Chromosomal distribution and organization of three cervid satellite DNAs in Chinese water deer (Hydropotes inermis)

Molecular mechanisms and topological consequences of drastic chromosomal rearrangements of muntjac deer

Muntjac deer have experienced drastic karyotype changes during their speciation, making it an ideal model for studying mechanisms and functional consequences of mammalian chromosome evolution. Here we generated chromosome-level genomes for Hydropotes inermis (2n = 70), Muntiacus reevesi (2n = 46), female and male M. crinifrons (2n = 8/9) and a contig-level genome for M. gongshanensis (2n = 8/9). These high-quality genomes combined with Hi-C data allowed us to reveal the evolution of 3D chromatin architectures during mammalian chromosome evolution. We find that the chromosome fusion events of muntjac species did not alter the A/B compartment structure and topologically associated domains near the fusion sites, but new chromatin interactions were gradually established across the fusion sites. The recently borne neo-Y chromosome of M. crinifrons, which underwent male-specific inversions, has dramatically restructured chromatin compartments, recapitulating the early evolution of canonical mammalian Y chromosomes. We also reveal that a complex structure containing unique centromeric satellite, truncated telomeric and palindrome repeats might have mediated muntjacs' recurrent chromosome fusions. These results provide insights into the recurrent chromosome tandem fusion in muntjacs, early evolution of mammalian sex chromosomes, and reveal how chromosome rearrangements can reshape the 3D chromatin regulatory conformations during species evolution.

Satellite DNA in Neotropical Deer Species

The taxonomy and phylogenetics of Neotropical deer have been mostly based on morphological criteria and needs a critical revision on the basis of new molecular and cytogenetic markers. In this study, we used the variation in the sequence, copy number, and chromosome localization of satellite I-IV DNA to evaluate evolutionary relationships among eight Neotropical deer species. Using FISH with satI-IV probes derived from Mazama gouazoubira, we proved the presence of satellite DNA blocks in peri/centromeric regions of all analyzed deer. Satellite DNA was also detected in the interstitial chromosome regions of species of the genus Mazama with highly reduced chromosome numbers. In contrast to Blastocerus dichotomus, Ozotoceros bezoarticus, and Odocoileus virginianus, Mazama species showed high abundance of satIV DNA by FISH. The phylogenetic analysis of the satellite DNA showed close relationships between O. bezoarticus and B. dichotomus. Furthermore, the Neotropical and Nearctic populations of O. virginianus formed a single clade. However, the satellite DNA phylogeny did not allow resolving the relationships within the genus Mazama. The high abundance of the satellite DNA in centromeres probably contributes to the formation of chromosomal rearrangements, thus leading to a fast and ongoing speciation in this genus, which has not yet been reflected in the satellite DNA sequence diversification.

Sequence Analysis and FISH Mapping of Four Satellite DNA Families among Cervidae

Centromeric and pericentromeric chromosome regions are occupied by satellite DNA. Satellite DNAs play essential roles in chromosome segregation, and, thanks to their extensive sequence variability, to some extent, they can also be used as phylogenetic markers. In this paper, we isolated and sequenced satellite DNA I-IV in 11 species of Cervidae. The obtained satellite DNA sequences and their chromosomal distribution were compared among the analysed representatives of cervid subfamilies Cervinae and Capreolinae. Only satI and satII sequences are probably present in all analysed species with high abundance. On the other hand, fluorescence in situ hybridisation (FISH) with satIII and satIV probes showed signals only in a part of the analysed species, indicating interspecies copy number variations. Several indices, including FISH patterns, the high guanine and cytosine (GC) content, and the presence of centromere protein B (CENP-B) binding motif, suggest that the satII DNA may represent the most important satellite DNA family that might be involved in the centromeric function in Cervidae. The absence or low intensity of satellite DNA FISH signals on biarmed chromosomes probably reflects the evolutionary reduction of heterochromatin following the formation of chromosome fusions. The phylogenetic trees constructed on the basis of the satellite I-IV DNA relationships generally support the present cervid taxonomy.

Organization and evolution of a novel cervid satellite DNA with yeast CDEI-like repeats

Background

It has been proposed that pericentromeric satellite DNA arises from the progressive proximal expansion of ancient centromeric DNA. In an attempt to recover putative ancestral centromeric DNA, we microdissected the pericentromeric/centromeric DNA from the chromosome X + 3 of Indian muntjac (Muntiacus muntjak vaginalis) and constructed a microclone-library of the X + 3 centromeric DNA.

