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

Abstract

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.

Early diversification and karyotype evolution of flowering plants

“…In addition, ancient polymorphisms in macrostructural genomic variations in the ancestral species may also lead to ILS when using such a trait for phylogenetic inference. However, chromosomal fusions usually result in rapid speciation with reproductive isolation 27,28,37,38 , therefore reducing such a possibility. Despite this, further evidence is needed to exclude this likeliness during rapid radiation of three ANA lineages.…”

Repression and 3D-restructuring resolves regulatory conflicts in evolutionarily rearranged genomes

“…Indeed, many TADs generated by evolution contain multiple genes with non-overlapping expression, despite all promoters contacting the same enhancers ( Dixon et al., 2016 ). Likewise, mutations that create novel ectopic enhancer-promoter contacts within rearranged TADs frequently do so without driving corresponding gene misexpression or phenotypic change ( Despang et al., 2019 ; Ghavi-Helm et al., 2019 ; Laugsch et al., 2019 ; Yin et al., 2021 ). Evolutionary altered regulatory landscapes must therefore employ additional mechanisms that further refine how and when promoters use enhancer activities.…”

Chromosomal conservatism vs chromosomal megaevolution: enigma of karyotypic evolution in Lepidoptera

“…The situation has changed quite recently due to the use of chromosome-level genome assemblies for karyotype analysis (Huang et al, 2022; Wang et al, 2022). This led to the first attempts to analyze rapid karyotypic evolution in different groups (Mudd et al, 2020; Yin et al, 2021), including Lepidoptera (Hill et al, 2019; Cicconardi et al, 2021; Mackintosh et al, 2021). However, to the best of our knowledge, no one has studied groups of organisms in which both evolutionary trends (chromosomal conservatism and chromosomal megaevolution) occur simultaneously.…”