A revamped rat reference genome improves the discovery of genetic diversity in laboratory rats

de Jong, T. V.; Pan, Y.; Rastas, P.; Munro, D.; Tutaj, M.; Akil, H.; Benner, Ch.; Chen, D.; Chitre, A. S.; Chow, W.; Colonna, V.; Dalgard, C. L.; Demos, W. M.; Doris, P. A.; Garrison, E.; Geurts, A.M.; Gunturkun, H. M.; Guryev, V.; Hourlier, T.; Howe, K.; Huang, J.; Kalbfleisch, T.; Kim, P.; Li, L.; Mahaffej, S.; Martin, F. J.; Mohammadi, P.; Ozel, A. B.; Polesskaya, O.; Pravenec, Michal; Prins, P.; Sebat, J.; Smith, J. R.; Woods, L. C. S.; Tabakoff, B.; Tracey, A.; Uliano-Silva, M.; Villani, F.; Wang, H.; Sharp, B. M.; Telese, F.; Jiang, Z.; Saba, L.; Wang, X.; Murphy, T. D.; Palmer, A. A.; Kwitek, A.E.; Dwinell, M. R.; Williams, R. W.; Li, J. Z.; Chen, H.

doi:https://dx.doi.org/10.1016/j.xgen.2024.100527

Number of the records: 1

A revamped rat reference genome improves the discovery of genetic diversity in laboratory rats

1.

SYSNO ASEP	0585369
Document Type	J - Journal Article
R&D Document Type	Journal Article
Subsidiary J	Ostatní články
Title	A revamped rat reference genome improves the discovery of genetic diversity in laboratory rats
Author(s)	de Jong, T. V. (US) Pan, Y. (US) Rastas, P. (FI) Munro, D. (US) Tutaj, M. (US) Akil, H. (US) Benner, Ch. (US) Chen, D. (US) Chitre, A. S. (US) Chow, W. (GB) Colonna, V. (IT) Dalgard, C. L. (US) Demos, W. M. (US) Doris, P. A. (US) Garrison, E. (US) Geurts, A.M. (US) Gunturkun, H. M. (US) Guryev, V. (NL) Hourlier, T. (GB) Howe, K. (GB) Huang, J. (US) Kalbfleisch, T. (US) Kim, P. (US) Li, L. (US) Mahaffej, S. (US) Martin, F. J. (GB) Mohammadi, P. (US) Ozel, A. B. (US) Polesskaya, O. (US) Pravenec, Michal (FGU-C)_{RID, ORCID} Prins, P. (US) Sebat, J. (US) Smith, J. R. (US) Woods, L. C. S. (US) Tabakoff, B. (US) Tracey, A. (GB) Uliano-Silva, M. (GB) Villani, F. (US) Wang, H. (US) Sharp, B. M. (US) Telese, F. (US) Jiang, Z. (US) Saba, L. (US) Wang, X. (US) Murphy, T. D. (US) Palmer, A. A. (US) Kwitek, A.E. (US) Dwinell, M. R. (US) Williams, R. W. (US) Li, J. Z. (US) Chen, H. (US)
Article number	100527
Source Title	Cell Genomics Roč. 4, č. 4 (2024)
Language	eng - English
Country	US - United States
Keywords	rat ; reference genome ; mRatBN7.2 ; Rnor_6.0 ; hybrid rat diversity panel ; heterogeneous stock ; genetic map ; phylogenetic tree ; inbred strains ; recombinant inbred
OECD category	Genetics and heredity (medical genetics to be 3)
R&D Projects	LX22NPO5104 GA MŠMT - Ministry of Education, Youth and Sports (MEYS)
Method of publishing	Open access
Institutional support	FGU-C - RVO:67985823
DOI	10.1016/j.xgen.2024.100527
Annotation	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.
Workplace	Institute of Physiology
Contact	Lucie Trajhanová, lucie.trajhanova@fgu.cas.cz, Tel.: 241 062 400
Year of Publishing	2025
Electronic address	https://doi.org/10.1016/j.xgen.2024.100527

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