. 2024 Apr 10;4(4):100527.

doi: 10.1016/j.xgen.2024.100527. Epub 2024 Mar 26.

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

Tristan V de Jong¹, Yanchao Pan², Pasi Rastas³, Daniel Munro⁴, Monika Tutaj⁵, Huda Akil⁶, Chris Benner⁷, Denghui Chen⁸, Apurva S Chitre⁸, William Chow⁹, Vincenza Colonna¹⁰, Clifton L Dalgard¹¹, Wendy M Demos⁵, Peter A Doris¹², Erik Garrison¹³, Aron M Geurts¹⁴, Hakan M Gunturkun¹, Victor Guryev¹⁵, Thibaut Hourlier¹⁶, Kerstin Howe⁹, Jun Huang¹, Ted Kalbfleisch¹⁷, Panjun Kim¹³, Ling Li¹⁸, Spencer Mahaffey¹⁹, Fergal J Martin¹⁶, Pejman Mohammadi²⁰, Ayse Bilge Ozel², Oksana Polesskaya⁸, Michal Pravenec²¹, Pjotr Prins¹³, Jonathan Sebat⁸, Jennifer R Smith⁵, Leah C Solberg Woods²², Boris Tabakoff¹⁹, Alan Tracey⁹, Marcela Uliano-Silva⁹, Flavia Villani¹³, Hongyang Wang²³, Burt M Sharp¹³, Francesca Telese⁸, Zhihua Jiang²³, Laura Saba¹⁹, Xusheng Wang¹⁸, Terence D Murphy²⁴, Abraham A Palmer²⁵, Anne E Kwitek⁵, Melinda R Dwinell⁵, Robert W Williams¹³, Jun Z Li²⁶, Hao Chen²⁷

Affiliations

¹ Department of Pharmacology, Addiction Science, and Toxicology, University of Tennessee Health Science Center, Memphis, TN, USA.
² Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA.
³ Institute of Biotechnology, University of Helsinki, Helsinki, Finland.
⁴ Department of Psychiatry, University of California San Diego, San Diego, CA, USA; Department of Integrative Structural and Computational Biology, Scripps Research, San Diego, CA, USA.
⁵ Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA; Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA.
⁶ Michigan Neuroscience Institute, University of Michigan, Ann Arbor, MI, USA.
⁷ Department of Medicine, University of California San Diego, San Diego, CA, USA.
⁸ Department of Psychiatry, University of California San Diego, San Diego, CA, USA.
⁹ Tree of Life, Wellcome Sanger Institute, Cambridge, UK.
¹⁰ Institute of Genetics and Biophysics, National Research Council, Naples, Italy; Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA.
¹¹ Department of Anatomy, Physiology & Genetics, The American Genome Center, Uniformed Services University of the Health Sciences, Bethesda, MD, USA.
¹² The Brown Foundation Institute of Molecular Medicine, Center for Human Genetics, University of Texas Health Science Center, Houston, TX, USA.
¹³ Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA.
¹⁴ Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA.
¹⁵ Genome Structure and Ageing, University of Groningen, UMC, Groningen, the Netherlands.
¹⁶ European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus in Hinxton, Cambridgeshire, UK.
¹⁷ Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Louisville, KY, USA.
¹⁸ Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA; Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, USA.
¹⁹ Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
²⁰ Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, WA, USA; Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, USA.
²¹ Institute of Physiology, Czech Academy of Sciences, Prague, Czechia.
²² Department of Internal Medicine, Section on Molecular Medicine, Wake Forest University School of Medicine, Winston-Salem, NC, USA.
²³ Department of Animal Sciences, Washington State University, Pullman, WA, USA.
²⁴ National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.
²⁵ Department of Psychiatry, University of California San Diego, San Diego, CA, USA; Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA.
²⁶ Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA. Electronic address: junzli@med.umich.edu.
²⁷ Department of Pharmacology, Addiction Science, and Toxicology, University of Tennessee Health Science Center, Memphis, TN, USA. Electronic address: hchen@uthsc.edu.

PMID: 38537634
PMCID: PMC11019364
DOI: 10.1016/j.xgen.2024.100527

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

Tristan V de Jong et al. Cell Genom. 2024.

. 2024 Apr 10;4(4):100527.

doi: 10.1016/j.xgen.2024.100527. Epub 2024 Mar 26.

