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

Tristan V. de Jong, Yanchao Pan, Pasi Rastas, Daniel Munro, Monika Tutaj, Huda Akil, Chris Benner, Denghui Chen, Apurva S. Chitre, William Chow, Vincenza Colonna, Clifton L. Dalgard, Wendy M. Demos, Peter A. Doris, Erik Garrison, Aron M. Geurts, Hakan M. Gunturkun, Victor Guryev, Thibaut Hourlier, Kerstin HoweJun Huang, Ted Kalbfleisch, Panjun Kim, Ling Li, Spencer Mahaffey, Fergal J. Martin, Pejman Mohammadi, Ayse Bilge Ozel, Oksana Polesskaya, Michal Pravenec, Pjotr Prins, Jonathan Sebat, Jennifer R. Smith, Leah C. Solberg Woods, Boris Tabakoff, Alan Tracey, Marcela Uliano-Silva, Flavia Villani, Hongyang Wang, Burt M. Sharp, Francesca Telese, Zhihua Jiang, Laura Saba, Xusheng Wang, Terence D. Murphy, Abraham A. Palmer, Anne E. Kwitek, Melinda R. Dwinell, Robert W. Williams, Jun Z. Li*, Hao Chen*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

Abstract

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.

Original languageEnglish
Article number100527
JournalCell Genomics
Volume4
Issue number4
DOIs
StatePublished - 10 Apr 2024
Externally publishedYes

Keywords

  • genetic map
  • heterogeneous stock
  • hybrid rat diversity panel
  • inbred strains
  • mRatBN7.2
  • phylogenetic tree
  • rat
  • recombinant inbred
  • reference genome
  • Rnor_6.0

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