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Published online before print
September 13, 2004, 10.1101/gr.2663304 Genome Res. 14:1851-1860, 2004 ©2004 by Cold Spring Harbor Laboratory Press; ISSN 1088-9051/04 $5.00
Letter Human, Mouse, and Rat Genome Large-Scale Rearrangements: Stability Versus Speciation1 The Institute for Genomic Research, Rockville, Maryland 20850, USA 2 BACPAC Resources, Children's Hospital Oakland Research Institute, Oakland, California 94609, USA
Using paired-end sequences from bacterial artificial chromosomes, we have constructed high-resolution synteny and rearrangement breakpoint maps among human, mouse, and rat genomes. Among the >300 syntenic blocks identified are segments of over 40 Mb without any detected interspecies rearrangements, as well as regions with frequently broken synteny and extensive rearrangements. As closely related species, mouse and rat share the majority of the breakpoints and often have the same types of rearrangements when compared with the human genome. However, the breakpoints not shared between them indicate that mouse rearrangements are more often interchromosomal, whereas intrachromosomal rearrangements are more prominent in rat. Centromeres may have played a significant role in reorganizing a number of chromosomes in all three species. The comparison of the three species indicates that genome rearrangements follow a path that accommodates a delicate balance between maintaining a basic structure underlying all mammalian species and permitting variations that are necessary for speciation.
The availability of the human (International Human Genome Sequencing Consortium 2001  ; Venter et al. 2001), mouse (Waterston et al. 2002), and rat (Rat Sequencing Project Consortium 2004) genomic sequences greatly facilitates mammalian genome evolution studies. Comparison of the three genomes reveals both conservation and variation, allowing the identification of both ancestral genome fragments and changes in chromosomal structure through evolution. Here, we have constructed a synteny and rearrangement breakpoint map for the three species using bacterial artificial chromosome (BAC) clones (Kim et al. 1996), which has allowed us to identify large-scale conservation and variation at a 100-300 kb resolution. The results indicate that whereas each genome tends to diverge, much of the basic structure is maintained. The study provides data to assess the balance of genome conservation and rearrangement in maintaining the fundamental functions and facilitating the evolutionary process including speciation.
Synteny and Rearrangement Breakpoint Map Construction Various methods (e.g., BLASTZ, Multiz, PatternHunter, Pash) have been used to compare mammalian genome sequences (Ma et al. 2002 ; Schwartz et al. 2003; Kalafus et al. 2004) and several synteny maps are currently available for mouse, rat, and human (e.g. www.ensembl.org and www.genome.ucsc.edu). We have taken a complementary approach by using the BAC end sequence (BES) resource that was generated for these three species, as well as a number of primates (Mahairas et al. 1999; Zhao et al. 2000, 2001; Fujiyama et al. 2002). We have mapped BACs by placing their paired BESs on the genome assemblies through sequence matches and examined the chromosomal locations, orientation, and distance of each paired mates on the genome (Zhao 2001). Clones that were successfully and uniquely assigned served as anchors for synteny/breakpoint map construction on the basis of clone order, BAC orientation, and distance between the clones. Owing to the large size (usually 80-300 kb) and orientation of BACs, as well as the additional mapping information provided by paired mates (e.g., location, orientation, and spanned distance on the genome) along with the BES sequence-match strength, our approach offers advantages in discriminating false matches originating from genome repeats and local misassemblies (see Discussion). For instance, we have resolved the synteny of at least additional 2.5 Mb sequences flanking the centromeric region of the human chromosome 9 (H9) that is currently missing at both www.ensembl.org and www.genome.ucsc.edu sites (see Supplemental material).
