Comparative Recombination Rates in the Rat, Mouse, and Human Genomes

Abstract

Levels of recombination vary among species, among chromosomes within species, and among regions within chromosomes in mammals. This heterogeneity may affect levels of diversity, efficiency of selection, and genome composition, as well as have practical consequences for the genetic mapping of traits. We compared the genetic maps to the genome sequence assemblies of rat, mouse, and human to estimate local recombination rates across these genomes. Humans have greater overall levels of recombination, as well as greater variance. In rat and mouse, the size of the chromosome and proximity to telomere have less effect on local recombination rate than in human. At the chromosome level, rat and mouse X chromosomes have the lowest recombination rates, whereas human chromosome X does not show the same pattern. In all species, local recombination rate is significantly correlated with several sequence variables, including GC%, CpG density, repetitive elements, and the neutral mutation rate, with some pronounced differences between species. Recombination rate in one species is not strongly correlated with the rate in another, when comparing homologous syntenic blocks of the genome. This comparative approach provides additional insight into the causes and consequences of genomic heterogeneity in recombination.

GC Content Evolution of the Human and Mouse Genomes: Insights from the Study of Processed Pseudogenes in Regions of Different Recombination Rates

“…So, low recombination rates seem to be a general characteristic of the murid lineage compared to the human lineage. The variance of recombination rate in processed pseudogenes was three times higher in human compared to mouse (0.42 compared to 0.13; Fisher test, p < 0.05), in agreement with a recent comparison of the variance of human and murid recombination rates (human, 0.396; mouse, 0.113; rat, 0.117 [Jensen-Seaman et al 2004]). …”

“…Moreover, the mean recombination rate in rat genome (0.62 cM/Mb) is also lower than the human one (Jensen-Seaman et al 2004). So, low recombination rates seem to be a general characteristic of the murid lineage compared to the human lineage.…”

High-density linkage mapping aided by transcriptomics documents ZW sex determination system in the Chinese mitten crab Eriocheir sinensis

“…Our linkage analysis successfully identified all 73 linkage groups. The linkage map provides high resolution, and the average recombination rate across all linkage groups in E. sinensis is 3.09 cM Mb − 1 , which is much higher than those reported in many other animals, such as mouse (0.5 cM Mb − 1 ), catfish (1.65 cM Mb − 1 ), zebrafish (1.35 cM Mb − 1 ), scallop (1.3 cM Mb − 1 ) and shrimp (1.9 cM Mb − 1 ) (Shimoda et al, 1999;Jensen-Seaman et al, 2004;Kucuktas et al, 2009;Huang et al, 2011;Baranski et al, 2014;Jiao et al, 2014). This suggests that QTLs, if identified, can be narrowed down to quite small genomic region in E. sinensis.…”

No effect of recombination on the efficacy of natural selection in primates

“…Comparison of the human genetic map to a preliminary map in rhesus macaques (Rogers et al 2006) suggests that rates over megabases may be similar. Moreover, centromeric regions tend to experience low rates of recombination, and telomeric regions tend to experience high rates across mammals (Jensen-Seaman et al 2004). These considerations suggest that our assumption is probably valid for the broad scale.…”