.uk/60239/1/Damas%20et%20al%202016%20-%20accepted%20manuscript.pdf Damas, J., O'Connor, Rebecca, Farré, Marta, Lenis, V.P.E., Martell, H.J., Mandawala, A., Fowler, K., Joseph, S., Swain, M.T., Griffin, Darren K., and others. Larkin, D.M. (hide) (2016) Upgrading short read animal genome assemblies to chromosome level using comparative genomics and a universal probe set. Genome Research, 27 . pp. 875-884. ISSN 1088-9051. (doi:10.1101/gr.213660.116 <https://doi.org/10.1101/gr.213660.116>) (KAR id:60239 </60239>) cc_by Q Science Article PeerReviewed 2016 ftkentuniv https://doi.org/10.1101/gr.213660.116 2023-03-12T19:10:48Z 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 sub-chromosomal 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. Multi-genome-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 level 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. Using chromosome breakpoint data, we established that avian interchromosomal breakpoints appear in the regions of low density of conserved non-coding 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. Article in Journal/Newspaper Falco peregrinus peregrine falcon University of Kent: KAR - Kent Academic Repository Genome Research 27 5 875 884 |
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University of Kent: KAR - Kent Academic Repository |
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ftkentuniv |
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English |
topic |
Q Science |
spellingShingle |
Q Science Damas, J. O'Connor, Rebecca Farré, Marta Lenis, V.P.E. Martell, H.J. Mandawala, A. Fowler, K. Joseph, S. Swain, M.T. Griffin, Darren K. Larkin, D.M. Upgrading short read animal genome assemblies to chromosome level using comparative genomics and a universal probe set |
topic_facet |
Q Science |
description |
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 sub-chromosomal 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. Multi-genome-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 level 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. Using chromosome breakpoint data, we established that avian interchromosomal breakpoints appear in the regions of low density of conserved non-coding 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. |
format |
Article in Journal/Newspaper |
author |
Damas, J. O'Connor, Rebecca Farré, Marta Lenis, V.P.E. Martell, H.J. Mandawala, A. Fowler, K. Joseph, S. Swain, M.T. Griffin, Darren K. Larkin, D.M. |
author_facet |
Damas, J. O'Connor, Rebecca Farré, Marta Lenis, V.P.E. Martell, H.J. Mandawala, A. Fowler, K. Joseph, S. Swain, M.T. Griffin, Darren K. Larkin, D.M. |
author_sort |
Damas, J. |
title |
Upgrading short read animal genome assemblies to chromosome level using comparative genomics and a universal probe set |
title_short |
Upgrading short read animal genome assemblies to chromosome level using comparative genomics and a universal probe set |
title_full |
Upgrading short read animal genome assemblies to chromosome level using comparative genomics and a universal probe set |
title_fullStr |
Upgrading short read animal genome assemblies to chromosome level using comparative genomics and a universal probe set |
title_full_unstemmed |
Upgrading short read animal genome assemblies to chromosome level using comparative genomics and a universal probe set |
title_sort |
upgrading short read animal genome assemblies to chromosome level using comparative genomics and a universal probe set |
publisher |
Cold Spring Harbour |
publishDate |
2016 |
url |
https://kar.kent.ac.uk/60239/ https://kar.kent.ac.uk/60239/19/Genome%20Res.-2017-Damas-875-84.pdf https://kar.kent.ac.uk/60239/1/Damas%20et%20al%202016%20-%20accepted%20manuscript.pdf https://doi.org/10.1101/gr.213660.116 |
genre |
Falco peregrinus peregrine falcon |
genre_facet |
Falco peregrinus peregrine falcon |
op_relation |
https://kar.kent.ac.uk/60239/19/Genome%20Res.-2017-Damas-875-84.pdf https://kar.kent.ac.uk/60239/1/Damas%20et%20al%202016%20-%20accepted%20manuscript.pdf Damas, J., O'Connor, Rebecca, Farré, Marta, Lenis, V.P.E., Martell, H.J., Mandawala, A., Fowler, K., Joseph, S., Swain, M.T., Griffin, Darren K., and others. Larkin, D.M. (hide) (2016) Upgrading short read animal genome assemblies to chromosome level using comparative genomics and a universal probe set. Genome Research, 27 . pp. 875-884. ISSN 1088-9051. (doi:10.1101/gr.213660.116 <https://doi.org/10.1101/gr.213660.116>) (KAR id:60239 </60239>) |
op_rights |
cc_by |
op_doi |
https://doi.org/10.1101/gr.213660.116 |
container_title |
Genome Research |
container_volume |
27 |
container_issue |
5 |
container_start_page |
875 |
op_container_end_page |
884 |
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1765995264013762560 |