Construction and evaluation of a new rat reference genome assembly, GRCr8, from long reads and long-range scaffolding. Genome Res 2024 Nov 20;34(11):2081-2093
Date
11/13/2024Pubmed ID
39516046Pubmed Central ID
PMC11610589DOI
10.1101/gr.279292.124Scopus ID
2-s2.0-85209718679 (requires institutional sign-in at Scopus site) 4 CitationsAbstract
We report the construction and analysis of a new reference genome assembly for Rattus norvegicus, the laboratory rat, a widely used experimental animal model organism. The assembly has been adopted as the rat reference assembly by the Genome Reference Consortium and is named GRCr8. The assembly has employed 40× Pacific Biosciences (PacBio) HiFi sequencing coverage and scaffolding using optical mapping and Hi-C. We used genomic DNA from a male BN/NHsdMcwi (BN) rat of the same strain and from the same colony as the prior reference assembly, mRatBN7.2. The assembly is at chromosome level with 98.7% of the sequence assigned to chromosomes. All chromosomes have increased in size compared with the prior assembly and k-mer analysis indicates that the subject animal is fully inbred and that the genome is represented as a single haploid assembly. Notable increases are observed in Chromosomes 3, 11, and 12 in the prospective rDNA regions. In addition, Chr Y has increased threefold in size and is more consistent with the rat karyotype than previous assemblies. Several other chromosomes have grown by the incorporation of sizable discrete new blocks. These contain highly repetitive sequences and encode numerous previously unannotated genes. In addition, centromeric sequences are incorporated in most chromosomes. Genome annotation has been performed by NCBI RefSeq, which confirms improvement in assembly quality and adds more than 1100 new protein coding genes. PacBio Iso-Seq data have been acquired from multiple tissues of the subject animal and are released concurrently with the new assembly to aid further analyses.
Author List
Li K, Smith ML, Blazier JC, Kochan KJ, Wood JMD, Howe K, Kwitek AE, Dwinell MR, Chen H, Ciosek JL, Masterson P, Murphy TD, Kalbfleisch TS, Doris PAAuthors
Melinda R. Dwinell PhD Associate Dean, Professor in the Physiology department at Medical College of WisconsinAnne E. Kwitek PhD Professor in the Physiology department at Medical College of Wisconsin
MESH terms used to index this publication - Major topics in bold
AnimalsGenome
Genomics
Male
Rats
Sequence Analysis, DNA