Authors

Affiliations

¹ Department of Pharmacology, Addiction Science, and Toxicology, University of Tennessee Health Science Center, Memphis, TN, USA.
² Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA.
³ Institute of Biotechnology, University of Helsinki, Helsinki, Finland.
⁴ Department of Psychiatry, University of California San Diego, San Diego, CA, USA; Department of Integrative Structural and Computational Biology, Scripps Research, San Diego, CA, USA.
⁵ Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA; Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA.
⁶ Michigan Neuroscience Institute, University of Michigan, Ann Arbor, MI, USA.
⁷ Department of Medicine, University of California San Diego, San Diego, CA, USA.
⁸ Department of Psychiatry, University of California San Diego, San Diego, CA, USA.
⁹ Tree of Life, Wellcome Sanger Institute, Cambridge, UK.
¹⁰ Institute of Genetics and Biophysics, National Research Council, Naples, Italy; Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA.
¹¹ Department of Anatomy, Physiology & Genetics, The American Genome Center, Uniformed Services University of the Health Sciences, Bethesda, MD, USA.
¹² The Brown Foundation Institute of Molecular Medicine, Center for Human Genetics, University of Texas Health Science Center, Houston, TX, USA.
¹³ Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA.
¹⁴ Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA.
¹⁵ Genome Structure and Ageing, University of Groningen, UMC, Groningen, the Netherlands.
¹⁶ European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus in Hinxton, Cambridgeshire, UK.
¹⁷ Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Louisville, KY, USA.
¹⁸ Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA; Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, USA.
¹⁹ Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
²⁰ Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, WA, USA; Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, USA.
²¹ Institute of Physiology, Czech Academy of Sciences, Prague, Czechia.
²² Department of Internal Medicine, Section on Molecular Medicine, Wake Forest University School of Medicine, Winston-Salem, NC, USA.
²³ Department of Animal Sciences, Washington State University, Pullman, WA, USA.
²⁴ National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.
²⁵ Department of Psychiatry, University of California San Diego, San Diego, CA, USA; Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA.
²⁶ Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA. Electronic address: junzli@med.umich.edu.
²⁷ Department of Pharmacology, Addiction Science, and Toxicology, University of Tennessee Health Science Center, Memphis, TN, USA. Electronic address: hchen@uthsc.edu.

PMID: 38537634
PMCID: PMC11019364
DOI: 10.1016/j.xgen.2024.100527

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.

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

PubMed Disclaimer

Conflict of interest statement

Declaration of interests The authors declare no competing interests.

Figures

**Figure 1**
mRatBN7.2 corrects structural errors in Rnor_6.0 (A) Genome-wide comparison between Rnor_6.0 and mRatBN7.2 showed many structural differences, such as a large inversion at proximal Chr 6 and many translocations between chromosomes. Image generated using the NCBI Comparative Genome Viewer. Numbers indicate chromosomes. Green lines indicate sequences in the forward alignment. Blue lines indicate reverse alignment. (B) The large inversion on proximal Chr 6 is shown in a dot plot between Rnor_6.0 and mRatBN7.2. (C) A rat genetic map generated using 150,835 binned markers from 1,893 heterogeneous stock rats showed an inversion at proximal Chr 6 between genetic distance and physical distance based on Rnor_6.0, indicating that the inversion is caused by assembly errors in Rnor_6.0. (D) Marker order and genetic distance from the genetic map on Chr 6 are in agreement with physical distance based on mRatBN7.2, indicating that the misassembly is fixed. (E–G) Genetic map confirms that many assembly errors on Chr 19 in Rnor_6.0 are fixed in mRatBN7.2.

**Figure 2**
mRatBN7.2 improved mapping statistics of whole-genome sequencing data Summary statistics from mapping 36 HXB/BXH WGS samples against Rnor_6.0 and mRatBN7.2 were compared. Using mRatBN7.2 increased the percentage of reads mapped (A), reduced regions on the reference genome with zero coverage (B), total number of SNPs (C), and indels (D). The presence of a large number of SNPs (E) and indels (F) that are shared by all samples (arrows), including BN/NHsdMcwi, indicates that they are base-level errors in the reference genome.

**Figure 3**
mRatBN7.2 improves eQTL and proteomic analysis Genome misassembly is associated with increased rates of calling spurious *trans*-eQTLs. (A) Each column represents a gene for which at least one *trans*-eQTL was found at p < 1 × 10⁻⁸ using Rnor_6.0. The color of bars indicate the number of *trans*-eQTL SNP-gene pairs in which the SNP and/or gene transcription start site (TSS) relocated to a different chromosome in mRatBN7.2 and whether the relocation would result in a reclassification to *cis*-eQTL (TSS distance < 1 Mb) or ambiguous (TSS distance is between 1–5 Mb). (B) Genomic location of one relocated *trans*-eQTL SNP from (A). The SNP is in a segment of Chr 13 in Rnor_6.0 that was relocated to Chr 3 in mRatBN7.2 (red stars), reclassifying the eQTL from *trans*-eQTL to *cis*-eQTL for both *Ly75* and *Itgb6* genes (red bars). (C) Histogram showing the distance between *cis*-pQTLs and TSS of the corresponding proteins. The distances of pQTLs in mRatBN7.2 tend to be closer than those in Rnor_6.0. (D) An example of *trans*-pQTL in Rnor_6.0 was detected as a *cis*-pQTL in mRatBN7.2. (E) Correlation of expression of the protein (the example in B) in Rnor_6.0 and mRatBN7.2. (F) Different annotations of the exemplar gene in Rnor_6.0 and mRatBN7.2.

