Improving the genome assembly of rabbits with long-read sequencing
dc.contributor.author | Bai, Y | |
dc.contributor.author | Lin, W | |
dc.contributor.author | Xu, J | |
dc.contributor.author | Song, J | |
dc.contributor.author | Yang, D | |
dc.contributor.author | Chen, YE | |
dc.contributor.author | Li, L | |
dc.contributor.author | Li, Y | |
dc.contributor.author | Wang, Z | |
dc.contributor.author | Zhang, J | |
dc.coverage.spatial | United States | |
dc.date.accessioned | 2022-10-05T14:35:40Z | |
dc.date.available | 2022-10-05T14:35:40Z | |
dc.date.issued | 2021-09-01 | |
dc.identifier.issn | 0888-7543 | |
dc.identifier.issn | 1089-8646 | |
dc.identifier.uri | https://www.ncbi.nlm.nih.gov/pubmed/34051323 | |
dc.identifier.uri | https://hdl.handle.net/2027.42/174882 | en |
dc.description.abstract | The European rabbit (Oryctolagus cuniculus) is important as a biomedical model given its unique features in immunity and metabolism. The current reference genome OryCun2.0 established with whole-genome shotgun sequencing was quite fragmented and had not been updated for ten years. In this work, we provided a new rabbit genome assembly UM_NZW_1.0 to improve OryCun2.0 by leveraging the contig lengths based on long-read sequencing and a wealth of available Illumina paired-end sequence data. UM_NZW_1.0 showed a remarkable increase of continuity compared with OryCun2.0, with 5 times longer contig N50 and approximately 75% gaps closed. Many of the closed gaps were overlapped with protein-coding genes or transcriptional features, resulting in an enhancement of gene annotations. In particular, UM_NZW_1.0 presented a more complete landscape of the MHC region and the IGH locus, therefore provided a valuable resource for future researches on rabbits. | |
dc.format.medium | Print-Electronic | |
dc.language | eng | |
dc.publisher | Elsevier | |
dc.subject | Gap closing | |
dc.subject | Long-read sequencing | |
dc.subject | Rabbit genomes | |
dc.subject | Reference assembly | |
dc.subject | Animals | |
dc.subject | High-Throughput Nucleotide Sequencing | |
dc.subject | Molecular Sequence Annotation | |
dc.subject | Rabbits | |
dc.subject | Sequence Analysis, DNA | |
dc.subject | Whole Genome Sequencing | |
dc.title | Improving the genome assembly of rabbits with long-read sequencing | |
dc.type | Article | |
dc.identifier.pmid | 34051323 | |
dc.description.bitstreamurl | http://deepblue.lib.umich.edu/bitstream/2027.42/174882/2/2021-Genomics-rabbit-PacBio.pdf | |
dc.identifier.doi | 10.1016/j.ygeno.2021.05.031 | |
dc.identifier.doi | https://dx.doi.org/10.7302/6511 | |
dc.identifier.source | Genomics | |
dc.description.version | Published version | |
dc.date.updated | 2022-10-05T14:35:37Z | |
dc.identifier.orcid | 0000-0003-2449-8651 | |
dc.identifier.orcid | 0000-0003-2357-7825 | |
dc.identifier.volume | 113 | |
dc.identifier.issue | 5 | |
dc.identifier.startpage | 3216 | |
dc.identifier.endpage | 3223 | |
dc.identifier.name-orcid | Bai, Y | |
dc.identifier.name-orcid | Lin, W | |
dc.identifier.name-orcid | Xu, J | |
dc.identifier.name-orcid | Song, J | |
dc.identifier.name-orcid | Yang, D; 0000-0003-2449-8651 | |
dc.identifier.name-orcid | Chen, YE; 0000-0003-2357-7825 | |
dc.identifier.name-orcid | Li, L | |
dc.identifier.name-orcid | Li, Y | |
dc.identifier.name-orcid | Wang, Z | |
dc.identifier.name-orcid | Zhang, J | |
dc.working.doi | 10.7302/6511 | en |
dc.owningcollname | Internal Medicine, Department of |
Files in this item
Remediation of Harmful Language
The University of Michigan Library aims to describe library materials in a way that respects the people and communities who create, use, and are represented in our collections. Report harmful or offensive language in catalog records, finding aids, or elsewhere in our collections anonymously through our metadata feedback form. More information at Remediation of Harmful Language.
Accessibility
If you are unable to use this file in its current format, please select the Contact Us link and we can modify it to make it more accessible to you.