Abstract
The number of rodent species examined by modern comparative genomic approaches, particularly chromosome painting, is limited. The use of human whole-chromosome painting probes to detect regions of homology in the karyotypes of the rodent index species, the mouse and rat, has been hindered by the highly rearranged nature of their genomes. In contrast, recent studies have demonstrated that non-murid rodents display more conserved genomes, underscoring their suitability for comparative genomic and higher-order systematic studies. Here we provide the first comparative chromosome maps between human and representative rodents of three major rodent lineages Castoridae, Pedetidae and Dipodidae. A comprehensive analysis of these data and those published for Sciuridae show (1) that Castoridae, Pedetidae and Dipodidae form a monophyletic group, and (2) that the European beaver Castor fiber (Castoridae) and the birch mouse Sicista betulina (Dipodidae) are sister species to the exclusion of the springhare Pedetes capensis (Pedetidae), thus resolving an enduring trifurcation in rodent higher-level systematics. Our results together with published data on the Sciuridae allow the formulation of a putative rodent ancestral karyotype (2n = 50) that is thought to comprise the following 26 human chromosomal segments and/or segmental associations: HSA1pq, 1q/10p, 2pq, 2q, 3a, 3b/19p, 3c/21, 4b, 5, 6, 7a, 7b/16p, 8p/4a/8p, 8q, 9/11, 10q, 12a/22a, 12b/22b, 13, 14/15, 16q/19q, 17, 18, 20, X and Y. These findings provide insights into the likely composition of the ancestral rodent karyotype and an improved understanding of placental genome evolution.
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Supplementary Figure S1
Examples of selected human (HSA) chromosome painting probes hybridized to beaver and springhare chromosomes. (JPEG 293 kb)
Supplementary Figure S2
Examples of selected human (HSA) chromosome painting probes hybridized to birch mouse chromosomes. (JPEG 185 kb)
Supplementary Figure S3
Examples of chipmunk (TSE) chromosome 18 probe (which corresponds to HSA7/16) hybridized to beaver chromosomes. (JPEG 83.1 kb)
Supplementary Table S1
Matrix of chromosomal characters corresponding to presence (1) or absence (0) of segmental associations of human chromosomal fragments (e.g., ‘1/2’ corresponds to the segmental association of HSA(1) and HSA(2)), and to inversions. Note that none of the characters was polarized a priori (i.e. there was no a priori assumption about fusion vs. fission). See text for details. (DOC 91kb)
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Graphodatsky, A.S., Yang, F., Dobigny, G. et al. Tracking genome organization in rodents by Zoo-FISH. Chromosome Res 16, 261–274 (2008). https://doi.org/10.1007/s10577-007-1191-5
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DOI: https://doi.org/10.1007/s10577-007-1191-5