Most foundational work on the evolution and migration of plant species relies on genomic data from contemporary samples. Ancient plant samples can give us access to allele sequences and distributions on the landscape dating back to the mid Holocene or earlier (Gugerli et al., 2005). Nuclear DNA from ancient wood, however, has been mostly inaccessible until now. In a From the Cover article in this issue of Molecular Ecology, Wagner et al. (2023) present the first nuclear genomes from ancient to subfossil oak wood, including two samples dated to the 15th century and one that dates to more than 3,500 years ago. These first assembled nuclear genomes from ancient trees open the possibility for investigating species adaptation, migration, divergence, and hybridization in the deep past. They pave the way for what we hope will be a new era in the use of paleogenomics to study Holocene tree histories.

Holocentric organisms, unlike typical monocentric organisms, have kinetochore activity distributed along almost the whole length of the chromosome. Because of this, chromosomal rearrangements through fission and fusion are more likely to become fixed in holocentric species, which may account for their extraordinary rates of chromosome evolution. Genome synteny has been reported to be conserved in animals with holocentric chromosomes despite high rates of chromosome rearrangements. Comparing genomes of Carex species and a genome of a distantly related Cyperaceae we have characterised conserved vs. rearranged genome regions across pairs of species that range in time since divergence between 2 and 50 million years. We have compared a C. scoparia genome with a linkage map of the same species to study rearrangements at a population level and suppression of recombination patterns. We found a surprisingly conserved genome synteny even between very distantly related species and extraordinarily high rates of chromosome evolution in genus Carex. Comparing the distribution of repetitive DNA and gene density between conserved and rearranged genomic regions, we found repetitive DNA to be related to holocentromeres and as well as rearranged regions of the genome. This evidence of extremely conserved synteny in sedges and the massive events of chromosome fission and fusion found across the evolution of genus Carex suggests the presence of common genomic hotspots of chromosome evolution related to repetitive DNA.