A revamped rat reference genome improves the discovery of genetic diversity in laboratory rats
Copyright © 2024 The Authors. Published by Elsevier Inc. All rights reserved..
The seventh iteration of the reference genome assembly for Rattus norvegicus-mRatBN7.2-corrects numerous misplaced segments and reduces base-level errors by approximately 9-fold and increases contiguity by 290-fold compared with its predecessor. Gene annotations are now more complete, improving the mapping precision of genomic, transcriptomic, and proteomics datasets. We jointly analyzed 163 short-read whole-genome sequencing datasets representing 120 laboratory rat strains and substrains using mRatBN7.2. We defined ∼20.0 million sequence variations, of which 18,700 are predicted to potentially impact the function of 6,677 genes. We also generated a new rat genetic map from 1,893 heterogeneous stock rats and annotated transcription start sites and alternative polyadenylation sites. The mRatBN7.2 assembly, along with the extensive analysis of genomic variations among rat strains, enhances our understanding of the rat genome, providing researchers with an expanded resource for studies involving rats.
| Errataetall: | |
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| Medienart: |
E-Artikel |
| Erscheinungsjahr: |
2024 |
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| Erschienen: |
2024 |
| Enthalten in: |
Zur Gesamtaufnahme - volume:4 |
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| Enthalten in: |
Cell genomics - 4(2024), 4 vom: 10. Apr., Seite 100527 |
| Sprache: |
Englisch |
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| Beteiligte Personen: |
de Jong, Tristan V [VerfasserIn] |
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| Links: |
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| Themen: |
Genetic map |
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| Anmerkungen: |
Date Completed 15.04.2024 Date Revised 25.04.2024 published: Print-Electronic UpdateOf: bioRxiv. 2023 Sep 28;:. - PMID 37214860 Citation Status MEDLINE |
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| doi: |
10.1016/j.xgen.2024.100527 |
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| funding: |
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| 245 | 1 | 2 | |a A revamped rat reference genome improves the discovery of genetic diversity in laboratory rats |
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| 500 | |a UpdateOf: bioRxiv. 2023 Sep 28;:. - PMID 37214860 | ||
| 500 | |a Citation Status MEDLINE | ||
| 520 | |a Copyright © 2024 The Authors. Published by Elsevier Inc. All rights reserved. | ||
| 520 | |a The seventh iteration of the reference genome assembly for Rattus norvegicus-mRatBN7.2-corrects numerous misplaced segments and reduces base-level errors by approximately 9-fold and increases contiguity by 290-fold compared with its predecessor. Gene annotations are now more complete, improving the mapping precision of genomic, transcriptomic, and proteomics datasets. We jointly analyzed 163 short-read whole-genome sequencing datasets representing 120 laboratory rat strains and substrains using mRatBN7.2. We defined ∼20.0 million sequence variations, of which 18,700 are predicted to potentially impact the function of 6,677 genes. We also generated a new rat genetic map from 1,893 heterogeneous stock rats and annotated transcription start sites and alternative polyadenylation sites. The mRatBN7.2 assembly, along with the extensive analysis of genomic variations among rat strains, enhances our understanding of the rat genome, providing researchers with an expanded resource for studies involving rats | ||
| 650 | 4 | |a Journal Article | |
| 650 | 4 | |a Rnor_6.0 | |
| 650 | 4 | |a genetic map | |
| 650 | 4 | |a heterogeneous stock | |
| 650 | 4 | |a hybrid rat diversity panel | |
| 650 | 4 | |a inbred strains | |
| 650 | 4 | |a mRatBN7.2 | |
| 650 | 4 | |a phylogenetic tree | |
| 650 | 4 | |a rat | |
| 650 | 4 | |a recombinant inbred | |
| 650 | 4 | |a reference genome | |
| 700 | 1 | |a Pan, Yanchao |e verfasserin |4 aut | |
| 700 | 1 | |a Rastas, Pasi |e verfasserin |4 aut | |
| 700 | 1 | |a Munro, Daniel |e verfasserin |4 aut | |
| 700 | 1 | |a Tutaj, Monika |e verfasserin |4 aut | |
| 700 | 1 | |a Akil, Huda |e verfasserin |4 aut | |
| 700 | 1 | |a Benner, Chris |e verfasserin |4 aut | |
| 700 | 1 | |a Chen, Denghui |e verfasserin |4 aut | |
| 700 | 1 | |a Chitre, Apurva S |e verfasserin |4 aut | |
| 700 | 1 | |a Chow, William |e verfasserin |4 aut | |
| 700 | 1 | |a Colonna, Vincenza |e verfasserin |4 aut | |
| 700 | 1 | |a Dalgard, Clifton L |e verfasserin |4 aut | |
| 700 | 1 | |a Demos, Wendy M |e verfasserin |4 aut | |
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