Results

A new cervid satellite DNA element, designated as satellite VI, was isolated from this library. Fluorescence in situ hybridization (FISH) studies revealed that satellite VI is predominately located on the distal pericentromeric region of the Indian muntjac chromosome X + 3 and on the pericentromeres of several Old World deer species studied. Its sequence is organized as 11-bp monomeric (ATCACGTGGGA) tandem repeats. Further sequencing on a BAC clone of Indian muntjac harboring this repeat showed that an array of this repeat stretches over approximately 5 kb followed by approximately 3 kb of interspersed repetitive sequences, such as long interspersed elements (LINEs), short interspersed elements (SINEs), and long terminal repeats (LTRs).

Conclusions

Based on the chromosomal localization, genomic and sequence organization, and copy numbers of satellite VI in deer species studied, we postulate that this newly found satellite DNA could be a putative ancient cervidic centromeric DNA that is still preserved in some Old World deer. Interestingly, the first eight nucleotides of the 11-bp monomeric consensus sequences are highly conserved and identical to the CDEI element in the centromere of the budding yeast Saccharomyces cerevisiae. The centromeric/pericentromeric satellite DNA harboring abundant copies of CDEI sequences is the first found in a mammalian species. Several zipper-like d (GGGA)2 motifs were also found in the (ATCACGTGGGA)n repeat of satellite VI DNA. Whether the satellite VI is structurally and functionally correlated with the CDEI of centromere of budding yeast and whether a zipper-like structure forms in satellite VI require further studies.

Centromere-competent DNA: structure and evolution

Although extant data favour centromere being an epigenetic structure, it is also clear that centromere formation is based on DNA, in particular, tandemly repeated satellite DNA and its transcripts. Presence of conserved structural motifs within satellite DNAs such as periodically distributed AT tracts, protein binding sites, or promoter elements indicate that despite sequence flexibility, there are structural determinants that are prerequisite for centromere function. In addition, existence of functional centromeric DNA transcripts indicates possible importance of structural elements at the level of RNA secondary or tertiary structure. Rapid centromere evolution is explained by homologous recombination followed by extrachromosomal rolling circle replication. This could lead to amplification of different satellite sequences within a genome. However, only those satellites that have inherent centromere-competence in the form of structural requirements necessary for centromere function are after amplification fixed in a population as a new centromere.

Species-specific shifts in centromere sequence composition are coincident with breakpoint reuse in karyotypically divergent lineages

The evolution of three classes of centromere sequences across nine species of macropodine marsupials were compared with that of other genes, showing that each species has experienced differential expansion and contraction of individual classes.

Background

It has been hypothesized that rapid divergence in centromere sequences accompanies rapid karyotypic change during speciation. However, the reuse of breakpoints coincident with centromeres in the evolution of divergent karyotypes poses a potential paradox. In distantly related species where the same centromere breakpoints are used in the independent derivation of karyotypes, centromere-specific sequences may undergo convergent evolution rather than rapid sequence divergence. To determine whether centromere sequence composition follows the phylogenetic history of species evolution or patterns of convergent breakpoint reuse through chromosome evolution, we examined the phylogenetic trajectory of centromere sequences within a group of karyotypically diverse mammals, macropodine marsupials (wallabies, wallaroos and kangaroos).

Results

The evolution of three classes of centromere sequences across nine species within the genus Macropus (including Wallabia) were compared with the phylogenetic history of a mitochondrial gene, Cytochrome b (Cyt b), a nuclear gene, selenocysteine tRNA (TRSP), and the chromosomal histories of the syntenic blocks that define the different karyotype arrangements. Convergent contraction or expansion of predominant satellites is found to accompany specific karyotype rearrangements. The phylogenetic history of these centromere sequences includes the convergence of centromere composition in divergent species through convergent breakpoint reuse between syntenic blocks.

Conclusion

These data support the 'library hypothesis' of centromere evolution within this genus as each species possesses all three satellites yet each species has experienced differential expansion and contraction of individual classes. Thus, we have identified a correlation between the evolution of centromere satellite sequences, the reuse of syntenic breakpoints, and karyotype convergence in the context of a gene-based phylogeny.