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

0585369 - FGÚ 2025 RIV US eng J - Článek v odborném periodiku
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.
A revamped rat reference genome improves the discovery of genetic diversity in laboratory rats.
Cell Genomics. Roč. 4, č. 4 (2024), č. článku 100527. E-ISSN 2666-979X
Grant CEP: GA MŠMT(CZ) LX22NPO5104
Institucionální podpora: RVO:67985823
Klíčová slova: rat * reference genome * mRatBN7.2 * Rnor_6.0 * hybrid rat diversity panel * heterogeneous stock * genetic map * phylogenetic tree * inbred strains * recombinant inbred
Obor OECD: Genetics and heredity (medical genetics to be 3)
Způsob publikování: Open access
https://doi.org/10.1016/j.xgen.2024.100527

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.
Trvalý link: https://hdl.handle.net/11104/0353096