With a total of 246,747 BACs aligned for human, 195,086 for mouse, and 160,683 for rat, the genome coverage by the clones is 12-, 14-, and 11-fold for the three species, respectively (see Supplemental material). With these BACs as markers, we performed two-way and three-way comparisons of the three species to identify syntenic blocks (a syntenic block is defined as a maximal chromosomal fragment in which a series of BACs are in the same order and with the same orientation in all species compared. Synteny here refers to the homology between chromosomal fragments from different species compared that form syntenic blocks). To reduce false results caused by local misassemblies and repeats matches, we excluded blocks with sizes <100 kb and a total clone number <6 for mouse versus rat, <3 for human versus mouse or rat, and <2 for the three species. In all cases, the syntenic blocks range from 100 kb to over 40 Mb (see Supplemental material), and are consistent with the fragile breakage model, but not with the random breakage model (Nadeau and Taylor 1984
Mouse/Rat Synteny and Rearrangements The synteny reveals interesting relationships among the chromosomes (Fig. 2). Except for mouse chromosome 9 (M9) and rat chromosome 8 (R8), as well as the X chromosomes that are exclusively syntenic to each other, all other chromosomes form a network, indicating that the exchange of genetic materials has occurred among the mouse or rat chromosomes within the network but not with outside members (e.g., M8/R9, MX/RX) since the mouse/rat divergence. Within the network, chromosomes also display varying degrees of complexity in synteny, with M17 having the most complex synteny (having blocks of synteny conserved with more rat chromosomes than do other mouse chromosomes; Fig. 2). However, these features are not apparent in other synteny plots such as those used by Rat Sequencing Project Consortium (2004 ), demonstrating the value of the presentation style shown in Figure 2. Our analyses indicate that some chromosomes are very conserved between mouse and rat. For instance, no other rearrangements were detected between M2 and R3, except for three blocks of 150-230 kb with 1-2 BACs inverted (possibly reflecting incorrect assemblies). Other chromosomes had more extensive rearrangements, for example, at least three major inversions involving regions as large as the entire R11 chromosome were found between M16 and R11. These inversions were not reported in nonsequence-based studies (Nilsson et al. 2001).
As expected, the mouse and rat genomes are very conserved compared with each other. Beside this great conservation, we want to know what changes have occurred in each lineage since the two species diverged. To do this, we need a reference genome. This is because comparing the two species will only tell us the differences between them, but cannot discriminate which species is more ancestral and which species has rearranged in regions that involve the differences. The ideal reference would be the most recent mouse/rat common ancestor, which, however, is un-realistic, because the genomic sequences of any mammalian ancestor are unknown. Fortunately, human provides an excellent alternative. This is because, as a more distant species (human and rodents diverged  75 million years ago, whereas mouse and rat diverged 12-24 million years ago [Waterston et al. 2002; Rat Sequencing Project Consortium 2004]), human has an equal genetic distance from both rodents. More importantly, compared with mouse and rat, human has been evolving from the human/rodent common ancestor at a slower rearrangement rate (O'Brien et al. 1999); thus, overall, its genome is more ancestral.
