ATTENTION: The software behind KU ScholarWorks is being upgraded to a new version. Starting July 15th, users will not be able to log in to the system, add items, nor make any changes until the new version is in place at the end of July. Searching for articles and opening files will continue to work while the system is being updated.
If you have any questions, please contact Marianne Reed at mreed@ku.edu .
De novo assembly of a chromosome-level reference genome for the California Scrub-Jay, Aphelocoma californica
dc.contributor.author | DeRaad, Devon A | |
dc.contributor.author | Escalona, Merly | |
dc.contributor.author | Benham, Phred M | |
dc.contributor.author | Marimuthu, Mohan P A | |
dc.contributor.author | Sahasrabudhe, Ruta M | |
dc.contributor.author | Nguyen, Oanh | |
dc.contributor.author | Chumchim, Noravit | |
dc.contributor.author | Beraut, Eric | |
dc.contributor.author | Fairbairn, Colin W | |
dc.contributor.author | Seligmann, William | |
dc.contributor.author | Bowie, Rauri C K | |
dc.contributor.author | Cicero, Carla | |
dc.contributor.author | McCormack, John E | |
dc.contributor.author | Wayne, Robert K | |
dc.contributor.editor | Sethuraman, Arun | |
dc.date.accessioned | 2024-06-17T19:55:00Z | |
dc.date.available | 2024-06-17T19:55:00Z | |
dc.date.issued | 2023-08-17 | |
dc.identifier.citation | DeRaad DA, Escalona M, Benham PM, Marimuthu MPA, Sahasrabudhe RM, Nguyen O, Chumchim N, Beraut E, Fairbairn CW, Seligmann W, Bowie RCK, Cicero C, McCormack JE, Wayne RK. De novo assembly of a chromosome-level reference genome for the California Scrub-Jay, Aphelocoma californica. J Hered. 2023 Nov 15;114(6):669-680. doi: 10.1093/jhered/esad047. PMID: 37589384; PMCID: PMC10650945 | en_US |
dc.identifier.uri | https://hdl.handle.net/1808/35199 | |
dc.description.abstract | We announce the assembly of the first de novo reference genome for the California Scrub-Jay (Aphelocoma californica). The genus Aphelocoma comprises four currently recognized species including many locally adapted populations across Mesoamerica and North America. Intensive study of Aphelocoma has revealed novel insights into the evolutionary mechanisms driving diversification in natural systems. Additional insights into the evolutionary history of this group will require continued development of high-quality, publicly available genomic resources. We extracted high molecular weight genomic DNA from a female California Scrub-Jay from northern California and generated PacBio HiFi long-read data and Omni-C chromatin conformation capture data. We used these data to generate a de novo partially phased diploid genome assembly, consisting of two pseudo-haplotypes, and scaffolded them using inferred physical proximity information from the Omni-C data. The more complete pseudo-haplotype assembly (arbitrarily designated “Haplotype 1”) is 1.35 Gb in total length, highly contiguous (contig N50 = 11.53 Mb), and highly complete (BUSCO completeness score = 97%), with comparable scaffold sizes to chromosome-level avian reference genomes (scaffold N50 = 66.14 Mb). Our California Scrub-Jay assembly is highly syntenic with the New Caledonian Crow reference genome despite ~10 million years of divergence, highlighting the temporal stability of the avian genome. This high-quality reference genome represents a leap forward in publicly available genomic resources for Aphelocoma, and the family Corvidae more broadly. Future work using Aphelocoma as a model for understanding the evolutionary forces generating and maintaining biodiversity across phylogenetic scales can now benefit from a highly contiguous, in-group reference genome. | en_US |
dc.publisher | Oxford University Press | en_US |
dc.rights | Copyright © The American Genetic Association. 2023. This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial License (https://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com | en_US |
dc.rights.uri | https://creativecommons.org/licenses/by-nc/4.0/ | en_US |
dc.subject | California Conservation Genomics Project | en_US |
dc.subject | CCGP | en_US |
dc.subject | Long-read sequencing | en_US |
dc.subject | N50 | en_US |
dc.subject | Omni-C | en_US |
dc.subject | PacBio | en_US |
dc.title | De novo assembly of a chromosome-level reference genome for the California Scrub-Jay, Aphelocoma californica | en_US |
dc.type | Article | en_US |
kusw.kuauthor | DeRaad, Devon A | |
kusw.kudepartment | Department of Ecology and Evolutionary Biology and Biodiversity Institute | en_US |
dc.identifier.doi | 10.1093/jhered/esad047 | en_US |
dc.identifier.orcid | https://orcid.org/0000-0003-3105-985X | en_US |
dc.identifier.orcid | https://orcid.org/0000-0003-0213-4777 | en_US |
dc.identifier.orcid | https://orcid.org/0000-0003-3276-6177 | en_US |
dc.identifier.orcid | https://orcid.org/0000-0001-8328-6021 | en_US |
dc.identifier.orcid | https://orcid.org/0000-0002-6282-2339 | en_US |
kusw.oaversion | Scholarly/refereed, publisher version | en_US |
kusw.oapolicy | This item meets KU Open Access policy criteria. | en_US |
dc.identifier.pmid | PMC10650945 | en_US |
dc.rights.accessrights | openAccess | en_US |
Files in this item
This item appears in the following Collection(s)
Except where otherwise noted, this item's license is described as: Copyright © The American Genetic Association. 2023.
This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial License (https://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com