**Figure 4**
Using WGS data to assess the quality of the Liftover from Rnor_6.0 to mRatBN7.2 (A) Overview of the workflow using a real WGS sample from a WKY rat. A higher portion of variants passed the quality filter for mRatBN7.2. Among them, 97.93% of the variants were liftable from Rnor_6.0 to mRatBN7.2. (B) The overlap between variants lifted from Rnor_6.0 and variants obtained by direct mapping sequence data to mRatBN7.2. Approximately 11.9% of the variants that were found from direct mapping were missing from the Liftover.

**Figure 5**
Phylogenetic relationship and genetic diversity of 120 strain/substrains of laboratory rats (A) The phylogenetic tree was constructed using 11.6 million biallelic SNPs from 163 samples. Strains/substrains with duplicated samples were condensed. Strains highlighted with bold fonts are parental strains for RI panels. Green, HXB/BXH RI panel; blue, FXLE/LEXF RI panel; orange, progenitors of the HS outbred population. (B) The HS progenitors contain 16,438,302 variants (i.e., 82.2% of the variants in our collection of 120 strain/substrains) based on analysis using mRatBN7.2. Among these, 10,895 are shared by all eight progenitor strains. The number of variants that are unique to each specific founder is noted. (C) The total number of variants per strain, with the total number unique to each strain marked. (D) The number of variants shared across strains per chromosome.

See this image and copyright information in PMC

Update of

A revamped rat reference genome improves the discovery of genetic diversity in laboratory rats.
de Jong TV, Pan Y, Rastas P, Munro D, Tutaj M, Akil H, Benner C, Chen D, Chitre AS, Chow W, Colonna V, Dalgard CL, Demos WM, Doris PA, Garrison E, Geurts AM, Gunturkun HM, Guryev V, Hourlier T, Howe K, Huang J, Kalbfleisch T, Kim P, Li L, Mahaffey S, Martin FJ, Mohammadi P, Ozel AB, Polesskaya O, Pravenec M, Prins P, Sebat J, Smith JR, Solberg Woods LC, Tabakoff B, Tracey A, Uliano-Silva M, Villani F, Wang H, Sharp BM, Telese F, Jiang Z, Saba L, Wang X, Murphy TD, Palmer AA, Kwitek AE, Dwinell MR, Williams RW, Li JZ, Chen H. de Jong TV, et al. bioRxiv [Preprint]. 2023 Sep 28:2023.04.13.536694. doi: 10.1101/2023.04.13.536694. bioRxiv. 2023. Update in: Cell Genom. 2024 Apr 10;4(4):100527. doi: 10.1016/j.xgen.2024.100527. PMID: 37214860 Free PMC article. Updated. Preprint.

References

1. Parker C.C., Chen H., Flagel S.B., Geurts A.M., Richards J.B., Robinson T.E., Solberg Woods L.C., Palmer A.A. Rats are the smart choice: Rationale for a renewed focus on rats in behavioral genetics. Neuropharmacology. 2014;76:250–258. - PMC - PubMed
1. Richter C.P. The effects of domestication and selection on the behavior of the Norway rat. J. Natl. Cancer Inst. 1954;15:727–738. - PubMed
1. Hulme-Beaman A., Orton D., Cucchi T. The origins of the domesticate brown rat (Rattus norvegicus) and its pathways to domestication. Anim. Front. 2021;11:78–86. - PMC - PubMed
1. Modlinska K., Pisula W. The Norway rat, from an obnoxious pest to a laboratory pet. Elife. 2020;9 doi: 10.7554/eLife.50651. - DOI - PMC - PubMed
1. Smith J.R., Hayman G.T., Wang S.-J., Laulederkind S.J.F., Hoffman M.J., Kaldunski M.L., Tutaj M., Thota J., Nalabolu H.S., Ellanki S.L.R., et al. The Year of the Rat: The Rat Genome Database at 20: a multi-species knowledgebase and analysis platform. Nucleic Acids Res. 2020;48:D731–D742. - PMC - PubMed

MeSH terms

Actions
Actions
Actions
Actions
Actions
Actions
Actions

Grants and funding

LinkOut - more resources

Full Text Sources

Save citation to file

Email citation

Add to Collections

Add to My Bibliography

Your saved search

Create a file for external citation management software

Your RSS Feed

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

Affiliations

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

Authors

Affiliations

Abstract

Conflict of interest statement

Figures

Update of

References

MeSH terms

Grants and funding

LinkOut - more resources

Full Text Sources