To identify the differences in rearrangements between the two rodents, we categorized the mouse/rat breakpoints on the human genome as shown in Table 2. As expected, mouse and rat share the majority of the breakpoints (266 of 348 total, 76%). In addition, among the shared breakpoints, 96% (255 of 266 total) involve the same type of rearrangements (either intrachromosomal or interchromosomal). For the remaining 4%, neither rodent seems to favor one rearrangement type over the other (five for mouse inter and rat intra, six for mouse intra and rat inter). However, a different picture was observed for species-specific breakpoints. Among a total of 35 mouse-specific breakpoints, 14 (40%) are interchromosomal. In addition, eight of the 25 total intrachromosomal breakpoints are closely associated with these interchromosomal rearrangements (e.g., subsequent inversion breakpoints. See Table 3), and therefore, only 17 (49%) are due to pure intrachromosomal events. For rat, however, nearly all breakpoints (46 of 47) are intrachromosomal. It is unlikely that the observed differences in the rearrangement pattern between mouse and rat are caused by genome misassemblies or repeats matches, as all mouse-specific interchromosomal breakpoints and many of the rat-specific intrachromosomal breakpoints involve syntenic blocks of >1 Mb and with >10 BACs (Tables 3,4). In addition, further examination has indicated that intrachromosomal rearrangements in rat are concentrated on several nearmeta- or metacentric chromosomes, which further argues against genome misassemblies as the reason. These observations are somewhat consistent with a reciprocal chromosomal painting study reporting at least three times more interchromosomal rearrangements in the mouse genome compared with the rat genome (Stanyon et al. 1999
Mouse Has More Interchromosomal Fission Rearrangements, Which Often Involve the Centromeric Regions The examination of the mouse-specific breakpoints has revealed 13 human fragments with 273 Mb total and from 10 chromosomes, each of which corresponds to a region in a single rat chromosome but is syntenic to fragments from multiple mouse chromosomes (Table 3). Thus, mouse is more rearranged than rat in these cases due to the extra fission (and subsequent fusion) events. Because these mouse-specific fissions were identified in 14 mouse chromosomes with homology to nine rat chromosomes with only one exception, (see Table 3 and Supplemental material), they represent a major rearrangement mechanism specific to mouse. Interestingly, 70% (nine of 13 total) of these rearrangements involve the centromeric regions, as the beginning of the euchromatic sequence of a total of 13 mouse chromosomes (chromosomal tip) was identified at the breakpoints (four tip-tip fissions, two tip-end fissions, and three tip-middle fragment fissions. See Table 3). This indicates that the centromeric regions of mouse chromosomes are very active for interchromosomal rearrangements, consistent with a study reporting that numerous Robertsonian fusions have resulted in six distinct chromosomal races (e.g., 2N = 20, 2N = 22, etc., instead of the normal 2N = 40) in the wild populations of M. musculus found in Maderia (Britton-Davidian et al. 2000).
The M5/M6 fission was previously identified by cytogenetic studies; recent duplications associated with this event were found in the pericentromeric regions of multiple mouse chromosomes, and two novel mouse satellite repeats were identified (Walentinsson et al. 2001
Rat Has More Intrachromosomal Rearrangements, With Several Nearmeta- or Metacentric Chromosomes More Extensively Rearranged
Intrachromosomal Rearrangements are Common in Human Both intra- and interchromosomal rearrangements are identified in human by examining its mouse/rat synteny (Table 5; see Supplemental material), however, intrachromosomal events are more frequent by using other species as an outgroup. For instance, by placing the same set of the BAC-end mate pairs that have been mapped to the human/mouse/rat genomes to the recently released dog genome, we have found that among a total of 20 mouse/rat breakpoints identified in H7, eight are mouse/rat specific, seven are human specific due to rearrangements within H7 chromosomal arms or between the arms, and five are common to mouse/rat/dog (Fig. 3). The observed intrachromosomal changes in H7 are consistent with studies indicating that the present day H7 is a fusion product of an acrocentric chromosome and one arm of a submetacentric chromosome in an ancestral placental mammal, followed by paracentric and pericentric inversions (Richard et al. 2000 ). Frequent cytogenetic changes associated with cancer and a high percentage of segmental duplication (8.3% vs. 5% of the entire genome) have been reported in H7 (Hillier et al. 2003), and it would be useful to find out whether these features are related to the observed rearrangements.
Similar to H7, intrachromosomal rearrangements have been identified in many other human chromosomes with the exception of 5, 6, 14, 19, 21, 22, and X. Using dog as the outgroup, in total, we have identified about 58 intrachromosomal breakpoints and four interchromosomal breakpoints that are specific to human. In addition, interarm rearrangements have been found in a number of chromosomes including 3, 7, 9, 11, 17, 18, and 20. The use of chicken as the outgoup also indicates significantly more intrachromosomal events. Thus, intrachromosomal rearrangements are more common in human.
