| Title: |
A revamped rat reference genome improves the discovery of genetic diversity in laboratory rats |
| Authors: |
de Jong, Tristan V.; Pan, Yanchao; Rastas, Pasi; Munro, Daniel; Tutaj, Monika; Akil, Huda; Benner, Chris; Chen, Denghui; Chitre, Apurva S.; Chow, William; Colonna, Vincenza; Dalgard, Clifton L.; Demos, Wendy M.; Doris, Peter A.; Garrison, Erik; Geurts, Aron M.; Gunturkun, Hakan M.; Guryev, Victor; Hourlier, Thibaut; Howe, Kerstin; Huang, Jun; Kalbfleisch, Ted; Kim, Panjun; Li, Ling; Mahaffey, Spencer; Martin, Fergal J.; Mohammadi, Pejman; Ozel, Ayse Bilge; Polesskaya, Oksana; Pravenec, Michal; Prins, Pjotr; Sebat, Jonathan; Smith, Jennifer R.; Woods, Leah C. Solberg; Tabakoff, Boris; Tracey, Alan; Uliano-Silva, Marcela; Villani, Flavia; Wang, Hongyang; Sharp, Burt M.; Telese, Francesca; Jiang, Zhihua; Saba, Laura; Wang, Xusheng; Murphy, Terence D.; Palmer, Abraham A.; Kwitek, Anne E.; Dwinell, Melinda R.; Williams, Robert W.; Li, Jun Z.; Chen, Hao |
| Contributors: |
Institute of Biotechnology; University of Helsinki |
| Publisher Information: |
Cell Press |
| Publication Year: |
2025 |
| Collection: |
Helsingfors Universitet: HELDA – Helsingin yliopiston digitaalinen arkisto |
| Subject Terms: |
Spontaneously hypertensive-rats; Insulin-resistance; Blood-pressure; Sequence; Traits; Identification; Annotation; Expression; Alignment; Accurate; Biomedicine; Biochemistry; cell and molecular biology; Genetics; developmental biology; physiology |
| Description: |
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. ; Peer reviewed |
| Document Type: |
article in journal/newspaper |
| File Description: |
application/pdf |
| Language: |
English |
| Relation: |
R24OD024617 to M.T.; NIH NIDA U01DA043098 to H.A.; NIH NIDA U01DA051972 to C.B.; NIH NHLBI R01HL064541 and Office of the Director R24OD024617 to W.M.D.; NIH NHLBI P01HL149620 and Office of the Director R24OD024617 to A.M.G.; Wellcome Trust WT222155/Z/20/Z to T.H.; NIH R01HG011252 to T.K.; Wellcome Trust WT222155/Z/20/Z to F.J.M.; NIH R01GM140287 to P.M.; a program from the National Institute for Research of Metabolic and Cardiovascular Diseases (Program EXCELES, ID project no. LX22NPO5104) funded by the European Union - Next Generation EU to M.P.; National Institute of Food and Agriculture, United States Department of Agricul-ture (2016-67015-24470/2020-67015-31733/2022-51300-38058/2023-67015-39566/2023-67015-40080) to Z.J.; NIH NIDA U01DA051234 to J.S.; NIH NHLBI R01HL064541, NHGRI U24HG010859, and Office of the Director R24OD024617 to J.R.S.; NIH NIDA P50DA037844 to L.C.S.W. (HS rats); NIH NIAAA R24AA013162 to B.T.; NIH NIDA U01DA050239 and U01DA051972 to F.T.; NIH NIDA P30DA044223 to L.S.; the National Center for Biotechnology Information of the National Library of Medicine (NLM) , National Institutes of Health to T.D.M.; NIH NHLBI R01HL064541 and P01HL149620, NHGRI U24HG010859, and Office of the Director R24OD024617 to A.E.K.; NIH Office of the Director grant R24OD024617 to M.R.D. (HRDP); NIH NIDA U01DA047638 and P30DA044223 to R.W.W.; NIH NIDA U01DA043098 to J.Z.L.; and NIH NIDA U01DA047638, P50DA037844, and R01DA048017 to H.C. The majority of the computation for this work was performed on the Univer-sity of Tennessee Infrastructure for Scientific Applications and Advanced Computing (ISAAC) computational resources. This work is dedicated to the memory of Dr. Mary Shimoyama.r R24OD024617 to M.T.; NIH NIDA U01DA043098 to H.A.; NIH NIDA U01DA051972 to C.B.; NIH NHLBI R01HL064541 and Office of the Director R24OD024617 to W.M.D.; NIH NHLBI P01HL149620 and Office of the Director R24OD024617 to A.M.G.; Wellcome Trust WT222155/Z/20/Z to T.H.; NIH R01HG011252 to T.K.; Wellcome Trust WT222155/Z/20/Z to F.J.M.; NIH R01GM140287 to P.M.; a program from the National Institute for Research of Metabolic and Cardiovascular Diseases (Program EXCELES, ID project no. LX22NPO5104) funded by the European Union - Next Generation EU to M.P.; National Institute of Food and Agriculture, United States Department of Agricul-ture (2016-67015-24470/2020-67015-31733/2022-51300-38058/2023-67015-39566/2023-67015-40080) to Z.J.; NIH NIDA U01DA051234 to J.S.; NIH NHLBI R01HL064541, NHGRI U24HG010859, and Office of the Director R24OD024617 to J.R.S.; NIH NIDA P50DA037844 to L.C.S.W. (HS rats); NIH NIDA U01DA047638 and P30DA044223 to R.W.W.; NIH NIDA U01DA043098 to J.Z.L.; and NIH NIDA U01DA047638, P50DA037844, and R01DA048017 to H.C. The majority of the computation for this work was performed on the Univer-sity of Tennessee Infrastructure for Scientific Applications and Advanced Computing (ISAAC) computational resources. This work is dedicated to the memory of Dr. Mary Shimoyama.; https://hdl.handle.net/10138/591160; 85189630510; 001230194400001 |
| Availability: |
https://hdl.handle.net/10138/591160 |
| Rights: |
cc_by ; info:eu-repo/semantics/openAccess ; openAccess |
| Accession Number: |
edsbas.D811F4BB |
| Database: |
BASE |