A revamped rat reference genome improves the discovery of genetic diversity in laboratory rats
Author:
de Jong Tristan VORCID, Pan YanchaoORCID, Rastas PasiORCID, Munro DanielORCID, Tutaj MonikaORCID, Akil HudaORCID, Benner ChrisORCID, Chen Denghui, Chitre Apurva SORCID, Chow WilliamORCID, Colonna VincenzaORCID, Dalgard Clifton LORCID, Demos Wendy MORCID, Doris Peter AORCID, Garrison ErikORCID, Geurts Aron MORCID, Gunturkun Hakan MORCID, Guryev VictorORCID, Hourlier Thibaut, Howe KerstinORCID, Huang Jun, Kalbfleisch TedORCID, Kim PanjunORCID, Li Ling, Mahaffey SpencerORCID, Martin Fergal JORCID, Mohammadi PejmanORCID, Ozel Ayse BilgeORCID, Polesskaya OksanaORCID, Pravenec MichalORCID, Prins PjotrORCID, Sebat JonathanORCID, Smith Jennifer R, Woods Leah C SolbergORCID, Tabakoff Boris, Tracey Alan, Uliano-Silva Marcela, Villani FlaviaORCID, Wang Hongyang, Sharp Burt M, Telese FrancescaORCID, Jiang ZhihuaORCID, Saba LauraORCID, Wang XushengORCID, Murphy Terence DORCID, Palmer Abraham AORCID, Kwitek Anne EORCID, Dwinell Melinda RORCID, Williams Robert WORCID, Li Jun ZORCID, Chen HaoORCID
Abstract
SummaryThe seventh iteration of the reference genome assembly forRattus norvegicus— mRatBN7.2—corrects numerous misplaced segments and reduces base-level errors by approximately 9-fold and increases contiguity by 290-fold compared to its predecessor. Gene annotations are now more complete, significantly improving the mapping precision of genomic, transcriptomic, and proteomics data sets. 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 18.7 thousand 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.
Publisher
Cold Spring Harbor Laboratory
Cited by
2 articles.
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