Synteny Across the Human Centromeres
An interesting association of rearrangements with the centromere formation has been found in H20. If we replace the centromeric region of H20 with its beginning 1.5 Mb inverted, the entire chromosome forms a single block syntenic to the last 50/54 Mb of M2/R3. On this basis, we propose a possible path for the evolution of H20 (Fig. 4), which suggests that the centromere in H20 appeared after primates diverged from rodents, and that the process was apparently related to the shuffling of the 1.5-Mb fragment, encoding at least 30 genes, including SOX12 and TCF15 (Deloukas et al. 2001
Comparative genomic studies have greatly advanced our understanding of biology (Mural et al. 2002 ; Waterston et al. 2002; Eichler and Sankoff 2003; Kirkness et al. 2003; Sankoff 2003; Thomas et al. 2003b; Rat Sequencing Project Consortium 2004) and provided opportunities to address questions that were unanswerable just a few years ago. Mouse and rat are important model systems for biomedical research, and a thorough comparison of their genomes in relation to the human genome is an important advance toward understanding differences and similarities of these species. Here, we report for the first time an analysis of chromosome-based whole-genome sequence comparison of the three species, focusing on large-scale rearrangements. Our study, together with other sequence analyses (e.g., micro-insertions and micro-deletions, nucleotide substitutions, duplications, etc.) provides the basis for a more complete picture of the evolutionary relationships of these species.
BES Mate Pairs for Mammalian Genome Comparison
This approach greatly lessens these problems. BACs are large (usually 80-300 kb) and we only used their two ends (
Stability vs. Speciation Our findings suggest that there is a basic structure underlying the three mammalian genomes that retains the fundamental function, and individual species tend to diverge from others provided this structure is maintained. As closely related species, mouse and rat share many of the breakpoints in the human genome and often have the same types of rearrangements. However, the breakpoints not shared between them indicate that mouse rearrangements tend to be more interchromosomal, whereas rat rearrangements are more often intrachromosomal. As a result (at least partially), compared with rat, mouse chromosomes display a large variation in the extent of rearrangement. X chromosomes provide another example (Fig. 5). Whereas the start and the end of MX correspond to HXp, a majority of its middle portion is syntenic to HXq. With rat, the opposite is observed. Considering that sex chromosomes rarely rearrange with autosomes, apparently mouse and rat differ from each other to the maximum allowed extent by a differential use of the two arms of HX.
The comparison between human and mouse/rat also supports this "stability versus speciation" theory. As described, H20 is beautifully preserved among the three species. A few other chromosomes, on the other hand, display highly rearranged synteny (e.g., H19 [Dehal et al. 2001 ] and H22, see Supplemental material). Large chromosomes usually mix both stable and fragile regions within themselves. For instance, whereas the p-arm and the last 103 Mb of H2 are conserved with segments as large as 55 Mb without rearrangements found, frequently broken synteny was detected at its 95-139 Mb region, where a head-to-head fusion of two ancestral primate chromosomes (Yunis and Prakash 1982; Ijdo et al. 1991) as well as intra- and interchromosomal duplications (Fan et al. 2002) were found. Thus, the broken synteny is likely also due to rearrangements within the human lineage.
