Three decades of rat genomics: approaching the finish(ed) line

Abstract

The rat, Rattus norvegicus, has provided an important model for investigation of a range of characteristics of biomedical importance. Here we survey the origins of this species, its introduction into laboratory research, and the emergence of genetic and genomic methods that utilize this model organism. Genomic studies have yielded important progress and provided new insight into several biologically important traits. However, some studies have been impeded by the lack of a complete and accurate reference genome for this species. New sequencing and genome assembly methods applied to the rat have resulted in a new reference genome assembly, GRCr8, which is a near telomere-to-telomere assembly of high base-level accuracy that incorporates several elements not captured in prior assemblies. As genome assembly methods continue to advance and production costs become a less significant obstacle, genome assemblies for multiple inbred rat strains are emerging. These assemblies will allow a rat pangenome assembly to be constructed that captures all the genetic variations in strains selected for their utility in research and will overcome reference bias, a limitation associated with reliance on a single reference assembly. By this means, the full utility of this model organism to genomic studies will begin to be revealed.

Keywords: genome annotation; genome assembly; repetitive regions; structural variation.

Graphical abstract

Figure 1.

Whole genome sequencing data from rats sampled at various global locations were used to model global rat population topology, yielding an inferred population tree topology and divergence times for the global expansion of brown rats. The approach allows adjustment of a number of operational parameters with the best-performing demographic model represented here. The notable observation is the rapid range expansion during the past 500–1,000 years into Southeast Asia, the Middle East, and Europe, which has been attributed to migration facilitated by human travel and transportation. From Puckett and Munshi-South (1) with permission.

Figure 2.

Left: extensive repeat arrays are important elements of the mammalian genome, but because of their repetitive nature, have not been assembled adequately using former methods. StainedGlass software allows tandem repeat arrays, such as those present in the centromeres to be visualized (44). A plot in the region of the centromere of chromosome 20 in the telomere-to-telomere assembly of the haploid human genome from the CHM13 cell line (NC_060944.1) reveals several different higher order repeat arrays, made apparent by the colored percent identity. Right: StainedGlass visualization of centromere of GRCr8 chromosome 15 indicates that this assembly likewise can capture complex repetitive elements such as centromeres, which have been absent from prior rat assemblies.

Figure 3.

Chromosome ideogram of rat genome showing new regions (black bars above chromosome) added to the GRCr8 assembly that were absent in the mRatBN7.2 assembly. Karyotype cytobands are also plotted based on data available at NCBI (https://ftp.ncbi.nlm.nih.gov/pub/gdp/ideogram_10116_GCF_036323745.1_NA_V1).

Figure 4.

Genome-to-genome alignment of GRCr8 and SHRSP across the chr15 T cell receptor locus reveals expansion of this locus through duplication in GRCr8. When two chromosomal regions arise identical by descent, the alignment of sequence can be represented by a dot plot in which the identical regions converge on the diagonal. Nonallelic homologous recombination across the T-cell receptor locus is visualized here using Nahrwhals software (50). This software captures genomic divergence that has arisen by expansion or contraction of structural variants. Such variants represent genomic segments that may have expanded by duplication or been lost by deletion. The approach allows the similarity between duplicated regions to be observed as a series of parallel diagonals. Here, the locus in the GRCr8 genome is of greater length than in SHRSP, but the inserted sequences share similarity both to each other and to a corresponding part of the SHRSP locus. This pattern suggests a serial structural variation attributable to local duplication events in this region.

Figure 5.

Pangenome graph representation of chromosome 19 in genomes of five distinct recently assembled inbred rat genomes. A pangenome graph is a mathematical representation of a data structure that reflects the mutual alignment of all variations in all the genomes incorporated into the model. Here, the alignment is limited to a single chromosome and was generated with PGGB software (65). Graph visualization was obtained using the ODGI software tool (66). Each strain’s chromosome reveals overall similar alignment, However, regions exist in which not all chromosomes align. Often such nonalignment is shared by more than one strain, indicating an ancestral haplotype variation that descended to some but not all inbred rat strains.