Karyotype relationships among selected deer species and cattle revealed by bovine FISH probes

Abstract

The Cervidae family comprises more than fifty species divided into three subfamilies: Capreolinae, Cervinae and Hydropotinae. A characteristic attribute for the species included in this family is the great karyotype diversity, with the chromosomal numbers ranging from 2n = 6 observed in female Muntiacus muntjak vaginalis to 2n = 70 found in Mazama gouazoubira as a result of numerous Robertsonian and tandem fusions. This work reports chromosomal homologies between cattle (Bos taurus, 2n = 60) and nine cervid species using a combination of whole chromosome and region-specific paints and BAC clones derived from cattle. We show that despite the great diversity of karyotypes in the studied species, the number of conserved chromosomal segments detected by 29 cattle whole chromosome painting probes was 35 for all Cervidae samples. The detailed analysis of the X chromosomes revealed two different morphological types within Cervidae. The first one, present in the Capreolinae is a sub/metacentric X with the structure more similar to the bovine X. The second type found in Cervini and Muntiacini is an acrocentric X which shows rearrangements in the proximal part that have not yet been identified within Ruminantia. Moreover, we characterised four repetitive sequences organized in heterochromatic blocks on sex chromosomes of the reindeer (Rangifer tarandus). We show that these repeats gave no hybridization signals to the chromosomes of the closely related moose (Alces alces) and are therefore specific to the reindeer.

Muntjac chromosome evolution and architecture

“…For convenience, we refer to chromosomal regions by their B. taurus (BTA) chromosome identifiers. We confirmed prior reports in literature [20] that: In the last common ancestor of cow and deer, segments corresponding to the two cow chromosomes BTA26 and BTA28 were present as a single chromosome in the last common ancestor of cervids and B. taurus . This ancestral state, corresponding to BTA26_28, is retained in C. elaphus and the muntjacs. Twelve chromosomes of the cervid ancestor arose by fission of chromosomes represented by six cow chromosomes (BTA1 => CEL19 and CEL31; BTA2 => CEL8 and CEL33; BTA5 => CEL3 and CEL22; BTA6 => CEL6 and CEL17; BTA8 => CEL16 and CEL29; and BTA9 => CEL26 and CEL28). Although chromosomes homologous to BTA17 and BTA19 are fused in the C. elaphus lineage as CEL5, this fusion is unique to the C. elaphus lineage, and these cow chromosomes correspond to distinct ancestral cervid chromosomes. In the muntjacs, we found six fusions shared by M. muntjak and M. reevesi (BTA7/BTA3, BTA5prox/BTA22, BTA2dist/BTA11, BTA18/BTA25/BTA26_28 (fusion of three ancestral chromosomes counted as two fusion events), and BTA27/BTA8dist; Figure S3).…”

“…In total, we found thirty-eight fusion events and no fissions separating the two muntjac species (Figure 1A). All twelve of the M. reevesi fusions identified by our comparative analysis are confirmed by BAC-FISH [20], and seventeen of the M. muntjak fusions are confirmed [29]. The additional fusions found in our analysis were not assayed by prior BAC-based studies.…”

“…The assembled chromosome numbers recapitulate the karyotypes reported in the literature (2n=6 for female M. muntjak [18] and 2n=46 for M. reevesi [19]). M. reevesi chromosomes were validated against previously published chromosome painting data [20]. For M. muntjak , we aligned 377 previously sequenced bacterial artificial chromosomes (BACs) [21–23] and, based on corresponding fluorescent in situ hybridization (FISH) location data, found that 360 (95%) of BACs align to the expected chromosomes.…”

“…The tree denotes the ancestral karyotype at each node and the six branches with fission and fusion events relative to the ancestral karyotype. The lack of fissions or fusions on the R. tarandus -specific branch as well as the timings of the cervid-specific and B. taurus -specific fissions are derived from literature [20]. [B] Plot with jcvi.graphics.karyotype (v0.8.12; https://github.com/tanghaibao/jcvi) using runs of collinearity containing at least 25 kb of aligned sequence between B. taurus , C. elaphus , M. reevesi , and M. muntjak .…”

“…To estimate the probability of such a reversion occurring by chance given the high rate of fusion in M. muntjak , we simulated a simplified model for karyotype change with four rules: (1) only one fission is allowed per chromosome; (2) all fissions occur first, followed by all fusions; (3) for each fission, a chromosome is chosen at random; and (4) for each fusion, chromosomes and chromosomal orientations are chosen at random. From a starting karyotype of n=29, representing the last common ancestor of cervids and B. taurus [20], we simulated the model of fissions and fusions to one million iterations per fission-fusion combination (Figure S5). The M. muntjak lineage, with six fissions and thirty-two fusions, had a 4% probability of at least one fusion reversing a prior fission.…”