Centromeres and Rearrangements
As described in previous sections, mouse- or rat-specific rearrangements are closely associated with centromeres. Rat acro- and metacentric chromosomes usually have a more complex synteny profile to mouse compared with the telocentrics, and several of them are more intrachromosomally rearranged (e.g., R1p, R19, R11, and R20). Mouse chromosomes are all acrocentric, and a majority of them are the products of extra interchromosomal fissions involving the centromeric regions (e.g., M1-M2, M4-M6, M10-M13, M15-M17, and M19. See Table 3). These observations raise many questions regarding the chromosomal morphology of the mouse/rat common ancestor and the centromere evolution in each rodent. For instance, R11 and R19 are presumably derived from ancestral chromosomes that were closer to M16 and M8, respectively. As the corresponding fragments of M16/M8 are noncentromeric, R11/R19 must have their centromere formed after the mouse/rat divergence. Did this cause the reorganization of these two chromosomes? If so, R18 (also metacentric) must follow a different mechanism, as it is also syntenic to noncentromeric regions in M18 (Fig. 2) but without rearrangements found, except for a few regions below 400 kb inverted. Did a new centromere form in R18, or did the old centromere disappear in M18? Rat metacentric chromosomes are usually more rearranged than the corresponding mouse chromosomes, suggesting that the mouse/rat ancestor consists of mostly acro- or telocentric chromosomes. If so, then why has the selection favored metacentrics in rat, and will more such chromosomes be formed in the future? As female meiosis drive can quickly change a species' karyotype (Pardo-Manuel de Villena and Sapienza 2001
Human chromosomes also display interesting features across their centromeric regions, some with the mouse/rat synteny broken, whereas others with the synteny uninterrupted (Table 5). These observations could be partially explained by the ancient centromere silencing and neocentromere emergence theory proposed for the centromere repositioning phenomenon observed in H6, H15, and HX in primates (Ventura et al. 2001
Rat Closer to Human? The rearrangement differences between the two rodents suggest that, except for the small inversions, overall, the rat genome might have a structure on a large scale closer to the human genome than the mouse genome. This is because, lacking the extra interchromosomal changes of mouse (Table 3), many rat fragments are closer to human. In addition, for those that are more rearranged (R1p, R11, and R19), the changes are mostly intra-chromosomal (Table 4), a mechanism that is also frequently seen in human (Table 5). In terms of chromosome morphology (and possibly the genome size as well), rat is also between mouse and human. However, a definite answer requires more complete sequencing (e.g., R12p and R13p may not be complete in the assembly), accurate assemblies, and thorough analyses.
Because the mouse and rat genomes are highly rearranged, it has been argued that these species may not mirror the genome organization of other mammals or other rodents (O'Brien et al. 2001
BAC Clone Placement The analyses were performed using genome assemblies of the human NCBI33 build, the dog genome canFam1 version, and the chicken genome version 2 downloaded from www.genome.ucsc.edu, the mouse NCBI30 build downloaded from ensembl (www.ensembl.org/Mus_musculus/), and the rat 3.1 version downloaded from www.ratgenome.hgsc.bcm.tmc.edu/. We compared 280,000 human BAC end sequence (BES) pairs, 192,000 mouse pairs, 138,000 rat pairs, as well as 100,000 pairs from other primate species (79,000 chimp pairs were downloaded from GenBank generated by RIKEN [Fujiyama et al. 2002]) to the three genomes as follows. BESs were first repeat-masked using Repeats-Masker (http://ftp.genome.washington.edu/RM/RepeatMasker.html) and then compared with the genome sequences using WU BLAST (http://sapiens.wustl.edu/blast/). Matches were selected on the basis of the alignment strength. When comparing BESs to the genome of the same species (e.g., human BESs to the human genome), matches with  90% sequence identities and at least half of the BES aligning onto the genome were selected. In cases involving different species (e.g., human BESs to the mouse genome), the best hit was selected for each BES from matches that had error rate <0.01 and length >100bp. For each clone that had both ends successfully placed on the genome, we examined three pieces of information as follows: (1) chromosome locations (its two ends on the same chromosome or not), (2) orientation (the two ends pointing toward each other or not, if on the same chromosome), and (3) distance between the two ends (if on the same chromosome, with the right orientation). We only selected clones that had two ends on the same chromosome, pointing toward each other, and with a distance of 1-400 kb between them.
Synteny Map Construction
We thank the US Department of Energy and the National Institutes of Health for funding the large-scale BAC end-sequencing project for human, mouse, and rat. We are grateful to the human, mouse, dog, rat, and chicken sequencing consortiums for sequencing these genomes.
3 Corresponding author. E-MAIL szhao{at}tigr.org; FAX (301) 838-0208.  [Supplemental material is available online at www.genome.org.] Article and publication are at http://www.genome.org/cgi/doi/10.1101/gr.2663304. Article published online before print in September 2004.
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ABSTRACT
RESULTS
