Analysis of muntjac deer genome and chromatin architecture reveals rapid karyotype evolution

Mudd, Austin B.; Bredeson, Jessen V.; Baum, Rachel; Hockemeyer, Dirk; Rokhsar, Daniel S.

doi:10.1038/s42003-020-1096-9

Cited by 42 publications

(49 citation statements)

References 93 publications

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“…These discoveries shed lights on the chromatin regulatory roles of chromosome rearrangement events during species evolution. It is noteworthy that a recent study comparing only M. reevesi and M. muntjak vaginalis without other species as control, concluded that the compartments are not well conserved between M. reevesi and M. muntjak vaginalis 52 , which is in contrast to our results. We downloaded their data and conducted careful comparison and found their analyses and conclusions had problems.…”

Section: Discussioncontrasting

confidence: 99%

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

et al. 2021

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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.

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Section: Discussioncontrasting

confidence: 99%

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

et al. 2021

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“…They would be in isolation since the reproductive fitness of a potential hybrid could be greatly aggravated by chromosomal imbalance, and thus being practically sterile ( Galindo et al, 2021 ). This is observed in hybrids or populations with the presence of heterozygous tandem fusion, which are considered highly deleterious chromosomal rearrangements, rapidly removed or fixed at meiosis during speciation ( King, 1993 ; Yang et al, 1997 ; Dobigny et al, 2017 ; Mudd et al, 2020 ). Although molecular data indicated the absence of reciprocal monophyly between Paraná and Carajás and suggested both as a single MOTU in the GMYC analyses, this needs to be further explored.…”

Section: Discussionmentioning

confidence: 99%

Revalidation of Mazama rufa (Illiger 1815) (Artiodactyla: Cervidae) as a Distinct Species out of the Complex Mazama americana (Erxleben 1777)

et al. 2021

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The red brocket deer Mazama americana Erxleben, 1777 is considered a polyphyletic complex of cryptic species with wide chromosomal divergence. Evidence indicates that the observed chromosomal divergences result in reproductive isolation. The description of a neotype for M. americana allowed its genetic characterization and represented a comparative basis to resolve the taxonomic uncertainties of the group. Thus, we designated a neotype for the synonym Mazama rufa Illiger, 1815 and tested its recognition as a distinct species from the M. americana complex with the analysis of morphological, cytogenetic and molecular data. We also evaluated its distribution by sampling fecal DNA in the wild. Morphological data from craniometry and body biometry indicated an overlap of quantitative measurements between M. rufa and the entire M. americana complex. The phylogenetic hypothesis obtained through mtDNA confirmed the reciprocal monophyly relationship between M. americana and M. rufa, and both were identified as distinct molecular operational taxonomic units by the General Mixed Yule Coalescent species delimitation analysis. Finally, classic cytogenetic data and fluorescence in situ hybridization with whole chromosome painting probes showed M. rufa with a karyotype of 2n = 52, FN = 56. Comparative analysis indicate that at least fifteen rearrangements separate M. rufa and M. americana (sensu stricto) karyotypes, which confirmed their substantial chromosomal divergence. This divergence should represent an important reproductive barrier and allow its characterization as a distinct and valid species. Genetic analysis of fecal samples demonstrated a wide distribution of M. rufa in the South American continent through the Atlantic Forest, Cerrado and south region of Amazon. Thus, we conclude for the revalidation of M. rufa as a distinct species under the concept of biological isolation, with its karyotype as the main diagnostic character. The present work serves as a basis for the taxonomic review of the M. americana complex, which should be mainly based on cytogenetic characterization and directed towards a better sampling of the Amazon region, the evaluation of available names in the species synonymy and a multi-locus phylogenetic analysis.

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“…Fourfold degenerate bases of one-to-one orthologs were obtained and reformatted from the MAFFT alignment as described in Mudd et al 145 (Supplementary Note 4). The maximumlikelihood phylogeny was obtained with RAxML 150 (v8.2.11) using the GTR+Gamma model of substitution with outgroup Ambystoma mexicanum.…”

Section: Phylogeny and Estimation Of Sequence Divergencementioning

confidence: 99%

“…Customized scripts 145 were used to extract pairwise alignments from the ROAST-merged MAF file and converted into runs of collinearity. The runs of collinearity were visualized with Circos 153 (v0.69-6) (Supplementary Note 4).…”

Section: Chromosome Evolutionmentioning

confidence: 99%

Conserved chromatin and repetitive patterns reveal slow genome evolution in frogs

Bredeson

Mudd

Medina-Ruiz

et al. 2021

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Frogs are an ecologically diverse and phylogenetically ancient group of living amphibians that include important vertebrate cell and developmental model systems, notably the genus Xenopus. Here we report a high-quality reference genome sequence for the western clawed frog, Xenopus tropicalis, along with draft chromosome-scale sequences of three distantly related emerging model frog species, Eleutherodactylus coqui, Engystomops pustulosus and Hymenochirus boettgeri. Frog chromosomes have remained remarkably stable since the Mesozoic Era, with limited Robertsonian (i.e., centric) translocations and end-to-end fusions found among the smaller chromosomes. Conservation of synteny includes conservation of centromere locations, marked by centromeric tandem repeats associated with Cenp-a binding, surrounded by pericentromeric LINE/L1 elements. We explored chromosome structure across frogs, using a dense meiotic linkage map for X. tropicalis and chromatin conformation capture (HiC) data for all species. Abundant satellite repeats occupy the unusually long (~20 megabase) terminal regions of each chromosome that coincide with high rates of recombination. Both embryonic and differentiated cells show reproducible association of centromeric chromatin, and of telomeres, reflecting a Rabl configuration similar to the "bouquet" structure of meiotic cells. Our comparative analyses reveal 13 conserved ancestral anuran chromosomes from which contemporary frog genomes were constructed.

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Analysis of muntjac deer genome and chromatin architecture reveals rapid karyotype evolution

Cited by 42 publications

References 93 publications

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

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

Revalidation of Mazama rufa (Illiger 1815) (Artiodactyla: Cervidae) as a Distinct Species out of the Complex Mazama americana (Erxleben 1777)

Conserved chromatin and repetitive patterns reveal slow genome evolution in frogs

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